[BioC] GenomicRanges countOverlaps error

Suraj Menon Suraj.Menon at cancer.org.uk
Wed Sep 8 14:31:28 CEST 2010

Hi Steve

Thanks very much for your response.

Yes I was indeed getting an error previously. 
However, I then updated the GenomicRanges devel version just before writing to the mailing list, and hadn't noticed that I was now getting just a warning instead of an error.


-----Original Message-----
From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com] 
Sent: 07 September 2010 21:32
To: Suraj Menon
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] GenomicRanges countOverlaps error

Hi Suraj,

On Tue, Sep 7, 2010 at 7:01 AM, Suraj Menon <Suraj.Menon at cancer.org.uk> wrote:
> Hi all
> I've been trying to use the GenomicRanges countOverlaps function. When I was using the release version of GenomicRanges, countOverlaps worked fine for coordinates from chromosomes 1-9, but gave me an error for the others.
> I switched to using the development version of GenomicRanges. The function now works for all chromosomes other than X and Y.
> Does anyone know a way around this?

I'm sorry, but I don't see what you're trying to get around?

Is it where you are querying with GRange from chrX and chrY here?


>> ## chrX
>> gr <- GRanges(seqnames = Rle("chrX", length(yst)),
> +      ranges = IRanges(yst, width = ywd))
>> counts <- countOverlaps(gr, aligns)
> Warning message:
> In .local(query, subject, maxgap, minoverlap, type, select, ...) :
>  'query' and 'subject' do not use a similiar naming convention for seqnames

The call to countOverlaps is simply (now) drawing your attention to
the fact that the seqnames of your query and subject GRanges aren't
exactly similar (via a "warning") -- the function call itself should
be working and return a result to you, no?

This thread actually drew attention to the problem. Originally we were
getting an error in these situation, but Herve has now switched this
to a warning:

Perhaps reading through that might shed more light on your issue, if
this is what you were asking about(?) If not, could you be a bit more
specific about the error/problem you are referring to?

Hope that helped,

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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