User: Malcolm Cook

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Malcolm Cook1.5k
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Posts by Malcolm Cook

<prev • 158 results • page 1 of 16 • next >
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Comment: C: CDS phase information missing from GenomicFeatures
... Yes, I am, Herve. Indeed. Let's back up a sec, and, for completeness let's make sure we are talking about the same thing. Here's my best reference - https://useast.ensembl.org/Help/Glossary where we find: Phase Exon The position of an exon/intron boundary within a codon. A phase of zero means the bo ...
written 1 day ago by Malcolm Cook1.5k
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Comment: C: CDS phase information missing from GenomicFeatures
... Just what I was looking for!  Except, upon review, I think the logic is off.  I've commented one line as #OLD and replaced it with proposed new line.   addCdsPhase <- function(cds_by_tx)    ## 'cds_by_tx' must be a GRangesList object obtained with cdsBy(txdb, by="tx") {   cds_phase <- pc(rep ...
written 1 day ago by Malcolm Cook1.5k
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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 4 months ago by Malcolm Cook1.5k
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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 4 months ago by Malcolm Cook1.5k
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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 6 months ago by Malcolm Cook1.5k
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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 9 months ago by Malcolm Cook1.5k
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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 11 months ago by Malcolm Cook1.5k
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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 11 months ago by Malcolm Cook1.5k
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Comment: C: Extract isoform-specific ranges
... @hwu12 - Glad to help!  The best thanks would be to accept my answer! ...
written 11 months ago by Malcolm Cook1.5k
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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 12 months ago by Malcolm Cook1.5k

Latest awards to Malcolm Cook

Scholar 15 months ago, created an answer that has been accepted. For A: Importing a .txt file with multiple headers into R
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Is Bioconductor 3.0 compatible with R 3.1.2?
Scholar 3.3 years ago, created an answer that has been accepted. For A: Importing a .txt file with multiple headers into R
Centurion 13.0 years ago, created 100 posts.

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