[BioC] filterBam using rname
vobencha at fhcrc.org
Thu Oct 18 19:02:03 CEST 2012
To read in only specific chromosomes (rnames) you can use 'which'.
This toy bam file has two 'chromosomes', seq1 and seq2. Here we specify
that we want a particular range of seq1. You can also request the entire
length of seq1.
which <- RangesList(seq1=IRanges(0, 2000))
If you only specify 'rname' in the 'what' then only that single field
that will be returned. Most likely you want several fields.
See ?ScanBamParam for details.
what <- c("rname", "strand", "pos", "qwidth", "seq")
Create the param and read in the data.
param <- ScanBamParam(which=which, what=what)
bamFile <- system.file("extdata", "ex1.bam", package="Rsamtools")
bam <- scanBam(bamFile, param=param)
On 10/18/2012 06:57 AM, rcaloger wrote:
> I have the necessity to filter a Bam file, keeping only reads
> associated to a subset of references.
> I wanted to do it with filterBam (Rsamtools)
> but I could not manage to find a way of doing it.
> If I use the code:
> filterBam("onlymapped.bam", "filtered.bam",
> param=ScanBamParam(which=my.rnames, what=scanBamWhat("rname")))
> I get:
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "ScanBamParam", for
> signature "character"
> checking the help it seems to me that ScanBamParam(which=) only
> support GRanges, RangesList, RangedData objects.
> There is any other way to filter a bam file on the basis of the rname?
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  ShortRead_1.14.4 latticeExtra_0.6-24 RColorBrewer_1.0-5
> lattice_0.20-10 Rsamtools_1.8.6
>  Biostrings_2.24.1 GenomicRanges_1.8.13 IRanges_1.14.4
> Biobase_2.16.0 BiocGenerics_0.2.0
> loaded via a namespace (and not attached):
>  bitops_1.0-4.1 grid_2.15.1 hwriter_1.3 stats4_2.15.1
> tools_2.15.1 zlibbioc_1.2.0
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