Just checked in something to make this work. Please let me know if it works as expected.
Michael On Wed, Oct 6, 2010 at 6:29 PM, Kasper Daniel Hansen < [email protected]> wrote: > Hi Michael > > For what it is worth, yesterday I "expected" the seqlength()<- thing > to work. So yes, I find that solution natural. > > Anything that allows you to do additional manipulation easily would be > welcome, for example like a drop unused levels. > > But seqlengths()<- will go a long way to help this out. > > Kasper > > On Wed, Oct 6, 2010 at 5:30 PM, Michael Lawrence > <[email protected]> wrote: > > 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 <[email protected]> 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 > >> [email protected] > >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > >> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
