Moderator: Patrick Aboyoun

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Patrick Aboyoun1.6k
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Posts by Patrick Aboyoun

<prev • 160 results • page 1 of 16 • next >
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Comment: C: IRanges: Need help speeding up sliding window analysis
... Michael, The IRanges package contains a number of built-in running window functions (runsum, runmean, runwtsum, runq) that you might want to consider for this operation. Also, if I am understanding what you are trying to do correctly, something like width <- 30 halfWidth <- width/2 halfWidthS ...
written 6.4 years ago by Patrick Aboyoun1.6k
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Comment: C: Subscripting GenomicRanges objects with [[ or $
... I am not sure where the design will lead, but another aspect of GRanges is that it has an accompanying GRangesList class for housing information such as the constituent exons in a transcript. There is a benefit for developers and script writers to having a similar mechanism for extracting these meta ...
written 6.5 years ago by Patrick Aboyoun1.6k
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Comment: C: Why is *ply-ing over a GRangesList much slower than *ply-ing over an IRangesList
... Steve, I haven't profiled the code yet to know what is going on, but I will address your followup question. I have a feeling that the GRangesList concept will be growing over time and I am not sure what the tipping point will be for changes in code to occur. I see two issues related to GRangesList. ...
written 6.5 years ago by Patrick Aboyoun1.6k
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Comment: C: A code kata: evening-out *Ranges ends.
... Steve, Riffing off of Martin's post, I would use the match function to do the mapping: fence.posts <- reduce(reads) ranges(reads) <- ranges(fence.posts)[match(reads, fence.posts)] It is not as fast as the Rle/cut based method by Martin, but it is more readable and, thus, easier to maintain ...
written 6.5 years ago by Patrick Aboyoun1.6k
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Comment: C: endoapply over GRangesList fails when an empty GRanges object is returned (Bug?)
... Steve, Thanks for reporting this issue. It turns out that the endoapply surfaced the error, but didn't cause it. The problem was upstream in the split,GRanges-method where there was a bug when splitting by a factor or 'factor' Rle that didn't have all levels present. (To check this try validObject ...
written 6.5 years ago by Patrick Aboyoun1.6k
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Comment: C: IRanges::Rle and missing values
... Kasper, I'll look to add na.rm arguments to the run* functions by the next release. Cheers, Patrick On 8/21/10 12:47 PM, Kasper Daniel Hansen wrote: > Thanks a lot for the fix. > > Some background. I have data associated with (very small) genomic > locations, irregularly space and ...
written 6.5 years ago by Patrick Aboyoun1.6k
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Comment: C: IRanges::Rle and missing values
... Kasper, I have addressed these two issues, which were caused by inappropriate comparisons using NA_REAL at the C-level for 'numeric' Rle objects. As with the runmed function in the stats package, I don't currently support missing values in the run* methods for Rle objects. Below is the current beh ...
written 6.5 years ago by Patrick Aboyoun1.6k
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Answer: A: IRanges::Rle and missing values
... Kasper, I'll take a look into this. The Rle constructor issue seems to be isolated to 'numeric' and 'complex' Rles. I'll have an update out soon. Patrick On 8/20/10 8:53 AM, Kasper Daniel Hansen wrote: > Would it make sense to allow missing values in Rle objects and also to > incorporate ...
written 6.5 years ago by Patrick Aboyoun1.6k
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Answer: A: feature request - pairwiseAlignment() in Biostrings
... Avril, I wont have time to extend pairwiseAlignment, but you are more then welcome to. It is written mainly in C with an R wrapper. You can grab it via svn at the URL https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biostrings with username: readonly and password: readonly. The particu ...
written 6.6 years ago by Patrick Aboyoun1.6k
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Answer: A: Biostrings - vcountPattern optimization
... Erik, Have you tried vcountPDict? It will use an Aho - Corasick matching algorithm (http://en.wikipedia.org/wiki/Aho?Corasick_string_matching_algorithm) that is pretty fast, albeit memory intensive. library(Biostrings) fragments<- DNAStringSet(c("ACTG","AAAA")) sequence_set<- DNAStringSet(c(" ...
written 6.6 years ago by Patrick Aboyoun1.6k

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Centurion 6.4 years ago, created 100 posts.

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