BamFile-methods {rtracklayer} | R Documentation

## 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

### See Also

The `readGAlignments` and `readGAlignmentPairs` functions for reading BAM files.

### 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 1.49.5 Index]