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Old 12-14-2010, 05:32 AM   #1
Location: us

Join Date: Nov 2010
Posts: 28
Default countOverlaps problem

I have problem using countOverlaps. Below is my code.


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?

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Old 12-14-2010, 06:57 AM   #2
(Jeremy Leipzig)
Location: Philadelphia, PA

Join Date: May 2009
Posts: 116

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
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Old 12-14-2010, 08:19 AM   #3
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Join Date: Nov 2010
Posts: 28

Thanks. It went through.
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