Moderator: Michael Lawrence

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Posts by Michael Lawrence

<prev • 1,348 results • page 1 of 135 • next >
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Answer: A: Coverage function assigns wrong weights for gapped alignments
... Seems like a bug in `coverage,GRangesList()`, because it should automatically expand the weights. For a relatively simple speed up, consider: ``` grl <- grglist(reads) weight <- mcols(reads)$weight[togroup(PartitioningByEnd(grl))] coverage(grl, weight) ``` ...
written 1 day ago by Michael Lawrence11k
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Comment: C: Can GenomicRanges findOverlaps ignore seqnames?
... Would you please provide more details on the use case? ...
written 2 days ago by Michael Lawrence11k
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Comment: C: Best way to subset one IRanges by list of IRanges
... I see, in that case I'm not sure if that is really a subset operation. It's more like `extractList()` except by overlap. ...
written 17 days ago by Michael Lawrence11k
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Comment: C: Best way to subset one IRanges by list of IRanges
... Would you be interested in contributing a `subsetByOverlaps()` method? Btw, I think you do need to reverse the arguments from your initial example, i.e., `subsetByOverlaps(slist, query)`. The simplest thing to do is `unlist(slist)`, perform the subset, then reform the list, which would be the slight ...
written 17 days ago by Michael Lawrence11k
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Comment: C: Best way to subset one IRanges by list of IRanges
... The reason this does not exist is that a RangesList defines ranges within separate spaces (typically chromosomes), named by the names of the list. An IRanges has no defined space. We could add a method that simply repeats the search across every space, but so far there has been no motivating use cas ...
written 17 days ago by Michael Lawrence11k
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Comment: C: Subsetting a GenomicRanges::GRanges with "%in%" fails
... Not exactly as there are generics specific to certain data types defined by the packages you mention and many others. Unless you are using a package for a very specific reason (like a single utility function), it's simplest to just import the package in bulk. ...
written 4 weeks ago by Michael Lawrence11k
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Comment: C: Checking if to DataFrames are identical
... Could be a lot of things. `all.equal()` is a good way to figure out which one(s). ...
written 5 weeks ago by Michael Lawrence11k
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Answer: A: Is it useful to define and export a setAs('BSgenome', 'GRanges')
... It depends on how obvious the conversion is. Sometimes, probably including this time, it's best to be explicit. Others may have a different opinion though. ...
written 5 weeks ago by Michael Lawrence11k
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Comment: C: Subsetting a GenomicRanges::GRanges with "%in%" fails
... You could always do something like ``IRanges::`%in%`(x, y)``. Keeping the workspace clean can be a pain though, because you'll constantly have to remember the origin of each function. ...
written 5 weeks ago by Michael Lawrence11k
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Answer: A: Filtering GFF3 file
... Assuming you want to do this with Bioconductor, you could do something like: ``` gr <- import("t.gff3") haveNotes <- !is.na(drop(test$Note)) gene <- drop(gr$Parent)[haveNotes] filtered <- subset(gr, gene == ID | haveNotes | startsWith(drop(Parent), paste0(gene, "."))) export(filtered, " ...
written 5 weeks ago by Michael Lawrence11k

Latest awards to Michael Lawrence

Scholar 3 months ago, created an answer that has been accepted. For A: Extract metadata from GRanges object for every genomic coordinate
Scholar 9 months ago, created an answer that has been accepted. For A: Subset GRanges object into new object
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: How can I create a GmapGenome that doesn't start at index 1?
Popular Question 9 months ago, created a question with more than 1,000 views. For Job Opening: Computational Biologist @ Genentech Bioinformatics
Scholar 9 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Scholar 9 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to use GenomicRanges to find overlaps by percentage covered of interval
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Importing Gene Symbols with makeTxDbFromGFF
Scholar 9 months ago, created an answer that has been accepted. For A: How to use GenomicRanges to find overlaps by percentage covered of interval
Scholar 9 months ago, created an answer that has been accepted. For A: DataFrame after splitting and back
Popular Question 9 months ago, created a question with more than 1,000 views. For views on Rle using GRanges object
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: Detecting Overlaps within Grange Object
Scholar 11 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 16 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 16 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Scholar 2.3 years ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: unlist a exons GRangeslist object and add a gene name column
Scholar 2.3 years ago, created an answer that has been accepted. For A: Subset GRanges object into new object
Scholar 2.3 years ago, created an answer that has been accepted. For A: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?

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