extractbams_output {DAMEfinder} | R Documentation

## 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!

[Package DAMEfinder version 1.2.0 Index]