User: Elizabeth Purdom

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USA/ Berkeley/UC Berkeley
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11 years, 11 months ago
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Posts by Elizabeth Purdom

<prev • 21 results • page 1 of 3 • next >
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Comment: C: getting gene ranges from a TranscriptDb (GenomicFeatures package)
... > > > Before I go further down this route, is there not a simple way to > get this information? > > > Stating the obvious, probably, but this is not a question with a > simple answer. You may have to settle on some sort of heuristic > (choose a random region, the ...
written 9.1 years ago by Elizabeth Purdom210
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getting gene ranges from a TranscriptDb (GenomicFeatures package)
... Hello, I would like to get the range of genes from a TranscriptDb object. Ideally, I would like to do: txdb <- loadFeatures(system.file("extdata", "UCSC_knownGene_sample.sqlite", package="GenomicFeatures")) genes(txdb) And have this return the entire genom ...
go transcriptdb written 9.1 years ago by Elizabeth Purdom210 • updated 9.1 years ago by Sean Davis21k
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Error in GenomicRanges trying to append two GRangesLists
... Hello, I am trying to append together two GRangesLists. I thought that either c() or append would allow me to do this, but I'm getting an error. My two GRangesLists have the same metadata column names. With both, I'm getting some kind of error about rownames that I don't understand and I just don' ...
written 9.1 years ago by Elizabeth Purdom210 • updated 9.1 years ago by Martin Morgan ♦♦ 23k
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biomaRt slow down?
... Hi, Lately when I make queries via biomaRt, they are onerously long as compared to before (last spring/early summer). For example, I frequently pull down the following information mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") WHAT <- c("ensembl_gene_id","ensembl_transcript_id", ...
biomart written 10.0 years ago by Elizabeth Purdom210
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Comment: C: IRanges: find containment and not just overlap
... Do I need a development version to have the function 'ranges' defined for the output of overlap? I get an error when I try to do this myself. Thanks, Elizabeth > isContained<-function(a,b){#a,b, ranges + require(IRanges) + ol<-overlap(a,b) + m<-as.matrix(ol) + containe ...
written 10.7 years ago by Elizabeth Purdom210
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IRanges: find containment and not just overlap
... Hi, I'm very happy with the efficiency of the overlap function and I was wondering if there is a fast way in IRanges to find which of the ranges in one set are completely contained by one or more ranges in another set (i.e. the same idea as overlap, but more restrictive criteria than any overlap)? I ...
iranges written 10.7 years ago by Elizabeth Purdom210 • updated 10.7 years ago by Michael Lawrence620
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Comment: C: IRanges: Trying to cut overlapping intervals into pieces
... Hi Michael, I think for what I want to do, actually, you need some extra sorts and uniques in the call to head and tail to make these calls completely remove the first/last positions -- they might be replicated (this is true even if you have unique intervals). This wasn't the case in the example I s ...
written 10.7 years ago by Elizabeth Purdom210
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Comment: C: IRanges: Trying to cut overlapping intervals into pieces
... It appears your solution assumes that the intervals are unique, right? Elizabeth Michael Lawrence wrote: > > > On Fri, Jan 23, 2009 at 10:24 PM, Elizabeth Purdom > > wrote: > > Hi, > > I am trying to take overlapping intervals and return a set of > interval ...
written 10.7 years ago by Elizabeth Purdom210
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Comment: C: IRanges: Trying to cut overlapping intervals into pieces
... Thanks for the help. It's much neater than what I had (and I do have gaps). If you are thinking about adding this kind of functionality, I'd be glad to tell you more specifically what I am doing if it helps to have a more general picture. I kept thinking the intersect or setdiff would help for diff ...
written 10.7 years ago by Elizabeth Purdom210
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IRanges: Trying to cut overlapping intervals into pieces
... Hi, I am trying to take overlapping intervals and return a set of intervals that are not overlapping but cover all of the region (and mantain the intervals that don't overlap). In particular, I don't want to merge intervals that overlap together (i.e. the reduce function in IRanges)-- I want to cut ...
iranges written 10.7 years ago by Elizabeth Purdom210 • updated 10.7 years ago by Michael Lawrence620

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