formatFromBSseq: Parsing output from the BSseq package

In kaiqiong/SOMNiBUS: Smooth modeling of bisulfite sequencing

Parsing output from the BSseq package

Description

This function reads and converts a BSseq object into a list of data.frames (one per chromosome) to a format compatible with SOMNiBUS' main functions runSOMNiBUS and binomRegMethModel.

Usage

formatFromBSseq(bsseq_dat, verbose = TRUE)

Arguments

bsseq_dat	an object of class BSseq.
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

BSseq for the BSseq class.

Other Parsing functions: formatFromBSmooth(), formatFromBismark()

Examples

M <- matrix(1:9, 3,3)
colnames(M) <- c("A1", "A2", "A3")
BStest <- bsseq::BSseq(pos = 1:3, chr = c("chr1", "chr2", "chr1"), 
M = M, Cov = M + 2)
dat <- formatFromBSseq(BStest, verbose = FALSE)

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