Running multiple pairs through Paired PSCBS

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Gaius Augustus

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Jun 9, 2016, 2:31:29 PM6/9/16
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Hello,
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])


Thanks,
Gaius

Amy Sherborne

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Nov 1, 2016, 9:47:17 AM11/1/16
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Hi Gaius,

I have just written an R script to do exactly the thing you you are asking about, I hope it helps.

Instead of calling the Tumor and Normal separately within the loop, I put them into a data frame and then just recalled the entire row - that way I had to change very little of the code from the PairedPSCBS vignette.

Using your example:
T <- c("Sample1_T.CEL", "Sample2_T.CEL", "Sample3_T.CEL")
N <- c("Sample1_N.CEL", "Sample2_N.CEL", "Sample3_N.CEL")
pair = data.frame(T, N, stringsAsFactors=F)

Then within my for loop I called csR <- csR[indexOf(csR, pair[i,])].

Full code is up on my github:
https://github.com/Sherbornator/Affy/blob/master/PairedPSCBS.R
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