celldata.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 147,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    " \n",
    "\n",
    "\n",
    "df_tissue = pd.read_csv('../arff/tissue_data.csv')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Gene</th>\n",
       "      <th>tissue1</th>\n",
       "      <th>tissue2</th>\n",
       "      <th>tissue3</th>\n",
       "      <th>tissue4</th>\n",
       "      <th>tissue5</th>\n",
       "      <th>tissue6</th>\n",
       "      <th>tissue7</th>\n",
       "      <th>tissue8</th>\n",
       "      <th>tissue9</th>\n",
       "      <th>...</th>\n",
       "      <th>tissue67</th>\n",
       "      <th>tissue68</th>\n",
       "      <th>tissue69</th>\n",
       "      <th>tissue70</th>\n",
       "      <th>tissue71</th>\n",
       "      <th>tissue72</th>\n",
       "      <th>tissue73</th>\n",
       "      <th>tissue74</th>\n",
       "      <th>tissue75</th>\n",
       "      <th>tissue76</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TSPAN6</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.7</td>\n",
       "      <td>0.4</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TNMD</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DPM1</td>\n",
       "      <td>7.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>...</td>\n",
       "      <td>3.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SCYL3</td>\n",
       "      <td>7.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>...</td>\n",
       "      <td>6.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>9.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>C1orf112</td>\n",
       "      <td>4.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>...</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>13.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 77 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       Gene  tissue1   tissue2   tissue3   tissue4   tissue5   tissue6  \\\n",
       "0    TSPAN6      0.0       0.0       8.0       1.0       0.0      13.0   \n",
       "1      TNMD      0.0       0.0       0.0       0.0       0.0       0.0   \n",
       "2      DPM1      7.0      16.0       8.0       2.0       2.0       1.0   \n",
       "3     SCYL3      7.0       9.0      11.0       8.0      10.0      11.0   \n",
       "4  C1orf112      4.0       5.0       6.0       3.0       5.0       8.0   \n",
       "\n",
       "    tissue7   tissue8   tissue9    ...       tissue67  tissue68   tissue69  \\\n",
       "0       1.0       0.0       3.0    ...            0.0       2.0        3.0   \n",
       "1       0.0       0.0       0.0    ...            0.0       0.0        0.1   \n",
       "2       4.0       3.0       2.0    ...            3.0       7.0        5.0   \n",
       "3       8.0      13.0      11.0    ...            6.0      12.0       13.0   \n",
       "4       5.0      16.0      11.0    ...            3.0       2.0        8.0   \n",
       "\n",
       "    tissue70   tissue71   tissue72   tissue73   tissue74   tissue75   tissue76  \n",
       "0        1.0        2.0        0.7        0.4        1.0        0.0        3.0  \n",
       "1        0.0        0.0        0.0        0.0        0.0        0.0        0.0  \n",
       "2        4.0        4.0        1.0        6.0        5.0        0.0        4.0  \n",
       "3       15.0       15.0       10.0       16.0       18.0        7.0        9.0  \n",
       "4        8.0       11.0        2.0        4.0       12.0        0.0       13.0  \n",
       "\n",
       "[5 rows x 77 columns]"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_tissue.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "result = pd.merge(df_data, df_tissue, how='left', on=['Gene', 'Gene'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Label</th>\n",
       "      <th>Chr</th>\n",
       "      <th>Position</th>\n",
       "      <th>RSID</th>\n",
       "      <th>Ref</th>\n",
       "      <th>Alt</th>\n",
       "      <th>Gene</th>\n",
       "      <th>GT</th>\n",
       "      <th>OMIM</th>\n",
       "      <th>CADD</th>\n",
       "      <th>...</th>\n",
       "      <th>tissue67</th>\n",
       "      <th>tissue68</th>\n",
       "      <th>tissue69</th>\n",
       "      <th>tissue70</th>\n",
       "      <th>tissue71</th>\n",
       "      <th>tissue72</th>\n",
       "      <th>tissue73</th>\n",
       "      <th>tissue74</th>\n",
       "      <th>tissue75</th>\n",
       "      <th>tissue76</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>4820844</td>\n",
       "      <td>rs397704705</td>\n",
       "      <td>GGAT</td>\n",
       "      <td>TGCTGTAAACTGTAACTGTAAA</td>\n",
       "      <td>AP5Z1</td>\n",
       "      <td>1</td>\n",
       "      <td>613647</td>\n",
       "      <td>29.500</td>\n",
       "      <td>...</td>\n",
       "      <td>14.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0</td>\n",
       "      <td>7</td>\n",
       "      <td>4833639</td>\n",
       "      <td>rs2880933</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>AP5Z1</td>\n",
       "      <td>1</td>\n",
       "      <td>613647</td>\n",
       "      <td>0.027</td>\n",
       "      <td>...</td>\n",
       "      <td>14.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>4827366</td>\n",
       "      <td>rs397704709</td>\n",
       "      <td>GGACCTGCCCTGCT</td>\n",
       "      <td>-</td>\n",
       "      <td>AP5Z1</td>\n",
       "      <td>1</td>\n",
       "      <td>613647</td>\n",
       "      <td>36.000</td>\n",
       "      <td>...</td>\n",
       "      <td>14.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0</td>\n",
       "      <td>7</td>\n",
       "      <td>4827366</td>\n",
       "      <td>rs397704709</td>\n",
       "      <td>GGACCTGCCCTGCT</td>\n",
       "      <td>-</td>\n",
       "      <td>AP5Z1</td>\n",
       "      <td>1</td>\n",
       "      <td>170500</td>\n",
       "      <td>36.000</td>\n",
       "      <td>...</td>\n",
       "      <td>14.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1</td>\n",
       "      <td>11</td>\n",
       "      <td>126145284</td>\n",
       "      <td>rs267606829</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>FOXRED1</td>\n",
       "      <td>1</td>\n",
       "      <td>252010</td>\n",
       "      <td>27.700</td>\n",
       "      <td>...</td>\n",
       "      <td>7.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>5.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 151 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   Label Chr   Position         RSID             Ref                     Alt  \\\n",
       "0      1   7    4820844  rs397704705            GGAT  TGCTGTAAACTGTAACTGTAAA   \n",
       "1      0   7    4833639    rs2880933               A                       C   \n",
       "2      1   7    4827366  rs397704709  GGACCTGCCCTGCT                       -   \n",
       "3      0   7    4827366  rs397704709  GGACCTGCCCTGCT                       -   \n",
       "4      1  11  126145284  rs267606829               C                       T   \n",
       "\n",
       "      Gene  GT    OMIM    CADD    ...       tissue67  tissue68   tissue69  \\\n",
       "0    AP5Z1   1  613647  29.500    ...           14.0       5.0       17.0   \n",
       "1    AP5Z1   1  613647   0.027    ...           14.0       5.0       17.0   \n",
       "2    AP5Z1   1  613647  36.000    ...           14.0       5.0       17.0   \n",
       "3    AP5Z1   1  170500  36.000    ...           14.0       5.0       17.0   \n",
       "4  FOXRED1   1  252010  27.700    ...            7.0       5.0        5.0   \n",
       "\n",
       "    tissue70   tissue71   tissue72   tissue73   tissue74   tissue75   tissue76  \n",
       "0       16.0       11.0       16.0       10.0       20.0       15.0        7.0  \n",
       "1       16.0       11.0       16.0       10.0       20.0       15.0        7.0  \n",
       "2       16.0       11.0       16.0       10.0       20.0       15.0        7.0  \n",
       "3       16.0       11.0       16.0       10.0       20.0       15.0        7.0  \n",
       "4        8.0        6.0        1.0        7.0       10.0        7.0        5.0  \n",
       "\n",
       "[5 rows x 151 columns]"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "result.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "result.sort_values(['OMIM'])\n",
    "\n",
    "result.replace('' , 0, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "result.to_csv('Master-Tissue.csv', index= None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "df = pd.read_csv('Master-Tissue.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Label</th>\n",
       "      <th>Chr</th>\n",
       "      <th>Position</th>\n",
       "      <th>RSID</th>\n",
       "      <th>Ref</th>\n",
       "      <th>Alt</th>\n",
       "      <th>Gene</th>\n",
       "      <th>GT</th>\n",
       "      <th>OMIM</th>\n",
       "      <th>CADD</th>\n",
       "      <th>...</th>\n",
       "      <th>tissue67</th>\n",
       "      <th>tissue68</th>\n",
       "      <th>tissue69</th>\n",
       "      <th>tissue70</th>\n",
       "      <th>tissue71</th>\n",
       "      <th>tissue72</th>\n",
       "      <th>tissue73</th>\n",
       "      <th>tissue74</th>\n",
       "      <th>tissue75</th>\n",
       "      <th>tissue76</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>4820844</td>\n",
       "      <td>rs397704705</td>\n",
       "      <td>GGAT</td>\n",
       "      <td>TGCTGTAAACTGTAACTGTAAA</td>\n",
       "      <td>AP5Z1</td>\n",
       "      <td>1</td>\n",
       "      <td>613647</td>\n",
       "      <td>29.500</td>\n",
       "      <td>...</td>\n",
       "      <td>14.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0</td>\n",
       "      <td>7</td>\n",
       "      <td>4833639</td>\n",
       "      <td>rs2880933</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>AP5Z1</td>\n",
       "      <td>1</td>\n",
       "      <td>613647</td>\n",
       "      <td>0.027</td>\n",
       "      <td>...</td>\n",
       "      <td>14.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>4827366</td>\n",
       "      <td>rs397704709</td>\n",
       "      <td>GGACCTGCCCTGCT</td>\n",
       "      <td>-</td>\n",
       "      <td>AP5Z1</td>\n",
       "      <td>1</td>\n",
       "      <td>613647</td>\n",
       "      <td>36.000</td>\n",
       "      <td>...</td>\n",
       "      <td>14.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0</td>\n",
       "      <td>7</td>\n",
       "      <td>4827366</td>\n",
       "      <td>rs397704709</td>\n",
       "      <td>GGACCTGCCCTGCT</td>\n",
       "      <td>-</td>\n",
       "      <td>AP5Z1</td>\n",
       "      <td>1</td>\n",
       "      <td>170500</td>\n",
       "      <td>36.000</td>\n",
       "      <td>...</td>\n",
       "      <td>14.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1</td>\n",
       "      <td>11</td>\n",
       "      <td>126145284</td>\n",
       "      <td>rs267606829</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>FOXRED1</td>\n",
