I noticed that upsetSamples will misbehave with a curatedTCGAData production, as the latter may have some hyphens in the assay names. So I have added a nameFilter parameter to the upsetSamples function, and default passage of check.names to FALSE when the data.frame needed by upset is created. It passes check cleanly in devel.
I noticed that upsetSamples will misbehave with a curatedTCGAData production, as the latter may have some hyphens in the assay names. So I have added a nameFilter parameter to the upsetSamples function, and default passage of check.names to FALSE when the data.frame needed by upset is created. It passes check cleanly in devel.