methylationDataList: The methylation data list

In DMRcaller: Differentially Methylated Regions caller

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).

DMRcaller documentation built on Nov. 8, 2020, 5:26 p.m.