Moderator: Michael Lawrence

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Posts by Michael Lawrence

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Comment: C: mm10 phastCons data for use with ATACseqQC
... Just a comment on the import, it would probably be best to use as="NumericList" for that type of data. It will probably still be pretty big though. You could loop over the chromosomes and use the which argument. ...
written 2 days ago by Michael Lawrence9.2k
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Answer: A: What is the proper way to modify mcols of a GRanges inside a GRangesList?
... This should work (as long as the column is not actually "new"): grl[,"newColumn"] <- newValue Someone should probably document that (I only found it by reading the code). But maybe it's better to do this: mcols(grl, level="within")$newColumn <- newValue Because it's more explicit, can ad ...
written 3 days ago by Michael Lawrence9.2k
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Answer: A: Genomicfeatures- Error: Image not found, dynamic loading, reputed error???
... Right now you'll need to install rtracklayer from source, or install openssl from homebrew. We're working on getting the binary to work out of the box. ...
written 7 days ago by Michael Lawrence9.2k
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Answer: A: Can I create a GmapGenome with a relative file path?
... Ok, I've fixed it in 1.19.1. ...
written 7 days ago by Michael Lawrence9.2k
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Comment: C: Can I create a GmapGenome with a relative file path?
... Does file.exists() return true for that path? Just making sure that e.g. the working directory is right. ...
written 10 days ago by Michael Lawrence9.2k
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Answer: A: Obtain exactly the interval that overlap
... Yes, it's basically pintersect(findOverlapPairs(gr1, gr2)).   ...
written 14 days ago by Michael Lawrence9.2k
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Answer: A: Split Genomic Ranges With Reference Overlaps (Centromere)
... Find the centromere for each range, and subtract it. The result is a GRangesList, because you need to group the result ranges by each input range. Metadata is carried over. centromeres <- centromeres[match(seqnames(ranges), seqnames(centromeres))] centromeres <- as(centromeres, "GRangesList" ...
written 17 days ago by Michael Lawrence9.2k
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Answer: A: trying to annotate overlaps with external file information
... It looks like you want what comes from the bedtools -wb option. It would write out the gene ranges after the intersections. The HelloRanges package maps bedtools command lines to IRanges code. For example, > bedtools_intersect("-a regions_of_interest.bed -b genes.bed -wb") { genome <- Se ...
written 19 days ago by Michael Lawrence9.2k
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Comment: C: Data structure for my dataset
... metadata() on GRanges is the same as metadata() on SummarizedExperiment. Maybe you are getting confused with mcols()? ...
written 21 days ago by Michael Lawrence9.2k
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Answer: A: Data structure for my dataset
... I think you could just store the metadata in a list as the metadata() component of the GRanges. ...
written 21 days ago by Michael Lawrence9.2k

Latest awards to Michael Lawrence

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 3 days ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 16 days ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 19 days ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 24 days ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 5 weeks ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 5 weeks ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 6 weeks ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 8 weeks ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 9 weeks ago, created an answer that has been accepted. For A: filtering VCF files
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Scholar 10 weeks ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 11 weeks 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: Genomic Ranges findOverlaps by sample
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: setdiff for GenomicRanges
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: Genomic Ranges findOverlaps by sample
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Operations across Lists of GenomicRanges?
Scholar 13 months ago, created an answer that has been accepted. For A: setdiff between GenomicRanges objects keeping metadata
Scholar 13 months ago, created an answer that has been accepted. For A: Operations across Lists of GenomicRanges?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Collapse/Reduce in GRanges by Metadata Column

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