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 http://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