       "      <td>1</td>\n",
       "      <td>252010</td>\n",
       "      <td>27.700</td>\n",
       "      <td>...</td>\n",
       "      <td>7.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>5.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 151 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   Label Chr   Position         RSID             Ref                     Alt  \\\n",
       "0      1   7    4820844  rs397704705            GGAT  TGCTGTAAACTGTAACTGTAAA   \n",
       "1      0   7    4833639    rs2880933               A                       C   \n",
       "2      1   7    4827366  rs397704709  GGACCTGCCCTGCT                       -   \n",
       "3      0   7    4827366  rs397704709  GGACCTGCCCTGCT                       -   \n",
       "4      1  11  126145284  rs267606829               C                       T   \n",
       "\n",
       "      Gene  GT    OMIM    CADD    ...       tissue67  tissue68   tissue69  \\\n",
       "0    AP5Z1   1  613647  29.500    ...           14.0       5.0       17.0   \n",
       "1    AP5Z1   1  613647   0.027    ...           14.0       5.0       17.0   \n",
       "2    AP5Z1   1  613647  36.000    ...           14.0       5.0       17.0   \n",
       "3    AP5Z1   1  170500  36.000    ...           14.0       5.0       17.0   \n",
       "4  FOXRED1   1  252010  27.700    ...            7.0       5.0        5.0   \n",
       "\n",
       "    tissue70   tissue71   tissue72   tissue73   tissue74   tissue75   tissue76  \n",
       "0       16.0       11.0       16.0       10.0       20.0       15.0        7.0  \n",
       "1       16.0       11.0       16.0       10.0       20.0       15.0        7.0  \n",
       "2       16.0       11.0       16.0       10.0       20.0       15.0        7.0  \n",
       "3       16.0       11.0       16.0       10.0       20.0       15.0        7.0  \n",
       "4        8.0        6.0        1.0        7.0       10.0        7.0        5.0  \n",
       "\n",
       "[5 rows x 151 columns]"
      ]
     },
     "execution_count": 43,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Remove BRCA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 152,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "df_data = pd.read_csv('PVP_new_data.csv')\n",
    "df_new = df_data[df_data.Gene.str.contains(\"BRCA\") == False]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 154,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "df_new.to_csv('PVP_data_no_brca.csv', index = None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 155,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "df_pvp = pd.read_csv('PVP_data_no_brca.csv')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Human Tissue Data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 157,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "df_human = pd.read_table('../arff/tissue_data_human.tsv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 158,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "del df_human['Gene ID']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 159,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Gene</th>\n",
       "      <th>adipose tissue</th>\n",
       "      <th>adrenal gland</th>\n",
       "      <th>brain</th>\n",
       "      <th>heart</th>\n",
       "      <th>kidney</th>\n",
       "      <th>liver</th>\n",
       "      <th>lung</th>\n",
       "      <th>ovary</th>\n",
       "      <th>pancreas</th>\n",
       "      <th>sigmoid colon</th>\n",
       "      <th>small intestine</th>\n",
       "      <th>spleen</th>\n",
       "      <th>testis</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TSPAN6</td>\n",
       "      <td>12.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>15.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TNMD</td>\n",
       "      <td>9.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.9</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DPM1</td>\n",
       "      <td>21.0</td>\n",
       "      <td>44.0</td>\n",
       "      <td>23.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>27.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>55.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>26.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>41.0</td>\n",
       "      <td>37.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SCYL3</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>4.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>C1orf112</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.5</td>\n",
       "      <td>3.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.7</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.7</td>\n",
       "      <td>0.8</td>\n",
       "      <td>0.4</td>\n",
       "      <td>2.0</td>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       Gene  adipose tissue  adrenal gland  brain  heart  kidney  liver  lung  \\\n",
       "0    TSPAN6            12.0            6.0    2.0    2.0    18.0   17.0  10.0   \n",
       "1      TNMD             9.0            0.0    0.0    0.0     0.9    0.0   0.0   \n",
       "2      DPM1            21.0           44.0   23.0   22.0    27.0   15.0  55.0   \n",
       "3     SCYL3             2.0            3.0    1.0    1.0     2.0    3.0   3.0   \n",
       "4  C1orf112             1.0            0.5    3.0    0.4     0.4    0.7   1.0   \n",
       "\n",
       "   ovary  pancreas  sigmoid colon  small intestine  spleen  testis  \n",
       "0   17.0       7.0            6.0             19.0     5.0    15.0  \n",
       "1    1.0       0.1            0.1              0.0     0.0     0.2  \n",
       "2   17.0      26.0           20.0             22.0    41.0    37.0  \n",
       "3    2.0       3.0            2.0              4.0     4.0     4.0  \n",
       "4    1.0       0.7            0.8              0.4     2.0     7.0  "
      ]
     },
     "execution_count": 159,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_human.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 160,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 161,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "final = final.sort_values(['OMIM'])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### empty cell fillup "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 162,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def recode_empty_cells(dataframe, list_of_columns):\n",
    "\n",
    "    for column in list_of_columns:\n",
    "      dataframe[column] = dataframe[column].replace(r'\\s+', np.nan, regex=True)\n",
    "      dataframe[column] = dataframe[column].fillna(0)\n",
    "\n",
    "    return dataframe"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 163,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Label</th>\n",
       "      <th>Chr</th>\n",
       "      <th>Position</th>\n",
       "      <th>RSID</th>\n",
       "      <th>Ref</th>\n",
       "      <th>Alt</th>\n",
       "      <th>Gene</th>\n",
       "      <th>GT</th>\n",
       "      <th>OMIM</th>\n",
       "      <th>CADD</th>\n",
       "      <th>...</th>\n",
       "      <th>heart</th>\n",
       "      <th>kidney</th>\n",
       "      <th>liver</th>\n",
       "      <th>lung</th>\n",
       "      <th>ovary</th>\n",
       "      <th>pancreas</th>\n",
       "      <th>sigmoid colon</th>\n",
       "      <th>small intestine</th>\n",
       "      <th>spleen</th>\n",
       "      <th>testis</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>60939</th>\n",
       "      <td>0</td>\n",
       "      <td>8</td>\n",
       "      <td>41791859</td>\n",
       "      <td>rs786200952</td>\n",
       "      <td>T</td>\n",
       "      <td>TT</td>\n",
       "      <td>KAT6A</td>\n",
       "      <td>0</td>\n",
       "      <td>100100</td>\n",
       "      <td>35.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
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       "      <td>3.0</td>\n",
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       "      <td>2.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>12.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26955</th>\n",
       "      <td>0</td>\n",
       "      <td>11</td>\n",
       "      <td>5275647</td>\n",
       "      <td>rs34474104</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>HBG2</td>\n",
       "      <td>0</td>\n",
       "      <td>100100</td>\n",
       "      <td>22.800000</td>\n",
       "      <td>...</td>\n",
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       "      <td>0.0</td>\n",
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       "      <td>0.1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>79875</th>\n",
       "      <td>0</td>\n",
       "      <td>8</td>\n",
       "      <td>61748664</td>\n",
       "      <td>rs886040990</td>\n",
       "      <td>GAAA</td>\n",
       "      <td>-</td>\n",
       "      <td>CHD7</td>\n",
       "      <td>1</td>\n",
       "      <td>100100</td>\n",
       "      <td>32.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.8</td>\n",
       "      <td>0.6</td>\n",
       "      <td>0.5</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.9</td>\n",
       "      <td>0.8</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35354</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>240071924</td>\n",
       "      <td>rs587776862</td>\n",
       "      <td>GCCTGAGGAGGA</td>\n",
       "      <td>T</td>\n",
       "      <td>CHRM3</td>\n",
       "      <td>1</td>\n",
       "      <td>100100</td>\n",
       "      <td>40.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.6</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83127</th>\n",
       "      <td>0</td>\n",
       "      <td>12</td>\n",
       "      <td>76740088</td>\n",
       "      <td>rs375413604</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>BBS10</td>\n",
       "      <td>1</td>\n",
       "      <td>100100</td>\n",
       "      <td>35.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>4.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1819</th>\n",
       "      <td>0</td>\n",
       "      <td>20</td>\n",
       "      <td>948667</td>\n",
       "      <td>rs74315420</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>RSPO4</td>\n",
       "      <td>1</td>\n",
       "      <td>100100</td>\n",
       "      <td>25.900000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.1</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.1</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75775</th>\n",
       "      <td>0</td>\n",
       "      <td>14</td>\n",
       "      <td>95579443</td>\n",
       "      <td>rs878855246</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>DICER1</td>\n",
       "      <td>0</td>\n",
       "      <td>100100</td>\n",
       "      <td>40.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>12.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10061</th>\n",
       "      <td>0</td>\n",
       "      <td>9</td>\n",
       "      <td>131284937</td>\n",
