bsseq (version 1.8.2)

read.bismark: Parsing output from the Bismark alignment suite.

Description

Parsing output from the Bismark alignment suite.

Usage

read.bismark(files, sampleNames, rmZeroCov = FALSE, strandCollapse = TRUE, fileType = c("cov", "oldBedGraph", "cytosineReport"), mc.cores = 1, verbose = TRUE)

Arguments

files

Input files. Each sample is in a different file. Input files are created by running Bismark's methylation extractor; see Note for details.

sampleNames

sample names, based on the order of files.

rmZeroCov

Should methylation loci that have zero coverage in all samples be removed. This will result in a much smaller object if the data originates from (targeted) capture bisulfite sequencing.

strandCollapse

Should strand-symmetric methylation loci, e.g., CpGs, be collapsed across strands. This option is only available if fileType = "cytosineReport" since the other file types do not contain the necessary strand information.

fileType

The format of the input file; see Note for details.

mc.cores

The number of cores used. Note that setting mc.cores to a value greater than 1 is not supported on MS Windows, see the help page for mclapply.

verbose

Make the function verbose.

Value

An object of class BSseq.

See Also

read.bsmooth for parsing output from the BSmooth alignment suite. read.umtab for parsing legacy (old) formats from the BSmooth alignment suite. collapseBSseq for collapse (merging or summing) the data in two different directories.

Examples

  infile <- system.file("extdata/test_data.fastq_bismark.bismark.cov.gz",
                        package = 'bsseq')
  bismarkBSseq <- read.bismark(files = infile,
                               sampleNames = "test_data",
                               rmZeroCov = FALSE,
                               strandCollapse = FALSE,
                               fileType = "cov",
                               verbose = TRUE)
  bismarkBSseq