BSreadBiSeq {MIRA} | R Documentation

## Read in files from biseq meth caller

### 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)

[Package MIRA version 1.12.0 Index]