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User: Jeff Johnston

gravatar for Jeff Johnston
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Posts by Jeff Johnston

<prev • 14 results • page 1 of 2 • next >
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Comment: C: breakTies for a Hits-object based on value in mcols?
... It looks like Hits need to stay sorted by query: hits <- sort(hits, by = ~ queryHits + val) breakTies(hits, "last") ...
written 14 months ago by Jeff Johnston90
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Comment: C: Extract coordinates of overlapping genomic intervals
... As the overlaps.gr is a GRanges object, you can use start(), end() and seqnames() to extract the coordinates of the overlapping intervals. ...
written 2.5 years ago by Jeff Johnston90
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Comment: C: Extract coordinates of overlapping genomic intervals
... Yes, it generates the overlapping interval for each row (a query/subject pair) in your Hits object. ...
written 2.5 years ago by Jeff Johnston90
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Answer: A: Extract coordinates of overlapping genomic intevals
... You can use pintersect: overlaps.gr <- pintersect(df1.gr[queryHits(dfs.ol)], df2.gr[subjectHits(dfs.ol)]) If you want all the results in one object, you can add the indices as metadata columns: overlaps.gr$df1_hit <- queryHits(dfs.ol) overlaps.gr$df2_hit <- subjectHits(dfs.ol)   ...
written 2.5 years ago by Jeff Johnston90
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Comment: C: Group GRanges and keep metadata
... Wasn't there talk at some point about modifying Views to support GRanges? That would allow convenient things like this: mcols(H1.chr22)$mean_score <- viewMeans(Views(rle, H1.chr22)) Currently this is a bit of a pain because coercing a GRanges into a RangesList modifies the order. ...
written 2.7 years ago by Jeff Johnston90
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Answer: A: export BSgenome directly in gzipped fasta
... This seems to work: library(BSgenome.Dmelanogaster.UCSC.dm3) export(Dmelanogaster, "dm3.fasta.gz", compress=TRUE)   ...
written 2.9 years ago by Jeff Johnston90
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Comment: C: Is there an easy way to extend coverage to seqlengths and fill with zeroes?
... In the case where you have existing coverage, you can coerce it back to a GRanges and then call coverage again with the desired width argument (or set the seqlengths of the GRanges first): gr <- as(cov, "GRanges") new_cv <- coverage(gr, weight="score", width=your_seqinfo)     ...
written 3.0 years ago by Jeff Johnston90
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Comment: C: updateObject() fails for old serialized GRanges objects
... Thanks Hervè. Here is a link for the object: https://dl.dropboxusercontent.com/u/726183/bioconductor/toll10b_k27ac_2to4h_1.ranges.RData We certainly have the ability to recreate all of these objects under a new version of Bioconductor using the original source data; the serialized GRanges objects a ...
written 4.3 years ago by Jeff Johnston90
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updateObject() fails for old serialized GRanges objects
... We have a number of serialized GRanges objects in RData format that cannot seem to be handled by updateObject() in Bioconductor 3.0. These all seem to have been created with Bioconductor 2.8. The version 2.9 objects appear to be working fine. Here's the output from calling updateObject(): > loa ...
genomicranges written 4.3 years ago by Jeff Johnston90 • updated 4.3 years ago by Hervé Pagès ♦♦ 13k
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Thread safety of BSgenome getSeq()
... Thanks for looking into this Herv? and Martin, and for the quick fix. It is working as expected now. I did have to install the updated packages from source as the binaries do not seem to be updating for Mac or Linux. Thanks, Jeff On Jun 18, 2014, at 1:14 PM, Hervé Pagès wrote: > Hi Jeff, > ...
cancer bsgenome process rsamtools written 4.6 years ago by Jeff Johnston90 • updated 4.6 years ago by Hervé Pagès ♦♦ 13k

Latest awards to Jeff Johnston

Scholar 2.9 years ago, created an answer that has been accepted. For A: export BSgenome directly in gzipped fasta
Scholar 2.9 years ago, created an answer that has been accepted. For A: export BSgenome directly in gzipped fasta

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