User: d r

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d r150
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Posts by d r

<prev • 31 results • page 1 of 4 • next >
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Unexpceted behaviour of RiboProfiling aroundPromoter() function when processing multi-exon CDSs
... Hello I have been experimenting with the script in RiboProfiling pacakge vigenette and have noticed an unexpected beahviour of aroundPromoter(). In line 84 of the script we have the call: oneBinRanges <- aroundPromoter(txdb, alnGRanges, percBestExpressed=0.001) This call returns a GRanges co ...
riboprofiling written 6 weeks ago by d r150
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Drawing a HeatMapList while retaining the original row order of each heat map
... The ComplexHeatmap documenation, under 'Making a list of Heatmaps' states that: "Under default mode, dendrograms from the second heatmap will be removed and row orders will be same as the first one." Is it possible to draw multiple heatmaps from a HeatMapList side by side while retaining the origi ...
complexheatmap written 9 months ago by d r150 • updated 9 months ago by Steve Lianoglou12k
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Problem with using GDC_queryMaf()
... Hello I am trying to use the TCGAbiolinks package to extract mutation data for several types of tumors I am interested in. I am using GDCquery_Maf, using exactly the syntax indicated in the help file: acc.maf <- GDCquery_Maf("ACC") However I then get the error: Error in missing(tumor) : 'm ...
maf tcgabiolinks mutations written 9 months ago by d r150 • updated 8 months ago by tiagochst100
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Comment: C: Intersecting a Granges and a GRangesList using within
... Thanks! just what I needed.   ...
written 2.3 years ago by d r150
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Comment: C: Intersecting a Granges and a GRangesList using within
... @Valerie Obenchain. Thanks for your reply. The output in your example seems what I want. However, In your call to lapply(), you iterate on an object called lst? Can you please tell me what it this object. I did not see it defined in your reply. Thanks again. ...
written 2.3 years ago by d r150
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Comment: C: ignore.strand option in range() when using GRangesList
... Thanks. I really appreciate the effort! ...
written 2.3 years ago by d r150
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Intersecting a Granges and a GRangesList using within
... Hello, I have a GRanges (gr) object and a GRangesList (grlist). I want to find elements in grlist that fully overlap elements of gr. That is, I want to know, for a given i and j if there is k such that grlist[j][[k]] is fully contained within gr[i]. It is important that the values of both i and ...
granges grangeslist findoverlaps written 2.3 years ago by d r150 • updated 2.2 years ago by Hervé Pagès ♦♦ 13k
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ignore.strand option in range() when using GRangesList
... Hello I note that while the range() function for GRanges objects has an ignore.strand argument, the equivalent function for GRangesList does not have this argument. Is there a particular reason that this option was not included in the GRangesList function? Also, what can I do if I do want to use ...
granges written 2.3 years ago by d r150
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Comment: C: Intersecting a Granges and a GRangesList elementwise
... Thanks! I did not know that mapply() works on GRangesList. Good to know. ...
written 2.3 years ago by d r150
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Comment: C: Intersecting a Granges and a GRangesList elementwise
... @Michael Lawerece Thanks for your reply. However,I think neither of your suggestions does what I want. What I want is to know, for a given i if there is k such that grlist[[i]][k] is within gr[i]. For example: gr<-GRanges(seqnames=c('chr1','chr2'), ranges=IRanges(start=c(10,20),end=(50,100)) gr1& ...
written 2.3 years ago by d r150

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Popular Question 8 months ago, created a question with more than 1,000 views. For GRanges DitancetoNearest query
Popular Question 2.2 years ago, created a question with more than 1,000 views. For GRanges DitancetoNearest query

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