User: Malcolm Cook

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Malcolm Cook1.5k
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Posts by Malcolm Cook

<prev • 164 results • page 1 of 17 • next >
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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 15 hours 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 16 hours 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 18 days 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 19 days 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 weeks ago by Malcolm Cook1.5k
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Comment: C: Function simplify fails when argument ont is set to "ALL" in enrichGO function i
... FWIW this problem similarly "stumped" me for a little while.... I do hope it is resolved in the future... tx  ...
written 5 weeks ago by Malcolm Cook1.5k
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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 9 weeks 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 9 weeks 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 6 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 6 months ago by Malcolm Cook1.5k

Latest awards to Malcolm Cook

Scholar 17 months ago, created an answer that has been accepted. For A: Importing a .txt file with multiple headers into R
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Is Bioconductor 3.0 compatible with R 3.1.2?
Scholar 3.5 years ago, created an answer that has been accepted. For A: Importing a .txt file with multiple headers into R
Centurion 13.2 years ago, created 100 posts.

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