Features/ft 885 refactor acgh survival analysis

Refactor the analysis pipeline for the aCGH survival analysis.
I saw it during my internship: I had a gene expression data set (in yeast)
where there were duplicate measurements for some of the genes, and there
were duplicate measurements for a mutant (comparable to patient in our
case). The data is confidential, so I can't show you.
It might indeed be the case that this situation will hardly ever occur, I'm
not sure. In doubt we could always consult the researchers what they think.
Another option is to just build in a check for duplicates and display a
warning if this ever occurs.


2014-07-15 10:59 GMT+02:00 kretep <notifications@github.com>:

> In web-app/Rscripts/aCGH/acgh-survival-test.R:
>
> >    calls <- as.matrix(dat[,grep('^flag\\.', colnames(dat))])
> >
> > +  # Filter for the calls that match the phenodata ids and have data
> > +  phenodataIds <- phenodata[, "PATIENT_NUM"]
> > +  highdimColumnsMatchingGroupIds <- pmatch(paste("flag.",phenodataIds,sep=""), colnames(calls))
>
> Could you point to an example where this is the case? I think at least for
> single high dim nodes, the (patient, concept) pair is unique, so there will
> be only one value per patient.
>
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