Moderator: Michael Lawrence

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Posts by Michael Lawrence

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Comment: C: GRanges object from gene list
... You'll want to use whatever annotations were used to generate the counts.  ...
written 5 weeks ago by Michael Lawrence9.9k
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Answer: A: GRanges object from gene list
... It depends on the source. For RefSeq in particular, you could use GenomicFeatures::makeTxDbFromUCSC() and ask for the "refGene" table (I think that's what it's called). Then, extract the desired features as a GRanges with e.g. genes(). There are probably resources available from AnnotationHub, as we ...
written 5 weeks ago by Michael Lawrence9.9k
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Comment: C: Make window around TSS and get values from another data.frame for bins of the sp
... I'll again recommend using promoters() to form exp_granges. subsetByOverlaps() will just return the elements of chip that overlap any range in exp_granges. Instead, I think you want to match the ranges up using findOverlaps() or similar.  But you probably want to group the scores by TSS, so somethin ...
written 6 weeks ago by Michael Lawrence9.9k
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Answer: A: Make window around TSS and get values from another data.frame for bins of the sp
... Use promoters() to generate the promoters, tile() to break them up into windows, and findOverlaps() to find which score windows overlap which promoter windows. Then you need to decide how to aggregate when multiple score windows overlap a single promoter window. ...
written 6 weeks ago by Michael Lawrence9.9k
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Answer: A: seqnames versus chrom
... Stick with seqnames(). The chrom() accessor is from before GRanges existed. Should probably be deprecated. ...
written 6 weeks ago by Michael Lawrence9.9k
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Comment: C: Add columns to granges object that sum score around range
... Might want to consider a loop. ...
written 7 weeks ago by Michael Lawrence9.9k
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Answer: A: Add columns to granges object that sum score around range
... One way to do this fast is to take advantage of the fixed width WIG data (200bp). Then it is easy to compute how many neighboring elements to include in the sum. window <- 10000L width <- 200L w <- resize(IRanges(seq_along(wig), width=1L), window/width, fix="center") w <- restrict(w, 1 ...
written 7 weeks ago by Michael Lawrence9.9k
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Comment: C: Add columns to granges object that sum score around range
... Needs some clarification. What sort of window do you want around each range? 10kb, centered on the midpoint of the range, or what? Btw, keepStandardChromosomes() might be helpful. ...
written 7 weeks ago by Michael Lawrence9.9k
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Answer: A: Generate 3' UTR and 5' UTR ranges from a gff file
... To get the ranges of the UTRs, as a GRangesList or GRanges object: library(rtracklayer) gtf <- import.gff3("tmp.gtf") tx <- subset(gtf, type == "mRNA") cds <- subset(gtf, type == "CDS") cds <- range(multisplit(cds, cds$Parent)) utrs <- psetdiff(tx, cds[tx$ID])       ...
written 8 weeks ago by Michael Lawrence9.9k
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Comment: C: breakTies for a Hits-object based on value in mcols?
... Well there is now in devel, S4Vectors 0.17.13. I also wanted to mention that the sort() failed, I think, because IRanges wasn't loaded. Some stuff still needs to be moved over. Jeff's comment on needing to include the queryHits is no longer true. Calling sort() on a "SortedByQueryHits" will coerce ...
written 9 weeks ago by Michael Lawrence9.9k

Latest awards to Michael Lawrence

Scholar 8 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 9 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 9 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 9 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 9 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 10 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 10 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 10 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 11 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 11 months ago, created an answer that has been accepted. For A: filtering VCF files
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Scholar 11 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 11 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 12 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 12 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 12 months ago, created an answer that has been accepted. For A: setdiff for GenomicRanges
Scholar 12 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 12 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Operations across Lists of GenomicRanges?
Scholar 22 months ago, created an answer that has been accepted. For A: setdiff between GenomicRanges objects keeping metadata
Scholar 22 months ago, created an answer that has been accepted. For A: Operations across Lists of GenomicRanges?

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