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  • countOverlaps problem

    I have problem using countOverlaps. Below is my code.

    counts=countOverlaps(tx_by_gene,"./s_1_sorted.bam")

    tx_by_gene is a GRangesList object which is a list of GRanges objects, where each GRanges object is a gene and the entries are the genomic coordinates of its transcripts.

    Then I get the error message.

    Error in function (classes, fdef, mtable) :
    unable to find an inherited method for function "countOverlaps", for signature "GRangesList", "character"

    What's wrong in my code? How could I run countOverlaps?

    Thanks,
    Dicty

  • #2
    right now "./s_1_sorted.bam" is just a character vector, a string

    load your BAM file into something compatible with the 'subject' of countOverlaps: a Ranges, RangesList, or RangedData. So check out scanBam or readBamGappedAlignments.
    --
    Jeremy Leipzig
    Bioinformatics Programmer
    --
    My blog
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    Comment


    • #3
      Thanks. It went through.

      Comment

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