User: Malcolm Cook

gravatar for Malcolm Cook
Malcolm Cook1.4k
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Posts by Malcolm Cook

<prev • 156 results • page 1 of 16 • next >
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Comment: C: nthreads option does NOT work in rsubread featureCounts
... It is true for me too that the majority of the time is spent in reading/decompressing. For this reason it would be nice if Rsubread::featureCounts allowed some degree to parallelization at this level. Ideally it might support new parameter, nbams, being how many .bams to process at a time (some smal ...
written 6 weeks ago by Malcolm Cook1.4k
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Comment: C: Error with featureCounts
... I can confirm that changing the tmpDir option to featureCounts to a drive where I have storage solved the issue for me, no longer terminating the with the error:   ||    Assign reads to features...                                             || ERROR: cannot write into the temporary file. Please c ...
written 6 weeks ago by Malcolm Cook1.4k
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coercion to Granges from empty data.frame ==> unexpected behavior ??
... Hello, I find it odd that coersion to GRanges with as fails in the case of an empty data.frame: This works fine: > as(data.frame(SeqID=c('s'),start=c(1),end=c(2)),'GRanges') GRanges object with 1 range and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> ...
granges coercion written 3 months ago by Malcolm Cook1.4k
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Answer: A: get vertex xy coords from igraph mst plot
... The graph does not holds its own plotting coordinates.   Look at ?layout_  ?plot.igraph ?igraph.plotting and you will learn how to get multiple different coordinates sets for the same plot depending upon choice of layout algorithm. To give you a sense: in the following example, the same graph, g, ...
written 7 months ago by Malcolm Cook1.4k
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Comment: C: Extract isoform-specific ranges
... Thanks. I reported your experience as an issue here: checkbox to accept response as answer does not appear in Safari browser #439 ...
written 8 months ago by Malcolm Cook1.4k
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Comment: C: Extract isoform-specific ranges
... To the left of every response to your question you should have the opportunity to click on a "thumb" to give the response +1 points and I think also a check-mark in a circle, which will turn green, which indicates that you have "accepted" the response as an answer.  I could not find documentation on ...
written 8 months ago by Malcolm Cook1.4k
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Comment: C: Extract isoform-specific ranges
... @hwu12 - Glad to help!  The best thanks would be to accept my answer! ...
written 9 months ago by Malcolm Cook1.4k
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Comment: C: Extract isoform-specific ranges
... Yes, except that it does not provide the info present in the revmap, being the association of each range with the to which it is unique isoform which I am assuming (perhaps incorrectly?) is desired result   > subset(GRanges(coverage(u)), score==1L) GRanges object with 2 ranges and 1 metadata c ...
written 9 months ago by Malcolm Cook1.4k
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Answer: A: Extract isoform-specific ranges
... Hello - I expect GenomicRanges:disjoin is your friend for this operation. Look: # editted for tightness and clarity, and to add a final split > g<-GRangesList(GeneA.1 = GRanges(seqnames="x", ranges=IRanges(1, 10), strand="+") + ,GeneA.2 = GRanges(seqnames="x", ranges=IRanges( ...
written 9 months ago by Malcolm Cook1.4k
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HowTo: install just html help on top of existing packages
... Is there an efficient way to install html help ONLY for all existing packages in an R installation some of which are BioConductor packages? ...
bioclite update package installation written 14 months ago by Malcolm Cook1.4k

Latest awards to Malcolm Cook

Scholar 12 months ago, created an answer that has been accepted. For A: Importing a .txt file with multiple headers into R
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Is Bioconductor 3.0 compatible with R 3.1.2?
Scholar 3.1 years ago, created an answer that has been accepted. For A: Importing a .txt file with multiple headers into R
Centurion 12.8 years ago, created 100 posts.

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