User: ccanchaya

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ccanchaya0
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Posts by ccanchaya

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intersect ranges from a GAlignment object with a GRangesList
... Hi, I would like to find the regions of my genome, overlapped by alignments in order to calculate the percentage of CDs that is covered by my GAligments. reduced_alignment <- reduce(intersect(as(x,"GRanges"),unlist(CDs_list_by_transcript)), ignore.strand=TRUE ) Unfortunately, I dont want to un ...
grangeslist intersect galignment written 6 months ago by ccanchaya0 • updated 6 months ago by Hervé Pagès ♦♦ 13k
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Views with RleLists and IRangesLists
... Hi, I am trying to have the read coverage on transcripts of a non-model genome.  I created an GenomicAlignment object from the bam file and I have the annotations usin txdb object. I would like to use Views to extract the coverage over the regions I am interested. reads<-readGAlignments("/Volu ...
coverage genomicalignments views irangeslist rlelist written 16 months ago by ccanchaya0 • updated 16 months ago by Hervé Pagès ♦♦ 13k
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Problem with GOstats - invalid names for slots of class GOHyperGResult
... Hi, I've been following the example for using GOstats at its manual at https://www.bioconductor.org/packages/release/bioc/vignettes/GOstats/inst/doc/GOstatsForUnsupportedOrganisms.pdf. Unfortunately I have an error Error in initialize(value, ...) : invalid names for slots of class “GOHyperGResu ...
gostats gostat written 17 months ago by ccanchaya0

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