formatFromBismark: Parsing output from the Bismark alignment suite

In kaiqiong/SOMNiBUS: Smooth modeling of bisulfite sequencing

Parsing output from the Bismark alignment suite

Description

This function reads and converts Bismark's 'genome wide cytosine report' and 'coverage' into a list of data.frames (one per chromosome) to a format compatible with SOMNiBUS' main functions runSOMNiBUS and binomRegMethModel.

Usage

formatFromBismark(..., verbose = TRUE)

Arguments

...	parameters from bsseq::read.bismark() function
verbose	logical indicates the level of information provided by the algorithm during the process. The default value is TRUE.

Value

This function returns a list of data.frames (one per chromosome). Each data.frame contains rows as individual CpGs appearing in all the samples. The first 4 columns contain the information of Meth_Counts (methylated counts), Total_Counts (read depths), Position (Genomic position for the CpG site) and ID (sample ID). The additional information (such as disease status, sex, age) extracted from the BSseq object are listed in column 5 and onwards and will be considered as covariate information by SOMNiBUS algorithms.

Author(s)

Audrey Lemaçon

See Also

read.bismark for parsing output from the Bismark alignment suite.

Other Parsing functions: formatFromBSmooth(), formatFromBSseq()

Examples

infile <- system.file("extdata/test_data.fastq_bismark.bismark.cov.gz",
package = "bsseq")
dat <- formatFromBismark(infile, verbose = FALSE)

kaiqiong/SOMNiBUS documentation built on Feb. 24, 2023, 5:38 a.m.