Cummerbund Help
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
1 answer
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.
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