User: cosmin

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cosmin0
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Posts by cosmin

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Comment: C: deconvole counts per feature from summerizedOverlaps with GRangesLists
... Thanks for pointing out the new resources.  I have tried GRangesList(gr1, ..gr12) and the result is a (12x nr of samples) object. So each component of the list yields an aggregated count. Not what I want. I want to have the ranges and the feature info preserved and it doesn't seem that GRangesList ...
written 19 months ago by cosmin0
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Comment: C: deconvole counts per feature from summerizedOverlaps with GRangesLists
...   http://www.bioconductor.org/packages//2.11/bioc/vignettes/GenomicRanges/inst/doc/summarizeOverlaps.pdf See page 4 ...
written 19 months ago by cosmin0
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Answer: A: deconvole counts per feature from summerizedOverlaps with GRangesLists
... Thank you Martin for taking the time and answer me. I'll try your suggestion.  As I am new at this, I followed the example given in the description of the summerizedOverlap  function grl <- GRangesList(c(gr1, gr2)).  In the meantime, I have created a vector of GRanges vector new_gr<- c(gr1 ...
written 19 months ago by cosmin0
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deconvole counts per feature from summerizedOverlaps with GRangesLists
...   I am trying to get the read counts over a number of annotated and newly created features from S, cerevisiae so that I can detect differentially expressed regions. The features are in a dozen or so txdbs GRanges I created and  I have tens of bam files to deal with on a 8Gb RAM laptop. To accompli ...

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