Moderator: Patrick Aboyoun

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Patrick Aboyoun1.6k
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Posts by Patrick Aboyoun

<prev • 160 results • page 2 of 16 • next >
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TranscriptDb and genomicranges questions
... Vincent, I am cc'ing the Bioconductor mailing list with the response to your e-mail so others can access it. The gaps,GRanges-method is strand specific, so when you pass a GRanges object containing the transcript bounds into gaps, you will get the gaps on the positive strand, the negative strand, a ...
transcriptdb iranges genomicranges written 7.4 years ago by Patrick Aboyoun1.6k
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Answer: A: bug: subsetByOverlaps(GRangesList, GRanges)
... Cei, The Details section of the relevant man page for subsetByOverlaps explains its functionality help("subsetByOverlaps,GRangesList,GRanges-method") In short the subsetByOverlaps function operates at the object's "top" level, not the within-element level, as the "[" operator behaves for a standar ...
written 7.4 years ago by Patrick Aboyoun1.6k
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Comment: C: Performing set ops with an IRanges object loaded with elementMetadata is like a
... Steve, Most of the methods for the IRanges class predate the introduction of the elementMetadata slot and these methods have not been tested when the elementMetadata is not NULL. I have some changes I can check in to BioC 2.7 to the gaps,IRanges-method and union,IRanges,IRanges-method that strips th ...
written 7.4 years ago by Patrick Aboyoun1.6k
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Comment: C: unexpected behaviour of pairwiseAlignment() in Biostrings
... Avril, I checked the versions of Biostrings that are available at bioconductor.org and they are either at or above the version number of the package that contains the patch. I also double-checked the packages in release and devel and both contain the fix. Could you please send session information fr ...
written 7.4 years ago by Patrick Aboyoun1.6k
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Comment: C: GRanges, strange behavior when chromosomes don't match
... Cei, I checked in a patch to BioC 2.6 (GenomicRanges 1.0.6) and BioC 2.7 (GenomicRanges 1.1.16) that fixes the issue you found in the intersect and setdiff methods for GRanges objects when the two objects don't have the same sequence names. These new packages will be available on bioconductor.org wi ...
written 7.4 years ago by Patrick Aboyoun1.6k
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Answer: A: GRanges, strange behavior when chromosomes don't match
... Cei, Thanks for the bug report. I am looking into the issue now and will have a patch out shortly. Cheers, Patrick On 7/8/10 9:22 AM, Cei Abreu-Goodger wrote: > Hello all, > > When you have two GRanges objects which don't have the same seqnames > factor, you can get very unexpected b ...
written 7.4 years ago by Patrick Aboyoun1.6k
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Answer: A: unexpected behaviour of pairwiseAlignment() in Biostrings
... Avril, Thanks for the bug report! It turns out that the dynamic programming traceback for local alignments by Biostrings::pairwiseAlignment was broken when the local alignment had a gap in it. I have fixed this bug in BioC 2.6 (Biostrings 2.16.7) and BioC 2.7 (2.17.13). This patched version will be ...
written 7.4 years ago by Patrick Aboyoun1.6k
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Comment: C: Error in loading "IRanges" package (version 1.6.1)
... I found a candidate replacement: > format(Sys.time(), "%Y-%m-%d %X %z (%a, %d %b %Y)") [1] "2010-05-12 21:19:17 -0700 (Wed, 12 May 2010)" The author of the original C code, Herve Pages, is currently on holiday and I don't know if he had a reason not to use the built in Sys.time function. If th ...
written 7.5 years ago by Patrick Aboyoun1.6k
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Comment: C: Error in loading "IRanges" package (version 1.6.1)
... Lilyana, Steve is right. We added an svn.time function to IRanges that produces a time/date stamp in the same format as the BioC Subversion server, e.g. "2007-12-07 10:03:15 -0800 (Fri, 07 Dec 2007)", for use by the GenomicFeatures package. We implemented a method in C that builds on Linux, Windows ...
written 7.5 years ago by Patrick Aboyoun1.6k
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Answer: A: IRanges bug? Running do.cal("c", list.of.IRanges.objects)
... Steve, This outcome is due to how the S4 generic for c is defined > args(getGeneric("c")) function (x, ..., recursive = FALSE) NULL The dispatch occurs off the argument x. Since all your list elements are named, but none are named "x", your object uses the primitive method > c function (. ...
written 7.6 years ago by Patrick Aboyoun1.6k

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Centurion 7.2 years ago, created 100 posts.

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