Moderator: Michael Lawrence

gravatar for Michael Lawrence
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Posts by Michael Lawrence

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Comment: C: (Big)wig file of complete chromosome
... I fixed this in devel. Work around is just not to use Rles, or coerce them to numeric vectors on export. The export routines are not that optimized for GPos anyway. ...
written 21 days ago by Michael Lawrence9.6k
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Comment: C: (Big)wig file of complete chromosome
... The approach described by Herve is not so bad, in general. You can pass the Seqinfo object to import, e.g., gr <- import(file, seqinfo=Seqinfo(genome="sacCer3"))   ...
written 4 weeks ago by Michael Lawrence9.6k
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Comment: C: (Big)wig file of complete chromosome
... It should come automatically from a BigWig file (it's embedded within the file). For bedGraph, unless the file has the genome indicated in a UCSC-style "track line", you will need to tell it the genome via the genome= argument (for example, "hg38").  It will look up the seqlengths automatically from ...
written 4 weeks ago by Michael Lawrence9.6k
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Comment: C: Extract isoform-specific ranges
... Could also do subset(GRanges(coverage(u)), score==1L)   ...
written 5 weeks ago by Michael Lawrence9.6k
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Comment: C: IRanges error from derfinder analyzeChr with custom TxDb?
... It looks like this is a dispatch issue, perhaps caused by some weird corruption of the methods cache. It might help to reinstall some of the packages involved, like BiocGenerics and S4Vectors. ...
written 5 weeks ago by Michael Lawrence9.6k
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Answer: A: Extract isoform-specific ranges
... Maybe you're looking for GenomicFeatures::mapToTranscripts()? ...
written 5 weeks ago by Michael Lawrence9.6k
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Answer: A: rtracklayer::lifOver one-to-many regions and not match UCSC
... The inconsistency is probably due to the UCSC lift over "smoothing over" the gaps in the alignment. rtracklayer takes a more literal interpretation of the chain file. Does this cause a problem for your use case? If a good case is made, I could add an option for the smoothing to rtracklayer. It would ...
written 5 weeks ago by Michael Lawrence9.6k
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Comment: C: IRanges from BAM file to GRanges convert
... Perhaps all you needed to do was extract the first (and only) element with test_bam_Iranges[[1]]. I also wonder whether you could have got what you wanted by replacing all of that with grglist(bam). ...
written 5 weeks ago by Michael Lawrence9.6k
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Comment: C: IRanges from BAM file to GRanges convert
... You actually have a RangesList, not a Ranges. How did you end up with one of those? Maybe you could show the code for importing the object from the BAM. ...
written 6 weeks ago by Michael Lawrence9.6k
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Comment: C: (Big)wig file of complete chromosome
... You want to use a GPos object. I thought this would be simple, but it turns out to require a couple lines: gpos <- GPos(gr) gpos$score <- rep(gr$score, width(gr))   ...
written 6 weeks ago by Michael Lawrence9.6k

Latest awards to Michael Lawrence

Scholar 3 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 4 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 4 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 4 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 4 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 5 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 5 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 5 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 6 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 6 months ago, created an answer that has been accepted. For A: filtering VCF files
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Scholar 6 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 6 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 7 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 7 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 7 months ago, created an answer that has been accepted. For A: setdiff for GenomicRanges
Scholar 7 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 7 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Operations across Lists of GenomicRanges?
Scholar 17 months ago, created an answer that has been accepted. For A: setdiff between GenomicRanges objects keeping metadata
Scholar 17 months ago, created an answer that has been accepted. For A: Operations across Lists of GenomicRanges?

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