Features/ft 885 refactor acgh survival analysis

Refactor the analysis pipeline for the aCGH survival analysis.
In some cases duplicate measurements  are done for a single individual ,
sample or gene, for example to test reproducibility or for some other
reason, so this issue might actually occur.


2014-07-14 14:50 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))
>
> I think we don't have to worry about duplicate ids or colnames, but it
> does sound like the pmatch call is a potential problem. Is there an
> equivalent match function that checks for the whole string?
>
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> <https://github.com/thehyve/Rmodules/pull/101/files#r14875913>.
>