SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Error Using CountOverlaps Function in R silverlining Bioinformatics 1 11-03-2013 03:07 AM
Raw readcounts for RNAseq data using CountOverlaps function in IRanges biofreak General 1 06-28-2011 01:32 PM
countOverlaps problem dicty Bioinformatics 1 12-15-2010 05:03 AM

Reply
 
Thread Tools
Old 12-14-2010, 05:32 AM   #1
dicty
Member
 
Location: us

Join Date: Nov 2010
Posts: 28
Default 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
dicty is offline   Reply With Quote
Old 12-14-2010, 06:57 AM   #2
Zigster
(Jeremy Leipzig)
 
Location: Philadelphia, PA

Join Date: May 2009
Posts: 116
Default

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
--
My blog
Twitter
Zigster is offline   Reply With Quote
Old 12-14-2010, 08:19 AM   #3
dicty
Member
 
Location: us

Join Date: Nov 2010
Posts: 28
Default

Thanks. It went through.
dicty is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:58 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO