rtracklayer: BamFile-methods – R documentation

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BamFile-methods

Export to BAM Files

Description

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

Usage

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

Arguments

`object`	The object to export, such as a `GAlignments` or `GAlignmentPairs`.
`con`	A path, URL, connection or `BamFile` object.
`format`	If not missing, should be “bam”.
`text`	Not supported.
`paired`	If `TRUE`, return a GAlignmentPairs object, otherwise a GAlignments.
`use.names`	Whether to parse QNAME as the names on the result.
`param`	The `ScanBamParam` object governing the import.
`genome`	Single string or `Seqinfo` object identifying the genome
`...`	Arguments that are passed to `ScanBamParam` if `param` is missing.

Details

BAM fields not formally present in the GAlignments[Pairs] 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)

rtracklayer

R interface to genome annotation files and the UCSC genome browser

v1.50.0

Artistic-2.0 + file LICENSE

Authors

Michael Lawrence, Vince Carey, Robert Gentleman

Initial release