       "      <td>rs386833693</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>GLE1</td>\n",
       "      <td>1</td>\n",
       "      <td>100100</td>\n",
       "      <td>7.085000</td>\n",
       "      <td>...</td>\n",
       "      <td>7.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>38.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17065</th>\n",
       "      <td>0</td>\n",
       "      <td>X</td>\n",
       "      <td>154124377</td>\n",
       "      <td>rs137852366</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>F8</td>\n",
       "      <td>1</td>\n",
       "      <td>100100</td>\n",
       "      <td>31.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>12.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>0.5</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.2</td>\n",
       "      <td>10.0</td>\n",
       "      <td>5.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>66717</th>\n",
       "      <td>0</td>\n",
       "      <td>10</td>\n",
       "      <td>99371271</td>\n",
       "      <td>rs756489804</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>HOGA1</td>\n",
       "      <td>1</td>\n",
       "      <td>100100</td>\n",
       "      <td>25.500000</td>\n",
       "      <td>...</td>\n",
       "      <td>6.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.1</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40683</th>\n",
       "      <td>0</td>\n",
       "      <td>14</td>\n",
       "      <td>24727586</td>\n",
       "      <td>rs398122900</td>\n",
       "      <td>TGGAA</td>\n",
       "      <td>-</td>\n",
       "      <td>TGM1</td>\n",
       "      <td>1</td>\n",
       "      <td>100100</td>\n",
       "      <td>26.700000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.6</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.6</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24607</th>\n",
       "      <td>0</td>\n",
       "      <td>16</td>\n",
       "      <td>47536948</td>\n",
       "      <td>rs121918022</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>PHKB</td>\n",
       "      <td>1</td>\n",
       "      <td>100300</td>\n",
       "      <td>28.200000</td>\n",
       "      <td>...</td>\n",
       "      <td>7.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>10.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37590</th>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>119132823</td>\n",
       "      <td>rs387907031</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>ARHGAP31</td>\n",
       "      <td>1</td>\n",
       "      <td>100300</td>\n",
       "      <td>35.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>5.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>6.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.2</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>53775</th>\n",
       "      <td>0</td>\n",
       "      <td>18</td>\n",
       "      <td>10671726</td>\n",
       "      <td>rs587777450</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>PIEZO2</td>\n",
       "      <td>1</td>\n",
       "      <td>100300</td>\n",
       "      <td>34.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.9</td>\n",
       "      <td>0.6</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.1</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25543</th>\n",
       "      <td>0</td>\n",
       "      <td>5</td>\n",
       "      <td>170837547</td>\n",
       "      <td>rs587776806</td>\n",
       "      <td>-</td>\n",
       "      <td>CATG</td>\n",
       "      <td>NPM1</td>\n",
       "      <td>0</td>\n",
       "      <td>100300</td>\n",
       "      <td>44.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>45.0</td>\n",
       "      <td>100.0</td>\n",
       "      <td>31.0</td>\n",
       "      <td>223.0</td>\n",
       "      <td>237.0</td>\n",
       "      <td>150.0</td>\n",
       "      <td>92.0</td>\n",
       "      <td>55.0</td>\n",
       "      <td>202.0</td>\n",
       "      <td>120.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37593</th>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>119102045</td>\n",
       "      <td>rs145326425</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>ARHGAP31</td>\n",
       "      <td>0</td>\n",
       "      <td>100300</td>\n",
       "      <td>11.920000</td>\n",
       "      <td>...</td>\n",
       "      <td>5.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>6.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.2</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37591</th>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>119135380</td>\n",
       "      <td>rs74767080</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>ARHGAP31</td>\n",
       "      <td>1</td>\n",
       "      <td>100300</td>\n",
       "      <td>0.003000</td>\n",
       "      <td>...</td>\n",
       "      <td>5.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>6.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.2</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37592</th>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>119132823</td>\n",
       "      <td>rs387907031</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>ARHGAP31</td>\n",
       "      <td>0</td>\n",
       "      <td>100300</td>\n",
       "      <td>35.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>5.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>6.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.2</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>50487</th>\n",
       "      <td>0</td>\n",
       "      <td>16</td>\n",
       "      <td>18804606</td>\n",
       "      <td>rs879255572</td>\n",
       "      <td>GTTT</td>\n",
       "      <td>-</td>\n",
       "      <td>ARL6IP1</td>\n",
       "      <td>1</td>\n",
       "      <td>100800</td>\n",
       "      <td>39.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>8.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>77.0</td>\n",
       "      <td>52.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>55.0</td>\n",
       "      <td>39.0</td>\n",
       "      <td>71.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>66339</th>\n",
       "      <td>0</td>\n",
       "      <td>12</td>\n",
       "      <td>109994886</td>\n",
       "      <td>rs369296618</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>MMAB</td>\n",
       "      <td>1</td>\n",
       "      <td>100800</td>\n",
       "      <td>37.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>3.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28164</th>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>1803657</td>\n",
       "      <td>rs121913114</td>\n",
       "      <td>A</td>\n",
       "      <td>T</td>\n",
       "      <td>FGFR3</td>\n",
       "      <td>1</td>\n",
       "      <td>100800</td>\n",
       "      <td>25.300000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.8</td>\n",
       "      <td>6.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>24.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>9.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56335</th>\n",
       "      <td>0</td>\n",
       "      <td>16</td>\n",
       "      <td>89818545</td>\n",
       "      <td>rs587783028</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>FANCA</td>\n",
       "      <td>0</td>\n",
       "      <td>100800</td>\n",
       "      <td>25.500000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.3</td>\n",
       "      <td>1.0</td>\n",
       "      <td>4.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>79871</th>\n",
       "      <td>0</td>\n",
       "      <td>8</td>\n",
       "      <td>61743032</td>\n",
       "      <td>rs886040989</td>\n",
       "      <td>A</td>\n",
       "      <td>AA</td>\n",
       "      <td>CHD7</td>\n",
       "      <td>1</td>\n",
       "      <td>100800</td>\n",
       "      <td>32.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.8</td>\n",
       "      <td>0.6</td>\n",
       "      <td>0.5</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.9</td>\n",
       "      <td>0.8</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28166</th>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>1803657</td>\n",
       "      <td>rs121913114</td>\n",
       "      <td>A</td>\n",
       "      <td>T</td>\n",
       "      <td>FGFR3</td>\n",
       "      <td>0</td>\n",
       "      <td>100800</td>\n",
       "      <td>25.300000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.8</td>\n",
       "      <td>6.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>24.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>9.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28031</th>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>1803236</td>\n",
       "      <td>rs2305180</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>FGFR3</td>\n",
       "      <td>1</td>\n",
       "      <td>100800</td>\n",
       "      <td>11.620000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.8</td>\n",
       "      <td>6.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>24.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>9.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28077</th>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>1806519</td>\n",
       "      <td>rs3135890</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>FGFR3</td>\n",
       "      <td>0</td>\n",
       "      <td>100800</td>\n",
       "      <td>6.723000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.8</td>\n",
       "      <td>6.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>24.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>9.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28076</th>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>1807371</td>\n",
       "      <td>rs28933068</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>FGFR3</td>\n",
       "      <td>1</td>\n",
       "      <td>100800</td>\n",
       "      <td>27.800000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.8</td>\n",
       "      <td>6.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>24.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>9.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28038</th>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>1806104</td>\n",
       "      <td>rs75790268</td>\n",
       "      <td>G</td>\n",
       "      <td>T</td>\n",
       "      <td>FGFR3</td>\n",
       "      <td>0</td>\n",
       "      <td>100800</td>\n",
       "      <td>15.720000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.8</td>\n",
       "      <td>6.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>24.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>9.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28036</th>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>1806104</td>\n",
       "      <td>rs75790268</td>\n",
       "      <td>G</td>\n",
       "      <td>T</td>\n",
       "      <td>FGFR3</td>\n",
       "      <td>1</td>\n",
