read.bsmooth {bsseq} | R Documentation

## Parsing output from the BSmooth alignment suite

### Description

Parsing output from the BSmooth alignment suite.

### Usage

    read.bsmooth(dirs, sampleNames = NULL, seqnames = NULL,
      returnRaw = FALSE, qualityCutoff = 20, rmZeroCov = FALSE,
      verbose = TRUE)

### Arguments

`dirs` | Input directories. Usually each sample is in a different directory, or perhaps each (sample, lane) is a different directory.
`sampleNames` | sample names, based on the order of `dirs`. If `NULL` either set to `basename(dirs)` (if unique) or `dirs`.
`seqnames` | The default is to read all BSmooth output files in `dirs`. Using this argument, it is possible to restrict this to only files with names in `seqnames` (apart from `.cpg.tsv` and optionally `.gz`).
`returnRaw` | Should the function return the complete information in the output files?
`qualityCutoff` | Only use evidence (methylated and unmethylated evidence) for a given methylation loci, if the base in the read has a quality greater than this cutoff.
`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.
`verbose` | Make the function verbose.

### Value

Either an object of class `BSseq` (if `returnRaw = FALSE`) or a list of `GRanges` which each component coming from a directory.

### Note

Input files can either be gzipped or not. Gzipping the input files results in much greater speed of reading (and saves space), so it is recommended.

We are working on making this function faster and less memory hungry.

### Author(s)

Kasper Daniel Hansen khansen@jhsph.edu

### See Also

`read.umtab` for parsing legacy (old) formats from the BSmooth alignment suite. `collapseBSseq` for collapse (merging or summing) the data in two different directories.

[Package bsseq version 1.28.0 Index]