PYMAP PYTHON PACKAGE TO ANALYZE 450K METHYLATION DATA.

Example pipeline:

load submodules

import Annotation import Core

Load Annotations

annotation_file = "Data/HumanMethylation450_15017482_v1-2.csv" annotations = Annotation.Annotator()

load and parse a single methylation file that might contain info for one or more sample.

methyl_file = "EXAMPLE.txt" samples = Core.ParseFile(methyl_file)

load and parse multiple methylation files

methyl_directory = "Data/" samples = Core.ParseBatch(methyl_directory)

get probes associated with a gene

gene= "TP53" probe_list = annotations.get_probes_from_gene(gene) print(probe_list)

get sample name and beta values from parse data

for sample in samples: print(sample.name) beta_values = sample.probes # beta_values are loaded from each sample.

COMMAND LINE EXECUTABLES:

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