       "      <td>100800</td>\n",
       "      <td>15.720000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.8</td>\n",
       "      <td>6.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>24.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>9.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28089</th>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>1806519</td>\n",
       "      <td>rs3135890</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>FGFR3</td>\n",
       "      <td>1</td>\n",
       "      <td>100800</td>\n",
       "      <td>6.723000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.8</td>\n",
       "      <td>6.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>24.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>9.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>72713</th>\n",
       "      <td>0</td>\n",
       "      <td>X</td>\n",
       "      <td>148579839</td>\n",
       "      <td>rs113993947</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>IDS</td>\n",
       "      <td>1</td>\n",
       "      <td>617297</td>\n",
       "      <td>24.200000</td>\n",
       "      <td>...</td>\n",
       "      <td>10.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22755</th>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>47604160</td>\n",
       "      <td>rs606231204</td>\n",
       "      <td>C</td>\n",
       "      <td>CC</td>\n",
       "      <td>EPCAM</td>\n",
       "      <td>1</td>\n",
       "      <td>617297</td>\n",
       "      <td>23.500000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.1</td>\n",
       "      <td>121.0</td>\n",
       "      <td>0.9</td>\n",
       "      <td>60.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>80.0</td>\n",
       "      <td>30.0</td>\n",
       "      <td>690.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>18.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21099</th>\n",
       "      <td>0</td>\n",
       "      <td>X</td>\n",
       "      <td>153596100</td>\n",
       "      <td>rs137853318</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>FLNA</td>\n",
       "      <td>1</td>\n",
       "      <td>617303</td>\n",
       "      <td>27.900000</td>\n",
       "      <td>...</td>\n",
       "      <td>21.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>44.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>501.0</td>\n",
       "      <td>0.7</td>\n",
       "      <td>36.0</td>\n",
       "      <td>41.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52967</th>\n",
       "      <td>0</td>\n",
       "      <td>7</td>\n",
       "      <td>5569255</td>\n",
       "      <td>rs281875331</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>ACTB</td>\n",
       "      <td>1</td>\n",
       "      <td>617303</td>\n",
       "      <td>24.700000</td>\n",
       "      <td>...</td>\n",
       "      <td>96.0</td>\n",
       "      <td>440.0</td>\n",
       "      <td>218.0</td>\n",
       "      <td>953.0</td>\n",
       "      <td>753.0</td>\n",
       "      <td>333.0</td>\n",
       "      <td>1338.0</td>\n",
       "      <td>384.0</td>\n",
       "      <td>1320.0</td>\n",
       "      <td>354.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59253</th>\n",
       "      <td>0</td>\n",
       "      <td>19</td>\n",
       "      <td>42490320</td>\n",
       "      <td>rs606231427</td>\n",
       "      <td>T</td>\n",
       "      <td>A</td>\n",
       "      <td>ATP1A3</td>\n",
       "      <td>1</td>\n",
       "      <td>617303</td>\n",
       "      <td>28.400000</td>\n",
       "      <td>...</td>\n",
       "      <td>31.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.2</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.2</td>\n",
       "      <td>16.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>68189</th>\n",
       "      <td>0</td>\n",
       "      <td>18</td>\n",
       "      <td>6973129</td>\n",
       "      <td>rs797045182</td>\n",
       "      <td>G</td>\n",
       "      <td>-</td>\n",
       "      <td>LAMA1</td>\n",
       "      <td>1</td>\n",
       "      <td>617303</td>\n",
       "      <td>24.178707</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.6</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.1</td>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83764</th>\n",
       "      <td>1</td>\n",
       "      <td>12</td>\n",
       "      <td>122717464</td>\n",
       "      <td>rs767748011</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>VPS33A</td>\n",
       "      <td>1</td>\n",
       "      <td>617303</td>\n",
       "      <td>35.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>5.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>63387</th>\n",
       "      <td>0</td>\n",
       "      <td>17</td>\n",
       "      <td>42985496</td>\n",
       "      <td>rs267607508</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>GFAP</td>\n",
       "      <td>1</td>\n",
       "      <td>617303</td>\n",
       "      <td>22.800000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13789</th>\n",
       "      <td>0</td>\n",
       "      <td>21</td>\n",
       "      <td>45194641</td>\n",
       "      <td>rs147484110</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>CSTB</td>\n",
       "      <td>1</td>\n",
       "      <td>617303</td>\n",
       "      <td>24.400000</td>\n",
       "      <td>...</td>\n",
       "      <td>17.0</td>\n",
       "      <td>26.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>154.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>18.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83766</th>\n",
       "      <td>1</td>\n",
       "      <td>12</td>\n",
       "      <td>122717464</td>\n",
       "      <td>rs767748011</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>VPS33A</td>\n",
       "      <td>0</td>\n",
       "      <td>617303</td>\n",
       "      <td>35.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>5.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12450</th>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>38302530</td>\n",
       "      <td>rs72549389</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>CYP1B1</td>\n",
       "      <td>1</td>\n",
       "      <td>617315</td>\n",
       "      <td>23.100000</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>10.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>64007</th>\n",
       "      <td>0</td>\n",
       "      <td>12</td>\n",
       "      <td>20769228</td>\n",
       "      <td>rs794726864</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>PDE3A</td>\n",
       "      <td>1</td>\n",
       "      <td>617315</td>\n",
       "      <td>26.200000</td>\n",
       "      <td>...</td>\n",
       "      <td>27.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>1.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>50381</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>220327318</td>\n",
       "      <td>rs587777169</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>RAB3GAP2</td>\n",
       "      <td>1</td>\n",
       "      <td>617315</td>\n",
       "      <td>45.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>3.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33885</th>\n",
       "      <td>0</td>\n",
       "      <td>X</td>\n",
       "      <td>107863603</td>\n",
       "      <td>rs104886191</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>COL4A5</td>\n",
       "      <td>0</td>\n",
       "      <td>617315</td>\n",
       "      <td>24.300000</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>0.3</td>\n",
       "      <td>1.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>0.3</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>4.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52725</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>147231124</td>\n",
       "      <td>rs587777304</td>\n",
       "      <td>T</td>\n",
       "      <td>A</td>\n",
       "      <td>GJA5</td>\n",
       "      <td>1</td>\n",
       "      <td>617315</td>\n",
       "      <td>27.200000</td>\n",
       "      <td>...</td>\n",
       "      <td>6.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>0.5</td>\n",
       "      <td>15.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>3.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52905</th>\n",
       "      <td>0</td>\n",
       "      <td>16</td>\n",
       "      <td>731520</td>\n",
       "      <td>rs587777342</td>\n",
       "      <td>G</td>\n",
       "      <td>T</td>\n",
       "      <td>STUB1</td>\n",
       "      <td>1</td>\n",
       "      <td>617315</td>\n",
       "      <td>26.800000</td>\n",
       "      <td>...</td>\n",
       "      <td>16.0</td>\n",
       "      <td>23.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>23.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>23.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>10.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12619</th>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>166606311</td>\n",
       "      <td>rs267606841</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>GALNT3</td>\n",
       "      <td>1</td>\n",
       "      <td>617315</td>\n",
       "      <td>27.700000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.1</td>\n",
       "      <td>4.0</td>\n",
       "      <td>0.7</td>\n",
       "      <td>8.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>34.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>17.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>78415</th>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>239261575</td>\n",
       "      <td>rs750055952</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>TRAF3IP1</td>\n",
       "      <td>1</td>\n",
       "      <td>617315</td>\n",
       "      <td>26.300000</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>11.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3075</th>\n",
       "      <td>0</td>\n",
       "      <td>12</td>\n",
       "      <td>116413092</td>\n",
       "      <td>rs28940310</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>MED13L</td>\n",
       "      <td>0</td>\n",
       "      <td>617315</td>\n",
       "      <td>35.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>11.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12452</th>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>38302530</td>\n",
       "      <td>rs72549389</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>CYP1B1</td>\n",
       "      <td>0</td>\n",
       "      <td>617315</td>\n",
       "      <td>23.100000</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>10.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43293</th>\n",
       "      <td>0</td>\n",
       "      <td>11</td>\n",
       "      <td>76901153</td>\n",
       "      <td>rs111033178</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>MYO7A</td>\n",
       "      <td>1</td>\n",
       "      <td>617319</td>\n",
