Question: Cummerbund Help
gravatar for madkitty
6.8 years ago by
madkitty620 wrote:

I have 3 samples in 3 folders under the working directory of R,

  • ~/Sample1
  • ~/Sample2
  • ~/Sample3

How can I point to R the directory for each sample in one readCufflinks command? If I just call readCufflinks it returns 0 sample ..

 > cuff<-readCufflinks()
 > cuff
 CuffSet instance with:
     0 samples
     0 genes
     0 isoforms
     0 TSS
     0 CDS
     0 promoters
     0 splicing
     0 relCDS
R cummerbund • 2.9k views
ADD COMMENTlink modified 6.8 years ago by Johan870 • written 6.8 years ago by madkitty620
gravatar for Johan
6.8 years ago by
Johan870 wrote:

You can set the directory to read from by:

cuff <- readCufflinks(dir="/path/to/your/data")

However, if I'm not mistaken cummeRbund should be used to read cuffdiff results, i.ex. results from differential expression studies, which means that normally you would have all you output data in one place.

ADD COMMENTlink written 6.8 years ago by Johan870
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