readBismark2DGE: Read Bismark Coverage Files
In edgeR: Empirical Analysis of Digital Gene Expression Data in R

Description Usage Arguments Details Value Note Author(s) References

Read Bismark coverage files containing methylated and unmethylated read counts for CpG loci and create DGEList.

1	readBismark2DGE(files, sample.names=NULL, readr=TRUE, verbose=TRUE)

`files`	character vector of file names.
`sample.names`	character vector of sample names. If `NULL`, sample names will be extracted from the file names.
`readr`	logical. If `TRUE`, `readr` package is used to read the coverage files, otherwise `read.delim` is used.
`verbose`	logical. If `TRUE`, read progress messages are send to standard output.

This function reads tab-delimited coverage files output by Bismark software. Counts from multiple files are collated into a DGEList object.

A DGEList object with a row for each unique genomic loci found in the files and two columns (containing methylated and unmethylated counts) for each sample.

This function represents genomic loci as integers, so the largest locus position must be less than the maximum integer in R (about 2e9). The number of chromosomes times the largest locus position must be less than 1e16.

Gordon Smyth

Chen, Y, Pal, B, Visvader, JE, Smyth, GK (2017). Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR. F1000Research 6, 2055. https://f1000research.com/articles/6-2055

edgeR documentation built on Jan. 16, 2021, 2:03 a.m.