       "      <td>34.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.6</td>\n",
       "      <td>7.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.7</td>\n",
       "      <td>0.7</td>\n",
       "      <td>0.5</td>\n",
       "      <td>3.0</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83796</th>\n",
       "      <td>1</td>\n",
       "      <td>19</td>\n",
       "      <td>17014434</td>\n",
       "      <td>rs369858688</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>CPAMD8</td>\n",
       "      <td>1</td>\n",
       "      <td>617319</td>\n",
       "      <td>24.600000</td>\n",
       "      <td>...</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.1</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.5</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83794</th>\n",
       "      <td>1</td>\n",
       "      <td>19</td>\n",
       "      <td>17081703</td>\n",
       "      <td>rs756064750</td>\n",
       "      <td>G</td>\n",
       "      <td>GG</td>\n",
       "      <td>CPAMD8</td>\n",
       "      <td>0</td>\n",
       "      <td>617319</td>\n",
       "      <td>21.700000</td>\n",
       "      <td>...</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.1</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.5</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>78131</th>\n",
       "      <td>0</td>\n",
       "      <td>17</td>\n",
       "      <td>17125842</td>\n",
       "      <td>rs879255663</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>FLCN</td>\n",
       "      <td>0</td>\n",
       "      <td>617319</td>\n",
       "      <td>40.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>4.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>67717</th>\n",
       "      <td>0</td>\n",
       "      <td>7</td>\n",
       "      <td>116199283</td>\n",
       "      <td>rs797044871</td>\n",
       "      <td>TT</td>\n",
       "      <td>-</td>\n",
       "      <td>CAV1</td>\n",
       "      <td>1</td>\n",
       "      <td>617319</td>\n",
       "      <td>44.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>62.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>258.0</td>\n",
       "      <td>79.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>117.0</td>\n",
       "      <td>0.2</td>\n",
       "      <td>102.0</td>\n",
       "      <td>29.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1493</th>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>220022905</td>\n",
       "      <td>rs886037606</td>\n",
       "      <td>TAC</td>\n",
       "      <td>AA</td>\n",
       "      <td>NHEJ1</td>\n",
       "      <td>0</td>\n",
       "      <td>617319</td>\n",
       "      <td>28.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.2</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83798</th>\n",
       "      <td>1</td>\n",
       "      <td>19</td>\n",
       "      <td>17014434</td>\n",
       "      <td>rs369858688</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>CPAMD8</td>\n",
       "      <td>0</td>\n",
       "      <td>617319</td>\n",
       "      <td>24.600000</td>\n",
       "      <td>...</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.1</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.5</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70631</th>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>15581710</td>\n",
       "      <td>rs763735590</td>\n",
       "      <td>TG</td>\n",
       "      <td>-</td>\n",
       "      <td>CC2D2A</td>\n",
       "      <td>1</td>\n",
       "      <td>617319</td>\n",
       "      <td>27.200000</td>\n",
       "      <td>...</td>\n",
       "      <td>1.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>3.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>0.7</td>\n",
       "      <td>4.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>1.0</td>\n",
       "      <td>3.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83792</th>\n",
       "      <td>1</td>\n",
       "      <td>19</td>\n",
       "      <td>17081703</td>\n",
       "      <td>rs756064750</td>\n",
       "      <td>G</td>\n",
       "      <td>GG</td>\n",
       "      <td>CPAMD8</td>\n",
       "      <td>1</td>\n",
       "      <td>617319</td>\n",
       "      <td>21.700000</td>\n",
       "      <td>...</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.1</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.5</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2519</th>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>35782404</td>\n",
       "      <td>rs104893976</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>LHFPL5</td>\n",
       "      <td>1</td>\n",
       "      <td>617319</td>\n",
       "      <td>34.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>83800 rows × 88 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       Label Chr   Position         RSID           Ref   Alt      Gene  GT  \\\n",
       "60939      0   8   41791859  rs786200952             T    TT     KAT6A   0   \n",
       "26955      0  11    5275647   rs34474104             G     A      HBG2   0   \n",
       "79875      0   8   61748664  rs886040990          GAAA     -      CHD7   1   \n",
       "35354      1   1  240071924  rs587776862  GCCTGAGGAGGA     T     CHRM3   1   \n",
       "83127      0  12   76740088  rs375413604             G     C     BBS10   1   \n",
       "1819       0  20     948667   rs74315420             T     C     RSPO4   1   \n",
       "75775      0  14   95579443  rs878855246             G     A    DICER1   0   \n",
       "10061      0   9  131284937  rs386833693             A     G      GLE1   1   \n",
       "17065      0   X  154124377  rs137852366             C     G        F8   1   \n",
       "66717      0  10   99371271  rs756489804             C     T     HOGA1   1   \n",
       "40683      0  14   24727586  rs398122900         TGGAA     -      TGM1   1   \n",
       "24607      0  16   47536948  rs121918022             G     C      PHKB   1   \n",
       "37590      1   3  119132823  rs387907031             C     T  ARHGAP31   1   \n",
       "53775      0  18   10671726  rs587777450             C     T    PIEZO2   1   \n",
       "25543      0   5  170837547  rs587776806             -  CATG      NPM1   0   \n",
       "37593      0   3  119102045  rs145326425             C     T  ARHGAP31   0   \n",
       "37591      0   3  119135380   rs74767080             A     G  ARHGAP31   1   \n",
       "37592      1   3  119132823  rs387907031             C     T  ARHGAP31   0   \n",
       "50487      0  16   18804606  rs879255572          GTTT     -   ARL6IP1   1   \n",
       "66339      0  12  109994886  rs369296618             G     A      MMAB   1   \n",
       "28164      1   4    1803657  rs121913114             A     T     FGFR3   1   \n",
       "56335      0  16   89818545  rs587783028             C     A     FANCA   0   \n",
       "79871      0   8   61743032  rs886040989             A    AA      CHD7   1   \n",
       "28166      1   4    1803657  rs121913114             A     T     FGFR3   0   \n",
       "28031      0   4    1803236    rs2305180             C     T     FGFR3   1   \n",
       "28077      0   4    1806519    rs3135890             C     T     FGFR3   0   \n",
       "28076      1   4    1807371   rs28933068             C     A     FGFR3   1   \n",
       "28038      1   4    1806104   rs75790268             G     T     FGFR3   0   \n",
       "28036      1   4    1806104   rs75790268             G     T     FGFR3   1   \n",
       "28089      0   4    1806519    rs3135890             C     T     FGFR3   1   \n",
       "...      ...  ..        ...          ...           ...   ...       ...  ..   \n",
       "72713      0   X  148579839  rs113993947             C     G       IDS   1   \n",
       "22755      0   2   47604160  rs606231204             C    CC     EPCAM   1   \n",
       "21099      0   X  153596100  rs137853318             C     A      FLNA   1   \n",
       "52967      0   7    5569255  rs281875331             T     G      ACTB   1   \n",
       "59253      0  19   42490320  rs606231427             T     A    ATP1A3   1   \n",
       "68189      0  18    6973129  rs797045182             G     -     LAMA1   1   \n",
       "83764      1  12  122717464  rs767748011             G     A    VPS33A   1   \n",
       "63387      0  17   42985496  rs267607508             G     A      GFAP   1   \n",
       "13789      0  21   45194641  rs147484110             C     G      CSTB   1   \n",
       "83766      1  12  122717464  rs767748011             G     A    VPS33A   0   \n",
       "12450      1   2   38302530   rs72549389             A     G    CYP1B1   1   \n",
       "64007      0  12   20769228  rs794726864             C     G     PDE3A   1   \n",
       "50381      0   1  220327318  rs587777169             G     A  RAB3GAP2   1   \n",
       "33885      0   X  107863603  rs104886191             G     A    COL4A5   0   \n",
       "52725      0   1  147231124  rs587777304             T     A      GJA5   1   \n",
       "52905      0  16     731520  rs587777342             G     T     STUB1   1   \n",
       "12619      0   2  166606311  rs267606841             A     C    GALNT3   1   \n",
       "78415      0   2  239261575  rs750055952             T     G  TRAF3IP1   1   \n",
       "3075       0  12  116413092   rs28940310             C     T    MED13L   0   \n",
       "12452      1   2   38302530   rs72549389             A     G    CYP1B1   0   \n",
       "43293      0  11   76901153  rs111033178             G     A     MYO7A   1   \n",
       "83796      1  19   17014434  rs369858688             C     T    CPAMD8   1   \n",
       "83794      1  19   17081703  rs756064750             G    GG    CPAMD8   0   \n",
       "78131      0  17   17125842  rs879255663             C     T      FLCN   0   \n",
       "67717      0   7  116199283  rs797044871            TT     -      CAV1   1   \n",
       "1493       0   2  220022905  rs886037606           TAC    AA     NHEJ1   0   \n",
       "83798      1  19   17014434  rs369858688             C     T    CPAMD8   0   \n",
       "70631      0   4   15581710  rs763735590            TG     -    CC2D2A   1   \n",
       "83792      1  19   17081703  rs756064750             G    GG    CPAMD8   1   \n",
       "2519       0   6   35782404  rs104893976             C     T    LHFPL5   1   \n",
       "\n",
       "         OMIM       CADD   ...    heart  kidney  liver   lung  ovary  \\\n",
       "60939  100100  35.000000   ...      2.0     2.0    2.0    3.0   11.0   \n",
       "26955  100100  22.800000   ...      0.0     0.1    0.0    0.0    0.1   \n",
       "79875  100100  32.000000   ...      0.8     0.6    0.5    0.4    0.9   \n",
       "35354  100100  40.000000   ...      0.0     0.4    0.1    0.6    1.0   \n",
       "83127  100100  35.000000   ...      4.0     4.0    3.0   14.0    6.0   \n",
       "1819   100100  25.900000   ...      0.0     0.1    0.1    2.0    0.0   \n",
       "75775  100100  40.000000   ...      2.0     3.0    4.0    6.0    8.0   \n",
