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
On Thursday, 9 June 2016 19:31:29 UTC+1, Gaius Augustus wrote:
>
> 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
>
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
---
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to aroma-affymetrix+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
