methylationDataList {DMRcaller} | R Documentation

## The methylation data list

### Description

A `GRangesList` object containing the methylation data at each cytosine location in the genome in Wild Type (WT) and met1-3 mutant (met1-3) in Arabidopsis thaliana. The data only contains the first 1 Mbp from Chromosome 3.

### Format

The `GRanges` elements contain four metadata columns

context

  the context in which the DMRs are computed (`"CG"`, `"CHG"` or `"CHH"`).

readsM

  the number of methylated reads.

readsN

  the total number of reads.

trinucleotide_context

  the specific context of the cytosine (H is replaced by the actual nucleotide).

### Source

Each element was created by by calling `readBismark` function on the CX report files generated by Bismark http://www.bioinformatics.babraham.ac.uk/projects/bismark/ for http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM980986 dataset in the case of Wild Type (WT) and http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM981032 dataset in the case of met1-3 mutant (met1-3).

[Package DMRcaller version 1.16.0 Index]