       "10061  100100   7.085000   ...      7.0     8.0    7.0   11.0   13.0   \n",
       "17065  100100  31.000000   ...     12.0     3.0    2.0   22.0    5.0   \n",
       "66717  100100  25.500000   ...      6.0    15.0    8.0    0.4    0.1   \n",
       "40683  100100  26.700000   ...      0.1     0.3    0.1    0.6    0.2   \n",
       "24607  100300  28.200000   ...      7.0     8.0    4.0    8.0    6.0   \n",
       "37590  100300  35.000000   ...      5.0     2.0    0.4    6.0   10.0   \n",
       "53775  100300  34.000000   ...      0.0     0.3    0.9    0.6    2.0   \n",
       "25543  100300  44.000000   ...     45.0   100.0   31.0  223.0  237.0   \n",
       "37593  100300  11.920000   ...      5.0     2.0    0.4    6.0   10.0   \n",
       "37591  100300   0.003000   ...      5.0     2.0    0.4    6.0   10.0   \n",
       "37592  100300  35.000000   ...      5.0     2.0    0.4    6.0   10.0   \n",
       "50487  100800  39.000000   ...      8.0    40.0   35.0   77.0   52.0   \n",
       "66339  100800  37.000000   ...      3.0     5.0    4.0    4.0    3.0   \n",
       "28164  100800  25.300000   ...      0.8     6.0    8.0    4.0    0.0   \n",
       "56335  100800  25.500000   ...      0.0     0.0    0.4    0.4    0.2   \n",
       "79871  100800  32.000000   ...      0.8     0.6    0.5    0.4    0.9   \n",
       "28166  100800  25.300000   ...      0.8     6.0    8.0    4.0    0.0   \n",
       "28031  100800  11.620000   ...      0.8     6.0    8.0    4.0    0.0   \n",
       "28077  100800   6.723000   ...      0.8     6.0    8.0    4.0    0.0   \n",
       "28076  100800  27.800000   ...      0.8     6.0    8.0    4.0    0.0   \n",
       "28038  100800  15.720000   ...      0.8     6.0    8.0    4.0    0.0   \n",
       "28036  100800  15.720000   ...      0.8     6.0    8.0    4.0    0.0   \n",
       "28089  100800   6.723000   ...      0.8     6.0    8.0    4.0    0.0   \n",
       "...       ...        ...   ...      ...     ...    ...    ...    ...   \n",
       "72713  617297  24.200000   ...     10.0     7.0    3.0   17.0   28.0   \n",
       "22755  617297  23.500000   ...      0.1   121.0    0.9   60.0    0.4   \n",
       "21099  617303  27.900000   ...     21.0    13.0    5.0   18.0   44.0   \n",
       "52967  617303  24.700000   ...     96.0   440.0  218.0  953.0  753.0   \n",
       "59253  617303  28.400000   ...     31.0     0.0    0.0    0.0    0.2   \n",
       "68189  617303  24.178707   ...      0.0     0.6    0.0    0.0    2.0   \n",
       "83764  617303  35.000000   ...      1.0     1.0    1.0    3.0    4.0   \n",
       "63387  617303  22.800000   ...      0.3     0.2    0.0    0.0    0.1   \n",
       "13789  617303  24.400000   ...     17.0    26.0   15.0  154.0   32.0   \n",
       "83766  617303  35.000000   ...      1.0     1.0    1.0    3.0    4.0   \n",
       "12450  617315  23.100000   ...      2.0     5.0    1.0   25.0   11.0   \n",
       "64007  617315  26.200000   ...     27.0     2.0    0.4    1.0    7.0   \n",
       "50381  617315  45.000000   ...      3.0     3.0    3.0    4.0    4.0   \n",
       "33885  617315  24.300000   ...      2.0     3.0    0.3    1.0   13.0   \n",
       "52725  617315  27.200000   ...      6.0    15.0    0.5   15.0   13.0   \n",
       "52905  617315  26.800000   ...     16.0    23.0    7.0   23.0    2.0   \n",
       "12619  617315  27.700000   ...      0.1     4.0    0.7    8.0    1.0   \n",
       "78415  617315  26.300000   ...      2.0     2.0    2.0    3.0    5.0   \n",
       "3075   617315  35.000000   ...      2.0     2.0    2.0    3.0   11.0   \n",
       "12452  617315  23.100000   ...      2.0     5.0    1.0   25.0   11.0   \n",
       "43293  617319  34.000000   ...      0.4     0.6    7.0    0.4    1.0   \n",
       "83796  617319  24.600000   ...      3.0     1.0    0.1    1.0    0.3   \n",
       "83794  617319  21.700000   ...      3.0     1.0    0.1    1.0    0.3   \n",
       "78131  617319  40.000000   ...      3.0     1.0    2.0    2.0    3.0   \n",
       "67717  617319  44.000000   ...     62.0     6.0    4.0  258.0   79.0   \n",
       "1493   617319  28.000000   ...      0.1     0.2    0.2    0.2    0.1   \n",
       "83798  617319  24.600000   ...      3.0     1.0    0.1    1.0    0.3   \n",
       "70631  617319  27.200000   ...      1.0     5.0    0.4    3.0    4.0   \n",
       "83792  617319  21.700000   ...      3.0     1.0    0.1    1.0    0.3   \n",
       "2519   617319  34.000000   ...      0.0     0.0    0.0    0.0    0.0   \n",
       "\n",
       "       pancreas  sigmoid colon  small intestine  spleen  testis  \n",
       "60939       2.0            4.0              7.0     6.0    12.0  \n",
       "26955       0.0            0.0              0.0     0.4     0.0  \n",
       "79875       0.8            1.0              2.0     3.0     2.0  \n",
       "35354       1.0            2.0              0.4     0.3     0.8  \n",
       "83127       2.0            5.0              2.0    10.0     7.0  \n",
       "1819        0.0            0.2              0.1     0.1     1.0  \n",
       "75775       3.0            4.0              8.0    12.0    12.0  \n",
       "10061       7.0            9.0             11.0    15.0    38.0  \n",
       "17065       0.5            1.0              0.2    10.0     5.0  \n",
       "66717       2.0            0.0              0.0     0.0     0.4  \n",
       "40683       0.4            0.4              0.2     0.6     1.0  \n",
       "24607       6.0            5.0             10.0    10.0    10.0  \n",
       "37590       1.0            2.0              0.2     3.0     2.0  \n",
       "53775       0.1            1.0              0.0     0.4     0.9  \n",
       "25543     150.0           92.0             55.0   202.0   120.0  \n",
       "37593       1.0            2.0              0.2     3.0     2.0  \n",
       "37591       1.0            2.0              0.2     3.0     2.0  \n",
       "37592       1.0            2.0              0.2     3.0     2.0  \n",
       "50487      22.0           17.0             55.0    39.0    71.0  \n",
       "66339       4.0            2.0              2.0     2.0     3.0  \n",
       "28164      24.0            3.0             14.0     1.0     9.0  \n",
       "56335       0.2            0.4              0.3     1.0     4.0  \n",
       "79871       0.8            1.0              2.0     3.0     2.0  \n",
       "28166      24.0            3.0             14.0     1.0     9.0  \n",
       "28031      24.0            3.0             14.0     1.0     9.0  \n",
       "28077      24.0            3.0             14.0     1.0     9.0  \n",
       "28076      24.0            3.0             14.0     1.0     9.0  \n",
       "28038      24.0            3.0             14.0     1.0     9.0  \n",
       "28036      24.0            3.0             14.0     1.0     9.0  \n",
       "28089      24.0            3.0             14.0     1.0     9.0  \n",
       "...         ...            ...              ...     ...     ...  \n",
       "72713       7.0           12.0             10.0    17.0     7.0  \n",
       "22755      80.0           30.0            690.0     2.0    18.0  \n",
       "21099       8.0          501.0              0.7    36.0    41.0  \n",
       "52967     333.0         1338.0            384.0  1320.0   354.0  \n",
       "59253       0.2            1.0              0.0     0.2    16.0  \n",
       "68189       0.1            0.1              0.1     0.1     7.0  \n",
       "83764       1.0            2.0              2.0     3.0     5.0  \n",
       "63387       0.0            0.0              0.1     0.0     0.0  \n",
       "13789      14.0           12.0             13.0    17.0    18.0  \n",
       "83766       1.0            2.0              2.0     3.0     5.0  \n",
       "12450       3.0            1.0              0.0    35.0    10.0  \n",
       "64007       3.0           11.0             10.0     2.0     1.0  \n",
       "50381       3.0            3.0              5.0     6.0     6.0  \n",
       "33885       0.3            2.0              0.0     3.0     4.0  \n",
       "52725       1.0            2.0              0.0     3.0     3.0  \n",
       "52905      23.0           13.0             11.0    22.0    10.0  \n",
       "12619       9.0            1.0             34.0     7.0    17.0  \n",
       "78415       2.0            4.0              3.0     3.0    11.0  \n",
       "3075        2.0            4.0              5.0     7.0    11.0  \n",
       "12452       3.0            1.0              0.0    35.0    10.0  \n",
       "43293       0.7            0.7              0.5     3.0     6.0  \n",
       "83796       0.2            0.3              0.0     0.5     1.0  \n",
       "83794       0.2            0.3              0.0     0.5     1.0  \n",
       "78131       1.0            8.0              6.0     3.0     4.0  \n",
       "67717       8.0          117.0              0.2   102.0    29.0  \n",
       "1493        0.1            0.2              1.0     0.3     0.7  \n",
       "83798       0.2            0.3              0.0     0.5     1.0  \n",
       "70631       0.7            4.0              0.4     1.0     3.0  \n",
       "83792       0.2            0.3              0.0     0.5     1.0  \n",
       "2519        3.0            0.0              0.0     0.0     0.0  \n",
       "\n",
       "[83800 rows x 88 columns]"
      ]
     },
     "execution_count": 163,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "columns = ['adipose tissue', 'adrenal gland', 'brain', 'heart', 'kidney',\n",
    "       'liver', 'lung', 'ovary', 'pancreas', 'sigmoid colon',\n",
    "       'small intestine', 'spleen', 'testis']\n",
    "\n",
    "recode_empty_cells(final, columns)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 164,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "final.to_csv('Human_PVP_no_norm_brca.csv', index=None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 166,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'df_tissue' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-166-9c5f842f2e8c>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;32mdel\u001b[0m \u001b[0mdf_tissue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0;32mdel\u001b[0m \u001b[0mdf_data\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0;31m#del result\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mNameError\u001b[0m: name 'df_tissue' is not defined"
     ]
    }
   ],
   "source": [
    "del df_tissue\n",
    "del df_data\n",
    "#del result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 167,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "df_test1 = final.iloc[:3000, :]\n",
    "df_test2 = final.iloc[78000:, :]\n",
    "\n",
    "df_train = final.iloc[3000:78000, :]\n",
    "\n",
    "frames = [df_test1, df_test2]\n",
    "df_test = pd.concat(frames)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 168,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "df_test.to_csv('PVP_human_tis_no_norm_test.csv', index=None, header=True)\n",
