I have a few hundred paired samples that I'd like to run through Paired PSCBS. The example at http://www.aroma-project.org/vignettes/PairedPSCBS-lowlevel/
is very clear on how to set up this protocol for one pair of samples. In order to do a test run, I used a for loop to run Paired PSCBS on each pair one at a time.
Is there another way to do this?
For example, I have two vectors with file names
TumorSamples <- c("Sample1_T.CEL", "Sample2_T.CEL", "Sample3_T.CEL")
NormalSamples <- c("Sample1_N.CEL", "Sample2_N.CEL", "Sample3_N.CEL")
instead of pair <- c(T="GSM318736", N="GSM318737")
within a for loop, I ran TumorNormalpair <- c(T=dsT[i], N=dsN[i])