formatFromBSmooth: Parsing output from the BSmooth alignment suite

View source: R/format.R

formatFromBSmoothR Documentation

Parsing output from the BSmooth alignment suite


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


formatFromBSmooth(..., verbose = TRUE)



parameters from bsseq::read.bsmooth() function


logical indicates the level of information provided by the algorithm during the process. The default value is TRUE.


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.


Audrey Lema├žon

See Also

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

Other Parsing functions: formatFromBSseq(), formatFromBismark()


indir <- system.file("extdata/ev_bt2_tab", package = "SOMNiBUS")
dat <- formatFromBSmooth(indir, verbose = FALSE)

kaiqiong/SOMNiBUS documentation built on June 3, 2022, 9:16 a.m.