BS.chr21: BS.chr21: Whole-genome bisulfite sequencing for chromosome 21...

In kdkorthauer/dmrseq: Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

BS.chr21: Whole-genome bisulfite sequencing for chromosome 21 from Lister et al.

Description

This dataset represents chromosome 21 from the IMR90 and H1 cell lines sequenced in Lister et al. Only CpG methylation are included. The two samples from each cell line are two different extractions (ie. technical replicates), and are pooled in the analysis in the original paper.

Usage

data(BS.chr21)

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_h1_r1.tar.gz, mc_h1_r2.tar.gz, mc_imr90_r1.tar.gz, mc_imr90_r2.tar.gz A script which downloads these files and constructs the BS.chr21 object may be found in ‘inst/scripts/get_BS.chr21.R’ - this was based off of and modified from the get_BS.chr22.R script in the bsseq package. The object constructed here contains a different chromosome (22 instead of 21), and two additional samples (h1 and imr90 instead of just imr90) to enable identification of cell type-DMRs for examples.

References

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

Examples

  data(BS.chr21)
  BS.chr21

kdkorthauer/dmrseq documentation built on Sept. 26, 2024, 9:32 p.m.