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Moderator: Michael Lawrence

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Posts by Michael Lawrence

<prev • 1,308 results • page 1 of 131 • next >
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Comment: C: How can I create a GmapGenome that doesn't start at index 1?
... Sorry, I meant `mapFromTranscripts`. You could call variants in your restricted genome space and then map to the true genome using that function. ...
written 8 days ago by Michael Lawrence10k
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Answer: A: How can I create a GmapGenome that doesn't start at index 1?
... You'll have to map the resulting coordinates using e.g. `mapToTranscripts()`. See the GenomicAlignments package. ...
written 9 days ago by Michael Lawrence10k
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Answer: A: How to filter gff based on certain gene list in rtracklayer?
... I think you could just `import()` the file, subset the returned object by whatever criteria, and `export()` it back to the file. ...
written 15 days ago by Michael Lawrence10k
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Comment: C: mclapply to loop over a GRangesList object
... The infrastructure includes a good number of utilities for common use cases. Combined with the pattern Martin mentions above, the need for an actual `lapply()` is very rare. We've optimized `lapply()` to a reasonable extent, but the bottom line is that decompressing the GRangesList into an actual li ...
written 17 days ago by Michael Lawrence10k
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Comment: C: mclapply to loop over a GRangesList object
... `intronsByTranscript()` should probably be non-generic, as it should really just rely on functions in the "TxDb" API. But anyway, if you look at `selectMethod(intronsByTranscript, "TxDb")`, you will see the basic pattern for achieving what you want with ensembldb objects. ...
written 17 days ago by Michael Lawrence10k
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Comment: C: Bug in rtracklayer::import of amino acid fasta sequences
... It's just there for completeness (rtracklayer also provides 2bit import) and is a simple wrapper around Biostrings, which is probably the better way to go. ...
written 24 days ago by Michael Lawrence10k
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Answer: A: Bug in rtracklayer::import of amino acid fasta sequences
... You have to tell rtracklayer the type of sequence using the `type=` argument ("AA" in this case). ...
written 25 days ago by Michael Lawrence10k
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Comment: C: Unexpected behaviour of set operations on GRanges objects when dplyr is loaded
... I guess the point is that dispatch could be smarter. I went ahead and inverted the dispatch cascade in S4Vectors 0.21.10, so that it flows from S3 to S4. Should resolve this issue. ...
written 6 weeks ago by Michael Lawrence10k
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Answer: A: rtracklayer BigBed format
... No, there is no support for BigBed, nor is any planned. But we'd be open to contributions. ...
written 6 weeks ago by Michael Lawrence10k
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Answer: A: Speed efficient way to select the n-th element from GRangsList
... You could also use List-based subsetting. X[rep(IntegerList(5L), length(X))] That takes about twice the time as Martin's example but one could argue that is more comprehensible once one understands how to subset by a List. Also, instead of splitAsList(), you could just coerce the result to a GRa ...
written 9 weeks ago by Michael Lawrence10k

Latest awards to Michael Lawrence

Scholar 6 weeks 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: Detecting Overlaps within Grange Object
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 8 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 8 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Scholar 20 months ago, created an answer that has been accepted. For A: Subset GRanges object into new object
Scholar 20 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 20 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Scholar 20 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 20 months ago, created an answer that has been accepted. For A: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
Teacher 20 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 20 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 20 months ago, created an answer that has been accepted. For A: unlist a exons GRangeslist object and add a gene name column
Scholar 20 months ago, created an answer that has been accepted. For A: closest-features equivalent in Bioconductor for finding closest gene(s)
Scholar 20 months ago, created an answer that has been accepted. For A: reduce function after combining 2 GRanges objects from cn.mops output
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 20 months ago, created an answer that has been accepted. For A: issue renaming seqnames in genomic ranges
Scholar 20 months ago, created an answer that has been accepted. For A: does import.bw with the selection argument take into account strand?
Scholar 20 months ago, created an answer that has been accepted. For A: VariantAnnotation as.vranges with asterisk in ALT field
Scholar 20 months ago, created an answer that has been accepted. For A: Group GRanges and keep metadata
Teacher 20 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?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information

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