Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 20k
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Website:
http://bioconductor.org/
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3 hours ago
Joined:
11 years, 10 months ago
Email:
m************@roswellpark.org

Posts by Martin Morgan

<prev • 2,605 results • page 1 of 261 • next >
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Answer: A: appointing a new maintainer for my package
... Have you already identified a new maintainer, or are you looking to find one? If you're looking for a new maintainer, then advertising here and especially on the bioc-devel mailing list would be appropriate, but probably the most success will come from a 'power user' that you've interacted with alr ...
written 3 hours ago by Martin Morgan ♦♦ 20k
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Answer: A: GSEAbase: goSlim function, pb with counts
... Sorry for my slow response, but yes, this seems to be a bug; thanks! It is fixed in version 1.38.2, which should become available via biocLite() on Thursday after about 2pm Eastern, all being well. The updated output is > goSlim(currentCollecSet7, slim, "CC") Count Percent ...
written 3 days ago by Martin Morgan ♦♦ 20k
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Comment: C: How to construct a valid GRanges object from RCPP and pass back to R
... It would help a lot to have code that I could actually execute. For instance, it looks like fiveUTRs is a list-GRangesList ? but it could be any number of things. Can you make a simple fully reproducible example (one that takes just a few seconds to run). This of course requires that you provide the ...
written 3 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Implementing fast mathematical and statistical operations on genomic variables i
... Map() / mapply() also retain names. mendoapply() returns the same object as input, avoiding explicit coercion to RleList. ppoisRle <- function(q, lambda, ...) {   q <- as.numeric(q)   lambda <- as.numeric(lambda) value <- ppois(q = q, lambda = lambda, ...)   Rle(value) } ppoi ...
written 3 days ago by Martin Morgan ♦♦ 20k
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Comment: C: How to construct a valid GRanges object from RCPP and pass back to R
... As written, getFastqSeq() and find_in_frame_ORFs() are loop invariants (don't depend on iteration, and can be moved outside the lapply. The iteration is now dna <- getFastaSeq() ## function for finding orfs, returned as IRanges. ORFdef <- find_in_frame_ORFs(dna, longestORF = FALSE, minimumLe ...
written 3 days ago by Martin Morgan ♦♦ 20k
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Comment: C: How to construct a valid GRanges object from RCPP and pass back to R
... So can you construct a simple example of a GRanges object that is big, and a simple operation that you've implemented and that has driven you to C++? ...
written 4 days ago by Martin Morgan ♦♦ 20k
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Comment: C: How to construct a valid GRanges object from RCPP and pass back to R
... Hmm, reading your question all the way through ;) ... GRanges can easily work on millions of rows, but you're probably trying to do operations one row at a time, instead of on vectors. e.g.,  > gr = GRanges("chr1", IRanges(rep(1, 1000), width=10)) > system.time({ res0 <- lapply(gr, functi ...
written 4 days ago by Martin Morgan ♦♦ 20k
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Answer: A: How to construct a valid GRanges object from RCPP and pass back to R
... I created a file "CPPRanges.cpp" #include <Rcpp.h> using namespace Rcpp; // [[Rcpp::export]] S4 CPPRanges(Function GRanges, Function IRanges) { IntegerVector start = IntegerVector::create( 10, 20, 30 ); IntegerVector end = IntegerVector::create( 40 ); CharacterVector seqname = C ...
written 4 days ago by Martin Morgan ♦♦ 20k
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Comment: C: How to construct a valid GRanges object from RCPP and pass back to R
... Use the 'ADD REPLY' button rather than 'Add Answer'. I was thinking more along the lines of http://gallery.rcpp.org/articles/r-function-from-c++/ ...
written 4 days ago by Martin Morgan ♦♦ 20k
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Comment: C: How to construct a valid GRanges object from RCPP and pass back to R
... Direct slot access violates the API; I'd instead arrange to call the constructor (GenomicRanges::GRanges()) from C++. ...
written 4 days ago by Martin Morgan ♦♦ 20k

Latest awards to Martin Morgan

Scholar 12 weeks ago, created an answer that has been accepted. For A: BiocParallel: messages shown only when processes finished
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Error in GRanges: could not find symbol "recursive" in environment of the generi
Scholar 3 months ago, created an answer that has been accepted. For A: BiocParallel: messages shown only when processes finished
Scholar 3 months ago, created an answer that has been accepted. For A: BiocParallel: messages shown only when processes finished
Scholar 3 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 3 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 4 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Error in GRanges: could not find symbol "recursive" in environment of the generi
Appreciated 4 months ago, created a post with more than 5 votes. For Statistics and Computing in Genome Science (CSAMA) Course Material
Scholar 4 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 4 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 5 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Appreciated 5 months ago, created a post with more than 5 votes. For BioC 2015 Annual Conference
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Scholar 5 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 5 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 5 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Appreciated 6 months ago, created a post with more than 5 votes. For BioC 2015 Annual Conference
Scholar 6 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 6 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Scholar 6 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 7 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()

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