read.umtab {bsseq} | R Documentation

## Parsing UM tab files (legacy output) containing output from the BSmooth aligner.

### Description

Parsing UM tab files containing output from the bisulfite aligner `Merman`. This is two different legacy formats, which we keep around. These functions are likely to be deprecated in the future.

### Usage

    read.umtab(dirs, sampleNames = NULL, rmZeroCov = FALSE,
      pattern = NULL, keepU = c("U10", "U20", "U30", "U40"),
      keepM = c("M10", "M20", "M30", "M40"), verbose = TRUE)

    read.umtab2(dirs, sampleNames = NULL, rmZeroCov = FALSE,
      readCycle = FALSE, keepFilt = FALSE,
      pattern = NULL, keepU, keepM, verbose = TRUE)

### Arguments

`dirs` | Input directories. Usually each sample is in a different directory.
`pattern` | An optional pattern, see `list.files` in the base package.
`sampleNames` | sample names, based on the order of `dirs`.
`rmZeroCov` | Should methylation loci that have zero coverage in all samples be removed. This will result in a much smaller object if the data originates from (targeted) capture bisulfite sequencing.
`keepU` | A vector of U columns which are kept.
`keepM` | A vector of M columns which are kept.
`readCycle` | Should the cycle columns be returned?
`keepFilt` | Should the filter columns be returned?
`verbose` | Make the function verbose.

### Details

`read.umtab2` is newer than `read.umtab` and both process output from older versions of the BSmooth alignment suite (versions older than 0.6.1). These functions are likely to be deprecated in the future. Newer output from the BSmooth alignment suite can be parsed using `read.bsmooth`.

A script using this function can be found in the `bsseqData` package, in the file ‘scripts/create_BS.cancer.R’.

### Value

Both functions returns lists, the components are

`BSdata` | An object of class `BSseq` containing the methylation evidence.
`GC` | A vector of local GC content values.
`Map` | A vector of local mapability values.
`Mcy` | A matrix of the number of unique M cycles.
`Ucy` | A matrix of the number of unique U cycles.
`chr` | A vector of chromosome names.
`pos` | A vector of genomic positions.
`M` | A matrix representing methylation evidence.
`U` | A matrix representing un-methylation evidence.
`csums` | Description of 'comp2'

### Author(s)

Kasper Daniel Hansen khansen@jhsph.edu

### See Also

`read.bsmooth`.

### Examples

    ## Not run:
    require(bsseqData)
    umDir <- system.file("umtab", package = "bsseqData")
    sampleNames <- list.files(umDir)
    dirs <- file.path(umDir, sampleNames, "umtab")
    umData <- read.umtab(dirs, sampleNames)

    ## End(Not run)

[Package bsseq version 1.28.0 Index]