readBismark2DGE: Read Bismark Coverage Files

In OliverVoogd/edgeR: Empirical Analysis of Digital Gene Expression Data in R

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

OliverVoogd/edgeR documentation built on July 28, 2022, 10:13 p.m.