Moderator: Michael Lawrence

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Posts by Michael Lawrence

<prev • 1,263 results • page 2 of 127 • next >
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Answer: A: Subsetting GRanges objext
... This is the way factors work, and the behavior can be useful. To adjust the seqlevels, use a convenience function like keepSeqlevels(), or the seqlevels<-() setter. ...
written 5 weeks ago by Michael Lawrence10k
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Answer: A: Import Chain - Cannot Import Chain File
... Looks like the UCSC chain file format has changed, or at least they are using features that they weren't before. It may take a bit for me to fix the parser. ...
written 5 weeks ago by Michael Lawrence10k
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Answer: A: IRanges seqselect and subsetByRanges
... This should be possible just via x[ranges], or extractROWS(x, ranges). There's also extractList() for making a list with one element per range. ...
written 7 weeks ago by Michael Lawrence10k
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Answer: A: motifs order on importing the motifs from bigWig file
... This could be improved, but as it is, there are two options: Ensure that the GRanges is sorted by the seqlevels as they are in the BigWig file. The resulting NumericList contains a metadata() field named "ranges", which is the which ranges in the order of the result. ...
written 8 weeks ago by Michael Lawrence10k
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Comment: C: Compute average score across multiple bed files
... Sure, since the scores are always 3, so that happens to work, but I doubt all the scores are actually 3. ...
written 8 weeks ago by Michael Lawrence10k
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Comment: C: Compute average score across multiple bed files
... Here is one way to do it: abc <- c(a,b,c) r <- disjoin(abc, with.revmap = TRUE, ignore.strand = TRUE) r$mean.score <- sum(extractList(score(abc), r$revmap)) / 3L It really seems like you would want the zero ranges in this data though. You could have a zero-score GRanges for the entire ge ...
written 8 weeks ago by Michael Lawrence10k
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Comment: C: Compute average score across multiple bed files
... Shouldn't this average the scores, not count the ranges? ...
written 8 weeks ago by Michael Lawrence10k
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Comment: C: Replacement for lapply on a GRanges?
... There can be multiple transcript names per element of the GRanges. How do you want to resolve that case? If you know that there is exactly one per range, just unlist() it, otherwise you might want something like any(). The point is, you need to consider the complexity of the data.  ...
written 11 weeks ago by Michael Lawrence10k
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Comment: C: Problem when transforming Platypus vcf to VRanges
... You need to wait for the fix to appear in 1.27.2. ...
written 11 weeks ago by Michael Lawrence10k
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Answer: A: Problem when transforming Platypus vcf to VRanges
... Thanks, Should be fixed in 1.26.1 (also in devel). ...
written 11 weeks ago by Michael Lawrence10k

Latest awards to Michael Lawrence

Scholar 3 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Scholar 3 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 15 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 15 months ago, created an answer that has been accepted. For A: Subset GRanges object into new object
Scholar 15 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Scholar 15 months ago, created an answer that has been accepted. For A: closest-features equivalent in Bioconductor for finding closest gene(s)
Scholar 15 months ago, created an answer that has been accepted. For A: reduce function after combining 2 GRanges objects from cn.mops output
Scholar 15 months ago, created an answer that has been accepted. For A: unlist a exons GRangeslist object and add a gene name column
Scholar 15 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 15 months ago, created an answer that has been accepted. For A: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: unlist a exons GRangeslist object and add a gene name column
Scholar 15 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: annotate GRanges with upstream or downstream nearest gene
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 15 months ago, created an answer that has been accepted. For A: issue renaming seqnames in genomic ranges
Scholar 15 months ago, created an answer that has been accepted. For A: does import.bw with the selection argument take into account strand?
Scholar 15 months ago, created an answer that has been accepted. For A: VariantAnnotation as.vranges with asterisk in ALT field
Scholar 15 months ago, created an answer that has been accepted. For A: Group GRanges and keep metadata
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: What is the proper way to modify mcols of a GRanges inside a GRangesList?
Scholar 15 months ago, created an answer that has been accepted. For A: Why export of empty GRanges to GFF fails?
Scholar 15 months ago, created an answer that has been accepted. For A: VariantAnnotation - expand not working as intended for VCF

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