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