BS.chr22: Whole-genome bisulfite sequencing for chromosome 22 from...

In kasperdanielhansen/bsseq: Analyze, manage and store whole-genome methylation data

Whole-genome bisulfite sequencing for chromosome 22 from Lister et al.

Description

This dataset represents chromosome 22 from the IMR90 cell line sequenced in Lister et al. Only CpG methylation are included (there were very few non-CpG loci). The two samples are two different extractions from the same cell line (ie. technical replicates), and are pooled in the analysis in the original paper.

Usage

data(BS.chr22)

Format

An object of class BSseq.

Details

All coordinates are in hg18.

Source

Obtained from http://neomorph.salk.edu/human_methylome/data.html specifically the files mc_imr90_r1.tar.gz and mc_imr90_r2.tar.gz. A script which downloads these files and constructs the BS.chr22 object may be found in ‘inst/scripts/get_BS.chr22.R’, see the example.

References

R Lister et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature (2009) 462, 315-322.

Examples

data(BS.chr22)
BS.chr22

script <- system.file("scripts", "get_BS.chr22.R", package = "bsseq")
script
readLines(script)

kasperdanielhansen/bsseq documentation built on April 14, 2024, 2:19 a.m.