Cummerbund Help

Question

[madkitty]

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

Answer 1

[Johan]

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.