Moderator: Michael Lawrence

gravatar for Michael Lawrence
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Posts by Michael Lawrence

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Comment: C: cmetindex missing in gmapr? Not possible to do bisulfite alignments
... gmapR 1.21.1 (devel) should resolve this issue by exporting cmetindex and adding the missing coercion. ...
written 6 days ago by Michael Lawrence9.8k
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Answer: A: cmetindex missing in gmapr? Not possible to do bisulfite alignments
... I guess we were waiting for a post like this to motivate support for those. They look like they've been implemented, but they've never been tested. You could try calling them, passing the GmapGenome object. Let me know how it goes. Eventually we can export and document them. ...
written 11 days ago by Michael Lawrence9.8k
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Answer: A: unlist a exons GRangeslist object and add a gene name column
... stack(exons, "gene")   ...
written 12 days ago by Michael Lawrence9.8k
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Comment: C: How to build a RNA-seq table of counts for repeatmasker annotations
... Probably could just read it with read.table() and then coerce to GRanges. ...
written 18 days ago by Michael Lawrence9.8k
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Answer: A: How to build a RNA-seq table of counts for repeatmasker annotations
... You can always download the "rmsk" table from UCSC using rtracklayer. ...
written 18 days ago by Michael Lawrence9.8k
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Comment: C: Weaknesses with GRanges data type, or just me ?
... If you need the data as a GRangesList, then there is a choice: are you restricting the analysis to a single chromosome? If so, this does what you want: keepSeqlevels(grl, "chr1", pruning.mode="tidy") Or, be explicit: grl1 <- grl[seqnames(grl) == "chr1"] grl1[lengths(grl1) > 0]   ...
written 24 days ago by Michael Lawrence9.8k
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Comment: C: Subset GRanges object into new object
... It sounds like you might just want to get the transcripts as a GRanges directly, i.e., call transcripts() instead of transcriptsBy(). ...
written 25 days ago by Michael Lawrence9.8k
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Answer: A: Subset GRanges object into new object
... First, please avoid accessing the slots of the object, as they are an internal implementation detail. Code accessing the slots will be cryptic and fragile. Note that this object is not a GRanges but a GRangesList. You might want to simplify to a GRanges using something like: tscripts_gr <- sta ...
written 25 days ago by Michael Lawrence9.8k
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Answer: A: Weaknesses with GRanges data type, or just me ?
... Information will be lost through coercion to a more general data structure. I guess there could be a way to coerce from data.frame to GRangesList, making an inference on the grouping column based on its name.  Typically though this round trip should not be necessary. GRanges shares much of the same ...
written 25 days ago by Michael Lawrence9.8k
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Answer: A: Finding distance between end of all ORFs in utr and start of first cds exon in t
... Well merge() is vectorized but it's a more general case than you require, and so is slower than something simpler. I think you can sort the first exons, flatten them to a GRanges, flatten the ORFs and expand the first exons accordingly. It may be easier and faster in the long run to keep the data as ...
written 26 days ago by Michael Lawrence9.8k

Latest awards to Michael Lawrence

Scholar 4 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 6 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 6 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 6 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 6 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 7 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 7 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 7 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 7 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 8 months ago, created an answer that has been accepted. For A: filtering VCF files
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Scholar 8 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 8 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 9 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 9 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 9 months ago, created an answer that has been accepted. For A: setdiff for GenomicRanges
Scholar 9 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 9 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Operations across Lists of GenomicRanges?
Scholar 19 months ago, created an answer that has been accepted. For A: setdiff between GenomicRanges objects keeping metadata
Scholar 19 months ago, created an answer that has been accepted. For A: Operations across Lists of GenomicRanges?

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