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

[SongLi]

Hi

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

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