User: Malcolm Cook

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Malcolm Cook1.5k
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Posts by Malcolm Cook

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Comment: C: GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be termina
... The code underlying supportedUCSCFeatureDbTracks is > supportedUCSCFeatureDbTracks function (genome)  {     session <- browserSession()     genome(session) <- genome     query <- ucscTableQuery(session)     trx <- trackNames(ucscTableQuery(session))     supported <- makeWhiteList( ...
written 7 weeks ago by Malcolm Cook1.5k
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Comment: C: GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be termina
... Thanks, James, but I don't understand your response.  I commented on the function supportedUCSCFeatureDbTracks, which by my sights you did not exercise in your code, so, how could it address my issue? ...
written 7 weeks ago by Malcolm Cook1.5k
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GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c
... In my hands, supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c. Any debugging help very welcome. I've tried with hg19 in addition to dm6.  Below I report my linux setup, but it also fails under windows, R 3.5.1, GenomicFeatures_1.34.1 >  trks<-supportedUCSCFeature ...
genomicfeatures bug written 7 weeks ago by Malcolm Cook1.5k • updated 7 weeks ago by James W. MacDonald49k
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Comment: C: Reorder exons on negative strand in GRanges list
... Mike - thanks for offering to take a look, and even more so for the "spot on" comment about using flank... you're absolutely right, computing flanking.grl as below is ~100x faster           up.gr<-trim(flank(intron.gr,flankSize,T))         down.gr<-trim(flank(intron.gr,flankSize,F))         ...
written 12 weeks ago by Malcolm Cook1.5k
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Comment: C: Reorder exons on negative strand in GRanges list
... Here's timing produced by the five statements in the following function, to give you a sense of relative speed on my computer:    user  system elapsed   12.227   0.871  13.100     user  system elapsed   41.688   3.735  45.423     user  system elapsed  636.549  29.291 665.827     user  system elapse ...
written 3 months ago by Malcolm Cook1.5k
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Comment: C: Element-wise setdiff when psetdiff fails for GenomicRanges
... Hi Michael. I find that this does NOT work in R3.5.0 but have updated your approach  After noticing: ``` > t.a <- as(test.a, "List") > class(t.a) [1] "GRanges" attr(,"package") [1] "GenomicRanges" ``` Converting instead to GRangesList gets me further, but not much: ``` t.a <- as(tes ...
written 3 months ago by Malcolm Cook1.5k
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Comment: C: Reorder exons on negative strand in GRanges list
... It appears the case was never made.  revElements certainly works as suggested, but it is dreadfully slow. Is there any other new BioC juju that might make this operation sing (and, would it help that in my case ALL all my exonAll2 have exactly two elements)?   ...
written 3 months ago by Malcolm Cook1.5k
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Comment: C: makeTxDbFromGFF errors too many NAs and make.splicings
... did you should take a look at row 58427 as suggested in error msg?  what did you see? ...
written 3 months ago by Malcolm Cook1.5k
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Answer: A: extracting the genes associated with the groups or samples in pheatmap.
... You want to use cutree. Nice presentation at Question: extract dendrogram cluster from pheatmap ...
written 3 months ago by Malcolm Cook1.5k
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Answer: A: Counting exonic and intronic reads for differential gene expression
...   In short, the biochemistry and bioinformatics that you perform should both be aligned with the scientific questions you seek to ask. The degree to which RNA-Seq can be taken as an indirect or proxy measure of protein abundance has been the subject of lots of research. In a particular study, if ...
written 4 months ago by Malcolm Cook1.5k

Latest awards to Malcolm Cook

Scholar 20 months ago, created an answer that has been accepted. For A: Importing a .txt file with multiple headers into R
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Is Bioconductor 3.0 compatible with R 3.1.2?
Scholar 3.8 years ago, created an answer that has been accepted. For A: Importing a .txt file with multiple headers into R
Centurion 13.4 years ago, created 100 posts.

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