readBismark2DGE {edgeR} | R Documentation

## Read Bismark Coverage Files

### Description

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

### Usage

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

### Arguments

`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.

### Details

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

### Value

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.

### Note

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`.

### Author(s)

Gordon Smyth

### References

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

[Package edgeR version 3.24.3 Index]