Moderator: Michael Lawrence

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Posts by Michael Lawrence

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Comment: C: reduce granges if mcols value are ideitical with the next intervals
... Please provide an example of what you want to do. I'm pretty sure it's doable in a simple way. ...
written 7 days ago by Michael Lawrence9.3k
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Answer: A: matrix as a column of mcols of GRanges would not be extracted correctly by lappl
... This is because > extractROWS(gr$mat, NSBS(IRanges(1,2), gr$mat)) [1] 1 2 which dispatches to extractROWS,vector_or_factor,RangeNSBS() and fails to take into account the dimensions. For now, I've checked in a fallback to S4Vectors:::.extractROWSWithBracket() for arrays, but there would be some ...
written 11 days ago by Michael Lawrence9.3k
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Answer: A: Width in IRanges objects on "+" and "-" strand
... The resize() method on GRanges is strand aware, so you could do: gr <- GRanges(seqnames = Rle(c("chr1", "chr2", "chr3", "chr4")), ranges = IRanges(10:13, width=1L), strand = Rle(c("+", "-", "+", "-"))) resize(gr, 3L)   ...
written 11 days ago by Michael Lawrence9.3k
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Comment: C: Irange _ Start and End
... Are you using the latest version of Bioconductor (3.5)? Your installation may be too old. ...
written 13 days ago by Michael Lawrence9.3k
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Answer: A: Irange _ Start and End
... paste(as.character(x[[1]]), collapse=", ") ...
written 13 days ago by Michael Lawrence9.3k
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Comment: C: How to change seqlevels in a GRanges object
... Or even shorter: keepStandardChromosomes(gr, pruning.mode="coarse") ...
written 22 days ago by Michael Lawrence9.3k
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Comment: C: why merged paired end reads still have strand infomation?
... Please tell us how you are doing the merging. rtracklayer does not do any merging. If you give it strand information, it will output it. ...
written 25 days ago by Michael Lawrence9.3k
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Comment: C: How to change seqlevels in a GRanges object
... In other words, seqlevelsStyle(gr) <- "NCBI"   ...
written 27 days ago by Michael Lawrence9.3k
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Answer: A: Interpreting R code with GRanges object
... I don't think the start and end in that data frame are chromosomal locations. My guess is that they have computed contiguous sets of ranges that belong to the same segment or something. The code is really hard to follow. I wouldn't recommend reading their code if your goal is to learn about Biocondu ...
written 28 days ago by Michael Lawrence9.3k
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Comment: C: reduce function after combining 2 GRanges objects from cn.mops output
... Check out that link in my answer. It shows the basics of this approach, including that you can call findOverlaps() with only a single argument. ...
written 28 days ago by Michael Lawrence9.3k

Latest awards to Michael Lawrence

Scholar 4 weeks ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 9 weeks ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 11 weeks ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 11 weeks ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 12 weeks ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 3 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 3 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 3 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 4 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 4 months ago, created an answer that has been accepted. For A: filtering VCF files
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Scholar 4 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 4 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: Genomic Ranges findOverlaps by sample
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: setdiff for GenomicRanges
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: Genomic Ranges findOverlaps by sample
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Operations across Lists of GenomicRanges?
Scholar 15 months ago, created an answer that has been accepted. For A: setdiff between GenomicRanges objects keeping metadata
Scholar 15 months ago, created an answer that has been accepted. For A: Operations across Lists of GenomicRanges?

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