R: Sample from a BAM files

BamSampler {Rsamtools}

R Documentation

Sample from a BAM files

Description

Use BamSampler() to create a reference to a BAM file (and optionally its index). Calls to scanBam (and many functions that use scanBam) draw a random sample from the BAM file.

Usage


## Constructors

BamSampler(file, index = file, ..., yieldSize, obeyQname = FALSE, asMates = FALSE) 

## S4 method for signature 'BamSampler'
scanBam(file, index=file, ..., param=ScanBamParam(what=scanBamWhat()))

Arguments

`file`	character(1); BAM file path for `BamSampler`, or `BamSampler` index for `scanBam` and other functions.
`index`	character(1); the BAM index file path (for `BamFile`); ignored for other methods.
`...`	Additional arguments; see `BamFile-class`.
`yieldSize`	integer(1); number of records to yield each time the file is read from using `scanBam`.
`obeyQname`	logical(1); indicating whether the file is sorted by `qname` and if so, that qnames are not split between yields.
`asMates`	logical(1); indicating whether the records should be returned as mated pairs.
`param`	An optional `ScanBamParam` instance to further influence scanning, counting, or filtering.

Objects from the Class

Objects are created by calls of the form BamSampler().

Fields

The BamSampler class inherits fields from the BamFile class.

Functions and methods

BamSampler inherits methods from BamFile and can be used in place of BamFile in many functions.

Author(s)

Martin Morgan

Examples

library(GenomicAlignments)  # for readGAlignmentsFromBam()
fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
samp <- BamSampler(fl, yieldSize=1000)
## two independent samples
head(readGAlignmentsFromBam(samp))
head(readGAlignmentsFromBam(samp))

[Package Rsamtools version 1.16.0 Index]