[BioC] 'which' argument to readGappedAlignments
Steve Lianoglou
mailinglist.honeypot at gmail.com
Thu Feb 16 17:36:53 CET 2012
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
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