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

Arguments

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(rtracklayer)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/rtracklayer/BamFile-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BamFile-methods
> ### Title: Export to BAM Files
> ### Aliases: export,ANY,BamFile,ANY-method
> ###   export,GAlignments,BamFile,ANY-method
> ###   export,GAlignmentPairs,BamFile,ANY-method
> ###   import,BamFile,ANY,ANY-method
> 
> ### ** Examples
> 
>      library(Rsamtools)
Loading required package: Biostrings
Loading required package: XVector
>      ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
>      gal <- import(ex1_file, param=ScanBamParam(what="flag"))
>      gal.minus <- gal[strand(gal) == "-"]
> ## Not run: 
> ##D      export(gal, BamFile("ex1-minus.bam"))
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>