BSreadBiSeq: Read in files from biseq meth caller

In MIRA: Methylation-Based Inference of Regulatory Activity

Description

Parses the x/y format of methylation calls, splitting them into individual columns: "methylCount" column for number of methylated reads for site and "coverage" column for total number of reads covering that site. Input files should have the following columns: "chr", "start", "end", "meth", "rate", "strand".

Usage

BSreadBiSeq(files, contrastList = NULL, cores = 4,
  returnAsList = FALSE)

Arguments

files	a vector of file paths
contrastList	Generally not needed for MIRA. A list of named character vectors, each with length equal to the number of items in files. These will translate into column names in the final table.
cores	number of processors.
returnAsList	Whether to return the output as a list or as one big data.table.

Details

This can run into memory problems if there are too many files... because of the way parallel lacks long vector support. The solution is to just use a single core; or to pass mc.preschedule = FALSE; This makes it so that each file is processed as a separate job. Much better.

Value

Data from each input file joined together into one big data.table. If returnAsList = TRUE, then input from each file will be in its own data.table in a list.

Examples

shortBSDTFile <- system.file("extdata", "shortRRBS.bed", package = "MIRA") 
shortBSDT <- BSreadBiSeq(shortBSDTFile)

MIRA documentation built on Nov. 8, 2020, 4:51 p.m.