LandScape - A simple method to aggregate p values without a priori grouping

Paper: https://www.ncbi.nlm.nih.gov/pubmed/27269897

For help on how to run the program run the command: python landscape.py --help

If plink files are used as input, the package https://github.com/ymer/Plink is required.

Output files:

An output files containing the maximal segments and their values. This file is saved to [output]_[score_evaluation].txt. It contains the following columns: s - The start point of the maximal segment. e - The end point of the maximal segment. Y - The height of the highest point in the maximal segment. p_value - The p value of the maximal segment. adjusted_p_value - The p value of the maximal segment adjusted for multiple testing.

A file containing the A_k values. This file is saved to [output]_Ak.txt

Arguments:

--infile INFILE
The input file path

--outfile OUTFILE
The output file path

--input_format {text,gzip,plink} Default: text

--transformation {dichotomous,log,none} Transformation of the input data. dichotomous applies the 1/-1 transformation shown example 1, and log applies the log transformation shown in example 2. Default: log

--score_evaluation {A0,A1,A2} How to evaluate the scores. (See section 4.2-4.4).

--gamma GAMMA
The threshold of significance. (See Example 1 and 2). Default: 0.05

--no-lattice Set if Z is not a lattice variable. (See definition 8 and 9)

--permutations PERMUTATIONS The number of permutations that are performed if score_evaluation is A1 or A2. Default: If input_format is text or gzip, the number of lines in the input file.

--random_seed RANDOM_SEED Random seed for permutations if input_format is plink. Default: 1

--no-draw Do not draw the landscape