Moderator: Michael Lawrence

gravatar for Michael Lawrence
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Posts by Michael Lawrence

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Answer: A: Could not find function "makeTranscriptDbFromGFF"
... I think that function has been renamed to makeTxDbFromGFF() in accordance with the change in the name of the TxDb class, through an appropriate deprecation cycle. ...
written 1 day ago by Michael Lawrence9.6k
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Answer: A: Gene Size using GenomicFeatures
... No, there is no function in GenomicFeatures for that. You have a GRanges object, defined by the GenomicRanges package. There is a GRanges method on the generic function width() that will return what you want. You can check out ?GRanges for more on what you can do with a GRanges. ...
written 1 day ago by Michael Lawrence9.6k
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Comment: C: Implementing fast mathematical and statistical operations on genomic variables i
... I like GPos and it would be great if it were applicable to human-size genomes. It would be nice to have easy way (simple function call) of moving between GPos and the RLE representation in a GRanges. Sometimes you want to operate on runs, other times positions. ...
written 4 days ago by Michael Lawrence9.6k
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Answer: A: Implementing fast mathematical and statistical operations on genomic variables i
... I am not sure whether C/C++ would really help unless there is some library for numerical computing with RLEs. The code you propose for ppois() is OK but I would use mapply() for cleanliness and coerce to the numeric vector within the loop in order to save memory (at a time cost). We are working to ...
written 6 days ago by Michael Lawrence9.6k
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Answer: A: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
... I just pushed a change to devel that expects all BED files to be tab-separated. That's what the spec says, and it's what bedtools requires, so hopefully it does not cause too much havoc. ...
written 11 days ago by Michael Lawrence9.6k
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Comment: C: converting a GRangesList object with different lengths into a data frame
... Ok. I think you could make a plot like the above using the long form. Certainly in ggplot2 or lattice, and probably in base. One issue that may not apply in your case is splicing. The simple code above will not handle the case of an intron within the first 100 bp. For that, you'll want to look into ...
written 11 days ago by Michael Lawrence9.6k
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Answer: A: converting a GRangesList object with different lengths into a data frame
... I don't immediately see how arranging the data in this way is useful. But the best way would be to coerce to data.frame and then use reshape() to move to wide form. I guess the tricky part is getting a variable representing the subscript within each GRanges. I've called that "row" below. df <- ...
written 11 days ago by Michael Lawrence9.6k
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Answer: A: Error in normSplitFactor(f, x)
... I guess we could make this more obvious but the problem is that there is no gene_id column. ...
written 12 days ago by Michael Lawrence9.6k
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Answer: A: summarize scores of GRanges into bins
... I think you're aiming to generate 100 windows over the span of each gene. First, find the gene spans, then unlist to GRanges, and generate the tiles: tiles <- tile(unlist(range(gr.list)), n=100) We now need to figure out which positions overlap which tile. It is simplest to first simplify the ...
written 16 days ago by Michael Lawrence9.6k
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Comment: C: subsetting GRanges object based on gene IDs
... Did you consider using %in% instead of ==? ...
written 21 days ago by Michael Lawrence9.6k

Latest awards to Michael Lawrence

Scholar 3 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 4 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 4 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 4 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 4 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 5 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 5 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 5 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 6 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 6 months ago, created an answer that has been accepted. For A: filtering VCF files
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Scholar 6 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 6 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: Genomic Ranges findOverlaps by sample
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: setdiff for GenomicRanges
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: Genomic Ranges findOverlaps by sample
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Operations across Lists of GenomicRanges?
Scholar 17 months ago, created an answer that has been accepted. For A: setdiff between GenomicRanges objects keeping metadata
Scholar 17 months ago, created an answer that has been accepted. For A: Operations across Lists of GenomicRanges?

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