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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
    Hi

    I think you need to load the .bam file by Rsamtools, and use countOverlap after that.




    Originally posted by dicty View Post
    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

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