countOverlaps problem

[dicty]

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

[Zigster]

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.

[dicty]

Thanks. It went through.