[BioC] filterBam using rname

[Valerie Obenchain]

Hi Raffaele,

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)

Valerie


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?
> Cheers
> Raffaele
>
>
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods base
>
> other attached packages:
>  [1] ShortRead_1.14.4     latticeExtra_0.6-24  RColorBrewer_1.0-5 
> lattice_0.20-10      Rsamtools_1.8.6
>  [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):
> [1] bitops_1.0-4.1 grid_2.15.1    hwriter_1.3    stats4_2.15.1 
> tools_2.15.1   zlibbioc_1.2.0
> >
>