SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Cuffmerge command giving error- TypeError: 'str' object is not callable kumardeep RNA Sequencing 1 05-21-2012 04:21 AM
Getting Illumina export file into R as a GenomicRanges object? mkbehnke Illumina/Solexa 2 05-16-2012 11:07 AM
DEXSeq - creating new ExonCountSet from scratch ahmetz Bioinformatics 1 10-21-2011 05:04 AM
How to create a GRangesList object for genome not from UCSC? dicty Bioinformatics 2 02-16-2011 06:51 AM
how to create an annotation object dicty Bioinformatics 0 02-04-2011 10:33 AM

Reply
 
Thread Tools
Old 09-26-2012, 07:51 AM   #1
KHubbard
Junior Member
 
Location: Baltimore

Join Date: May 2011
Posts: 8
Default Making exonCountSet object using DEXSeq in R

The DEXSeq vignette states that a user can create and exonCountSet using DEXSeq in R only. Can anyone explain or point to a reference that explains how to do this? Thanks!
KHubbard is offline   Reply With Quote
Old 09-26-2012, 08:26 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

Use the python scripts that come with DEXSeq (they run htseq-count) and then just read.HTSeqCounts(...) in R.
dpryan 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 12:16 PM.


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