R: Export to BAM Files

BamFile-methods {rtracklayer}

R Documentation

Export to BAM Files

Description

Methods for import and export of GappedAlignments objects from and to BAM files, represented as BamFile objects.

Usage

## S4 method for signature 'BamFile,ANY,ANY'
import(con, format, text, use.names = FALSE,
                                   param = ScanBamParam(...), ...)
## S4 method for signature 'ANY,BamFile,ANY'
export(object, con, format, ...)

Arguments

`object`	The object to export, should be a `GappedAlignments` or one of its subclasses, like `GappedReads`.
`con`	A path, URL, connection or `BamFile` object.
`format`	If not missing, should be “bam”.
`text`	Not supported.
`use.names`	Whether to parse QNAME as the names on the result.
`param`	The `ScanBamParam` object governing the import.
`...`	Arguments that are passed to `ScanBamParam` if `param` is missing.

Details

BAM fields not formally present in the GappedAlignments object are extracted from the metadata columns, if present; otherwise, the missing value, “"."”, is output. The file is sorted and indexed. This can be useful for subsetting BAM files, although filterBam may eventually become flexible enough to be the favored alternative.

Author(s)

Michael Lawrence

Examples

     library(Rsamtools)
     ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
     gal <- import(ex1_file, param=ScanBamParam(what="flag"))
     gal.minus <- gal[strand(gal) == "-"]
## Not run: 
     export(gal, BamFile("ex1-minus.bam"))

## End(Not run)

[Package rtracklayer version 1.20.0 Index]