Moderator: Michael Lawrence

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Posts by Michael Lawrence

<prev • 1,251 results • page 1 of 126 • next >
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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 11 days 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 14 days 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 19 days 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 19 days 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 19 days 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 5 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 5 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 5 weeks ago by Michael Lawrence10k
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Comment: C: How do I do a bedtools like intersection in GenomicRanges?
... No. pintersect() after findOverlaps() ...
written 6 weeks ago by Michael Lawrence10k
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Answer: A: How do I do a bedtools like intersection in GenomicRanges?
... See the HelloRanges package for this. ...
written 6 weeks ago by Michael Lawrence10k

Latest awards to Michael Lawrence

Scholar 11 weeks ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Scholar 11 weeks ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Teacher 11 weeks ago, created an answer with at least 3 up-votes. 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: setdiff for GenomicRanges
Scholar 13 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 13 months ago, created an answer that has been accepted. For A: Subset GRanges object into new object
Scholar 13 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Scholar 13 months ago, created an answer that has been accepted. For A: closest-features equivalent in Bioconductor for finding closest gene(s)
Scholar 13 months ago, created an answer that has been accepted. For A: reduce function after combining 2 GRanges objects from cn.mops output
Scholar 13 months ago, created an answer that has been accepted. For A: unlist a exons GRangeslist object and add a gene name column
Scholar 13 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 13 months ago, created an answer that has been accepted. For A: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
Teacher 13 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 13 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: annotate GRanges with upstream or downstream nearest gene
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 13 months ago, created an answer that has been accepted. For A: issue renaming seqnames in genomic ranges
Scholar 13 months ago, created an answer that has been accepted. For A: does import.bw with the selection argument take into account strand?
Scholar 13 months ago, created an answer that has been accepted. For A: VariantAnnotation as.vranges with asterisk in ALT field
Scholar 13 months ago, created an answer that has been accepted. For A: Group GRanges and keep metadata
Teacher 13 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 13 months ago, created an answer that has been accepted. For A: Why export of empty GRanges to GFF fails?
Scholar 13 months ago, created an answer that has been accepted. For A: VariantAnnotation - expand not working as intended for VCF

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