I have 3 samples in 3 folders under the working directory of R, I did "Change directory" and pointed out one new folder "data" under the root C. "Data" contains our 3 samples outputed from cuffdiff.
How can I point to R the directory for each sample in one readCufflinks command?
If I just call readCufflinks() it returns 0 sample ..
I need to execute the following, and retrieve cuff, dispersion graph, density graph and boxplot graph:
- ~/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 ..
Code:
> cuff<-readCufflinks() > cuff CuffSet instance with: 0 samples 0 genes 0 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 relCDS
I need to execute the following, and retrieve cuff, dispersion graph, density graph and boxplot graph:
Code:
> cuff<-readCufflinks(system.file("extdata", package="cummeRbund")) > cuff > disp<-dispersionPlot(genes(cuff)) > disp > genes.scv<-fpkmSCVPlot(genes(cuff)) > isoforms.scv<-fpkmSCVPlot(isoforms(cuff)) > dens<-csDensity(genes(cuff)) > dens > b<-csBoxplot(genes(cuff)) > b
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