    "df_train.to_csv('PVP_human_tis_no_norm_train.csv', index=None, header=True) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 169,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "del df_train, df_test, df_test1, df_test2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Not normalized data (model 1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 170,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "df_1 = pd.read_csv('PVP_human_tis_no_norm_train.csv')\n",
    "df_2 = pd.read_csv('PVP_human_tis_no_norm_test.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 171,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "df_1.drop(['Chr', 'Position', 'RSID', 'Ref', 'Alt', 'Gene' , 'OMIM'], axis =1, inplace = True)\n",
    "df_2.drop(['Chr', 'Position', 'RSID', 'Ref', 'Alt', 'Gene' , 'OMIM'], axis = 1, inplace = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 110,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Label                        int64\n",
       "GT                           int64\n",
       "CADD                       float64\n",
       "GWAVA                      float64\n",
       "DANN                       float64\n",
       "Similarity_score           float64\n",
       "HP_0000078                   int64\n",
       "HP_0000291                   int64\n",
       "HP_0000708                   int64\n",
       "HP_0001001                   int64\n",
       "HP_0001939                   int64\n",
       "HP_0002086                   int64\n",
       "HP_0006476                   int64\n",
       "HP_0009126                   int64\n",
       "HP_0010515                   int64\n",
       "HP_0010948                   int64\n",
       "HP_0010987                   int64\n",
       "HP_0011017                   int64\n",
       "HP_0011025                   int64\n",
       "HP_0011277                   int64\n",
       "HP_0011482                   int64\n",
       "HP_0011915                   int64\n",
       "HP_0040063                   int64\n",
       "MP_0000003                   int64\n",
       "MP_0000358                   int64\n",
       "MP_0000428                   int64\n",
       "MP_0000462                   int64\n",
       "MP_0000516                   int64\n",
       "MP_0000685                   int64\n",
       "MP_0000716                   int64\n",
       "                            ...   \n",
       "MP_0004134                   int64\n",
       "MP_0005408                   int64\n",
       "MP_0005451                   int64\n",
       "MP_0005621                   int64\n",
       "MP_0009389                   int64\n",
       "MP_0010678                   int64\n",
       "MP_0010769                   int64\n",
       "MP_0012719                   int64\n",
       "MP_0013328                   int64\n",
       "Inheritence_mode_0           int64\n",
       "Inheritence_mode_1           int64\n",
       "Inheritence_mode_2           int64\n",
       "Inheritence_mode_3           int64\n",
       "CADD_impute                  int64\n",
       "GWAVA_impute                 int64\n",
       "Similarity_score_impute      int64\n",
       "DANN_impute                  int64\n",
       "adipose tissue             float64\n",
       "adrenal gland              float64\n",
       "brain                      float64\n",
       "heart                      float64\n",
       "kidney                     float64\n",
       "liver                      float64\n",
       "lung                       float64\n",
       "ovary                      float64\n",
       "pancreas                   float64\n",
       "sigmoid colon              float64\n",
       "small intestine            float64\n",
       "spleen                     float64\n",
       "testis                     float64\n",
       "dtype: object"
      ]
     },
     "execution_count": 110,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_1.dtypes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 172,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import os\n",
    "\n",
    "num_train_entries = df_1.shape[0]\n",
    "num_train_features = df_1.shape[1] - 1    \n",
    "\n",
    "num_test_entries = df_2.shape[0]\n",
    "num_test_features = df_2.shape[1] - 1    # The data frames are written as a temporary CSV file, as we still\n",
    "# need to modify the header row to include the number of rows and\n",
    "# columns present in the training and testing CSV files.\n",
    "df_1.to_csv('train_temp.csv', index=False, header=None)\n",
    "df_2.to_csv('test_temp.csv', index=False, header=None)    \n",
    "\n",
    "# Append onto the header row the information about how many\n",
    "# columns and rows are in each file as TensorFlow requires.\n",
    "open('tissue1_train.csv', 'w').write(str(num_train_entries) +\n",
    "                                     ',' + str(num_train_features) + ',CTRL,CASE\\n' +\n",
    "                                     open('train_temp.csv').read())    \n",
    "\n",
    "open('tissue1_test.csv', 'w').write(str(num_test_entries) +\n",
    "                                     ',' + str(num_test_features) + ',CTRL,CASE\\n' +\n",
    "                                     open('test_temp.csv').read())    # Remove the temporary CSV files that were generated above.\n",
    "os.remove('train_temp.csv')\n",
    "os.remove('test_temp.csv')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## -End-"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Row Normalized (Model2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 179,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "df =  pd.read_table('../arff/tissue_data_human.tsv')\n",
    "\n",
    "del df['Gene ID']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 180,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Gene</th>\n",
       "      <th>adipose tissue</th>\n",
       "      <th>adrenal gland</th>\n",
       "      <th>brain</th>\n",
       "      <th>heart</th>\n",
       "      <th>kidney</th>\n",
       "      <th>liver</th>\n",
       "      <th>lung</th>\n",
       "      <th>ovary</th>\n",
       "      <th>pancreas</th>\n",
       "      <th>sigmoid colon</th>\n",
       "      <th>small intestine</th>\n",
       "      <th>spleen</th>\n",
       "      <th>testis</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TSPAN6</td>\n",
       "      <td>12.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>15.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TNMD</td>\n",
       "      <td>9.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.9</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DPM1</td>\n",
       "      <td>21.0</td>\n",
       "      <td>44.0</td>\n",
       "      <td>23.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>27.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>55.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>26.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>41.0</td>\n",
       "      <td>37.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SCYL3</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>4.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>C1orf112</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.5</td>\n",
       "      <td>3.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.7</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.7</td>\n",
       "      <td>0.8</td>\n",
       "      <td>0.4</td>\n",
       "      <td>2.0</td>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       Gene  adipose tissue  adrenal gland  brain  heart  kidney  liver  lung  \\\n",
       "0    TSPAN6            12.0            6.0    2.0    2.0    18.0   17.0  10.0   \n",
       "1      TNMD             9.0            0.0    0.0    0.0     0.9    0.0   0.0   \n",
       "2      DPM1            21.0           44.0   23.0   22.0    27.0   15.0  55.0   \n",
       "3     SCYL3             2.0            3.0    1.0    1.0     2.0    3.0   3.0   \n",
       "4  C1orf112             1.0            0.5    3.0    0.4     0.4    0.7   1.0   \n",
       "\n",
       "   ovary  pancreas  sigmoid colon  small intestine  spleen  testis  \n",
       "0   17.0       7.0            6.0             19.0     5.0    15.0  \n",
       "1    1.0       0.1            0.1              0.0     0.0     0.2  \n",
       "2   17.0      26.0           20.0             22.0    41.0    37.0  \n",
       "3    2.0       3.0            2.0              4.0     4.0     4.0  \n",
       "4    1.0       0.7            0.8              0.4     2.0     7.0  "
      ]
     },
     "execution_count": 180,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 184,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "df = df.T\n",
    "\n",
    "df.to_csv('temp_norm_row_tissue.csv', header = None, index = None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 186,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
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       "    <tr style=\"text-align: right;\">\n",
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       "      <th>TSPAN6</th>\n",
       "      <th>TNMD</th>\n",
       "      <th>DPM1</th>\n",
       "      <th>SCYL3</th>\n",
       "      <th>C1orf112</th>\n",
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       "      <th>CFH</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>12.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>2.0</td>\n",
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       "      <td>11.0</td>\n",
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       "      <td>6.0</td>\n",
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       "      <td>0.2</td>\n",
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       "    <tr>\n",
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       "      <td>6.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>44.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>0.5</td>\n",
       "      <td>2.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>8.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.0</td>\n",
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       "      <td>0.1</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.6</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>23.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>0.6</td>\n",
       "      <td>2.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>1.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>18.0</td>\n",
       "      <td>0.9</td>\n",
       "      <td>27.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.5</td>\n",
       "      <td>6.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.3</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.2</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 57073 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   TSPAN6  TNMD  DPM1  SCYL3  C1orf112   FGR   CFH  FUCA2  GCLC  NFYA  \\\n",
       "0    12.0   9.0  21.0    2.0       1.0  11.0  18.0   16.0   6.0   6.0   \n",
       "1     6.0   0.0  44.0    3.0       0.5   2.0  14.0   32.0  11.0   8.0   \n",
       "2     2.0   0.0  23.0    1.0       3.0   0.6   2.0   18.0   7.0  12.0   \n",
