At the moment, this is extremely difficult and requires obscure hacks to
achieve. It's been brought up numerous times.

It happens all the time when comparing gene annotations to read alignments.
The gene annotations from GenomicFeatures include the entire set
chromosomes, which is nice, but the sequence reads are usually loaded in a
genome-independent way and only have the chromosomes present in the data. It
would be best to add the additional chromosomes to the read dataset, even if
there are no mappings, rather than throw away intervals from the other set.

The main problem is that the seqlengths and seqnames need to updated
simultaneously.  Really one should take precedence over the other, and I
recently changed the GRanges constructor to favor seqlengths, so that the
levels of seqnames are set to the names of seqlengths. Thus, it would be
nice if one could call seqlengths<- and have it add the necessary levels to
seqnames automatically.  Then you can just do:

seqlengths(reads) <- seqlengths(genes)

and be done with it. Of course, if seqnames contains values that are not
present in the new seqlengths, it should fail.

Comments? Should I make it work this way?

Michael

On Wed, Oct 6, 2010 at 2:10 PM, Chris Seidel <seidel@phaget4.org> wrote:

> Hello,
>
> How do I remove a factor level for the sequence names of a GRanges object?
>
> Sometimes I work with data sets that have not been aligned to all the
> same chromosomes. To make them comparable I have to remove or ignore
> reads for the odd chromosome. So if I have a GRanges object for which I
> want to remove all reads matching a given chromosome, e.g.:
>
> gr <- gr[seqnames(gr) != "chrXHet"]
>
> levels(seqnames(gr)) will return all original seqnames, but I would like
> to exclude "chrXHet" since I've removed all the reads matching that
> chromosome. How do I do this?
>
> -Chris
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>

	[[alternative HTML version deleted]]

