[BioC] 'which' argument to readGappedAlignments

[Steve Lianoglou]

Hi,

On Thu, Feb 16, 2012 at 11:04 AM, Juliet Hannah <juliet.hannah at gmail.com> wrote:
> All,
>
> I am studying the document "CountAndMeasure-lab.pdf" by Martin Morgan
> obtained from:
>
> http://www.bioconductor.org/help/course-materials/2011/BioC2011/
>
> In the code below, I am unable to get the following line working:
>
>> aln1 <- readBamGappedAlignments(bam[[1]], which=which)
> Error in readBamGappedAlignments(bam[[1]], which = which) :
>  unused argument(s) (which = which)

Seems the interface has changed some?

I think this should do it for you:

aln1 <- readBamGappedAlignments(bam[[1]], param=ScanBamParam(which=which))

or something similar.

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact