extractbams_output: extract_bams() output.

In markrobinsonuzh/DAMEfinder: Finds DAMEs - Differential Allelicly MEthylated regions

extract_bams() output.

Description

4 Patients from a previous study (Parker et al, 2018.) with colorectal cancer were sequenced and the normal and cancerous tissue of each patient was obtained. The data includes a subset of chromosome 19.

Usage

extractbams_output

Format

A large list with 8 elements. Each element is a list of GRanges for each sample. Each GRanges in the list includes the location of the CpG sites contained in the reads for each SNP. The GRanges metadata table contains:

cov.ref

Number of reads of "reference" allele in that SNP

cov.alt

Number of reads of "alternative" allele in that SNP

meth.ref

Number of methylated reads of "reference" allele in that SNP

cov.ref

Number of methylated reads of "alternative" allele in that SNP

snp

The SNP containing the reads

For further details, see https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6949/ sample names in in ArrayExpress do not necessarily match names given here!

markrobinsonuzh/DAMEfinder documentation built on April 7, 2023, 6:37 a.m.