       "3     2.0   0.0  22.0    1.0       0.4   1.0   6.0   11.0   4.0   3.0   \n",
       "4    18.0   0.9  27.0    2.0       0.4   0.5   6.0   32.0   5.0   3.0   \n",
       "\n",
       "       ...        RP11-65B7.2  GIMAP1-GIMAP5  RP11-274B21.13  AL359736.1  \\\n",
       "0      ...                0.1            0.0             5.0         0.0   \n",
       "1      ...                0.0            0.0             2.0         0.0   \n",
       "2      ...                0.0            0.0             1.0         0.0   \n",
       "3      ...                0.0            0.0             2.0         0.0   \n",
       "4      ...                0.0            0.0             0.3         0.0   \n",
       "\n",
       "   AF127936.7  CH17-132F21.5  RP11-439M15.1  SNORA50A.1  LINC01144  \\\n",
       "0         0.1            0.5            0.0         0.1        0.3   \n",
       "1         0.1            0.3            0.0         0.0        0.6   \n",
       "2         0.0            0.0            0.0         0.0        1.0   \n",
       "3         0.0            0.2            0.0         0.0        0.2   \n",
       "4         0.1            0.2            0.0         0.0        0.4   \n",
       "\n",
       "   RP11-418H16.1  \n",
       "0            0.2  \n",
       "1            0.0  \n",
       "2            0.1  \n",
       "3            0.1  \n",
       "4            0.1  \n",
       "\n",
       "[5 rows x 57073 columns]"
      ]
     },
     "execution_count": 186,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dft = pd.read_csv('temp_norm_row_tissue.csv')\n",
    "dft.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 189,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>TSPAN6</th>\n",
       "      <th>TNMD</th>\n",
       "      <th>DPM1</th>\n",
       "      <th>SCYL3</th>\n",
       "      <th>C1orf112</th>\n",
       "      <th>FGR</th>\n",
       "      <th>CFH</th>\n",
       "      <th>FUCA2</th>\n",
       "      <th>GCLC</th>\n",
       "      <th>NFYA</th>\n",
       "      <th>...</th>\n",
       "      <th>RP11-65B7.2</th>\n",
       "      <th>GIMAP1-GIMAP5</th>\n",
       "      <th>RP11-274B21.13</th>\n",
       "      <th>AL359736.1</th>\n",
       "      <th>AF127936.7</th>\n",
       "      <th>CH17-132F21.5</th>\n",
       "      <th>RP11-439M15.1</th>\n",
       "      <th>SNORA50A.1</th>\n",
       "      <th>LINC01144</th>\n",
       "      <th>RP11-418H16.1</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
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       "      <th>0</th>\n",
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       "      <td>1.0</td>\n",
       "      <td>0.150</td>\n",
       "      <td>0.333333</td>\n",
       "      <td>0.090909</td>\n",
       "      <td>0.206049</td>\n",
       "      <td>0.060493</td>\n",
       "      <td>0.307692</td>\n",
       "      <td>0.166667</td>\n",
       "      <td>0.096774</td>\n",
       "      <td>...</td>\n",
       "      <td>0.166667</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.620253</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.5</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.125</td>\n",
       "      <td>0.125</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.235294</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.725</td>\n",
       "      <td>0.666667</td>\n",
       "      <td>0.015152</td>\n",
       "      <td>0.035917</td>\n",
       "      <td>0.046975</td>\n",
       "      <td>0.923077</td>\n",
       "      <td>0.583333</td>\n",
       "      <td>0.161290</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.240506</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.5</td>\n",
       "      <td>0.6</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.500</td>\n",
       "      <td>0.0</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.200</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.393939</td>\n",
       "      <td>0.009452</td>\n",
       "      <td>0.006421</td>\n",
       "      <td>0.384615</td>\n",
       "      <td>0.250000</td>\n",
       "      <td>0.290323</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.113924</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000</td>\n",
       "      <td>1.000</td>\n",
       "      <td>0.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.175</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.017013</td>\n",
       "      <td>0.019939</td>\n",
       "      <td>0.115385</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.240506</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0.941176</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.300</td>\n",
       "      <td>0.333333</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.007561</td>\n",
       "      <td>0.019939</td>\n",
       "      <td>0.923077</td>\n",
       "      <td>0.083333</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.025316</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.5</td>\n",
       "      <td>0.4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.250</td>\n",
       "      <td>0.5</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 57073 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     TSPAN6  TNMD   DPM1     SCYL3  C1orf112       FGR       CFH     FUCA2  \\\n",
       "0  0.588235   1.0  0.150  0.333333  0.090909  0.206049  0.060493  0.307692   \n",
       "1  0.235294   0.0  0.725  0.666667  0.015152  0.035917  0.046975  0.923077   \n",
       "2  0.000000   0.0  0.200  0.000000  0.393939  0.009452  0.006421  0.384615   \n",
       "3  0.000000   0.0  0.175  0.000000  0.000000  0.017013  0.019939  0.115385   \n",
       "4  0.941176   0.1  0.300  0.333333  0.000000  0.007561  0.019939  0.923077   \n",
       "\n",
       "       GCLC      NFYA      ...        RP11-65B7.2  GIMAP1-GIMAP5  \\\n",
       "0  0.166667  0.096774      ...           0.166667            0.0   \n",
       "1  0.583333  0.161290      ...           0.000000            0.0   \n",
       "2  0.250000  0.290323      ...           0.000000            0.0   \n",
       "3  0.000000  0.000000      ...           0.000000            0.0   \n",
       "4  0.083333  0.000000      ...           0.000000            0.0   \n",
       "\n",
       "   RP11-274B21.13  AL359736.1  AF127936.7  CH17-132F21.5  RP11-439M15.1  \\\n",
       "0        0.620253         0.0         0.5            1.0            0.0   \n",
       "1        0.240506         0.0         0.5            0.6            0.0   \n",
       "2        0.113924         0.0         0.0            0.0            0.0   \n",
       "3        0.240506         0.0         0.0            0.4            0.0   \n",
       "4        0.025316         0.0         0.5            0.4            0.0   \n",
       "\n",
       "   SNORA50A.1  LINC01144  RP11-418H16.1  \n",
       "0       0.125      0.125            1.0  \n",
       "1       0.000      0.500            0.0  \n",
       "2       0.000      1.000            0.5  \n",
       "3       0.000      0.000            0.5  \n",
       "4       0.000      0.250            0.5  \n",
       "\n",
       "[5 rows x 57073 columns]"
      ]
     },
     "execution_count": 189,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from sklearn.preprocessing import MinMaxScaler\n",
    "scaler = MinMaxScaler()\n",
    "\n",
    "df_scaled = pd.DataFrame(scaler.fit_transform(dft), columns=dft.columns)\n",
    "\n",
    "df_scaled.head()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 191,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "df_scaled_row = df_scaled.T"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 193,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "df_scaled_row.to_csv('row_scaled_tissue.csv', header = True, index = True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Manually add 'Gene' as column name in the file"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Creating File"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 194,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "df_tissues = pd.read_csv('row_scaled_tissue.csv')\n",
    "df_pvp = pd.read_csv('PVP_data_no_brca.csv')\n",
    "\n",
    "final = pd.merge(df_pvp, df_human, how='left', on=['Gene', 'Gene'])\n",
    "\n",
    "final = final.sort_values(['OMIM'])\n",
    "\n",
    "columns = ['adipose tissue', 'adrenal gland', 'brain', 'heart', 'kidney',\n",
    "       'liver', 'lung', 'ovary', 'pancreas', 'sigmoid colon',\n",
    "       'small intestine', 'spleen', 'testis']\n",
    "\n",
    "recode_empty_cells(final, columns)\n",
    "\n",
    "\n",
    "final.to_csv('Human_PVP_no_norm_brca.csv', index=None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 195,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "df_test1 = final.iloc[:4000, :]\n",
    "df_test2 = final.iloc[77000:, :]\n",
    "\n",
    "df_train = final.iloc[4000:77000, :]\n",
    "\n",
    "frames = [df_test1, df_test2]\n",
    "df_test = pd.concat(frames)\n",
    "\n",
    "\n",
    "df_test.to_csv('PVP_human_tis_row_norm_test.csv', index=None, header=True)\n",
    "df_train.to_csv('PVP_human_tis_row_norm_train.csv', index=None, header=True)\n",
    "\n",
    "\n",
    "\n",
    "df_1 = pd.read_csv('PVP_human_tis_row_norm_train.csv')\n",
    "df_2 = pd.read_csv('PVP_human_tis_row_norm_test.csv')\n",
    "\n",
    "df_1.drop(['Chr', 'Position', 'RSID', 'Ref', 'Alt', 'Gene' , 'OMIM'], axis =1, inplace = True)\n",
    "df_2.drop(['Chr', 'Position', 'RSID', 'Ref', 'Alt', 'Gene' , 'OMIM'], axis = 1, inplace = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 196,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import os\n",
    "\n",
    "num_train_entries = df_1.shape[0]\n",
    "num_train_features = df_1.shape[1] - 1    \n",
    "\n",
    "num_test_entries = df_2.shape[0]\n",
    "num_test_features = df_2.shape[1] - 1    # The data frames are written as a temporary CSV file, as we still\n",
    "# need to modify the header row to include the number of rows and\n",
    "# columns present in the training and testing CSV files.\n",
    "df_1.to_csv('train_temp.csv', index=False, header=None)\n",
    "df_2.to_csv('test_temp.csv', index=False, header=None)    \n",
    "\n",
    "# Append onto the header row the information about how many\n",
    "# columns and rows are in each file as TensorFlow requires.\n",
    "open('tissue2_train.csv', 'w').write(str(num_train_entries) +\n",
    "                                     ',' + str(num_train_features) + ',CTRL,CASE\\n' +\n",
    "                                     open('train_temp.csv').read())    \n",
    "\n",
    "open('tissue2_test.csv', 'w').write(str(num_test_entries) +\n",
    "                                     ',' + str(num_test_features) + ',CTRL,CASE\\n' +\n",
    "                                     open('test_temp.csv').read())    # Remove the temporary CSV files that were generated above.\n",
    "os.remove('train_temp.csv')\n",
    "os.remove('test_temp.csv')"
   ]
  }
 ],
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