PyMAP is a python package for efficient and fast analyzing of Illumina 450K methylation data. This package is available under GNU version 2 license agreement. Please contact mahpour[at-sign]outlook.com for support.

Please head over to https://pymap.readthedocs.org for examples and detailed documentations of the pyMAP package.

convertbed.py creates a BED file that contains all information about probes that are associated with a specified gene.

USAGE:

./convertbed.py -file Data/METHYL_DATA.txt -out TP53.bed -gene TP53

getidfromgene.py generates a text file that contains probe ids associated with a gene

USAGE:

./getidfromgene.py -gene TP53 -out y

samplebed.py create multiple BED files that each represent a sample. the gene is also need to be specified.

USAGE:

./samplebed.py -file Data/GSE42308.txt -out Export/TP53 -gene TP53

PlotProbe.py generates heatmap plot of probes that are associated with a gene.

USAGE:

./PlotProbes.py -gene TP53 -out out.png -data Data/methyl_data.txt