RFE: Allow subsetting samples in the GISTIC class

[lbeltrame]

As the issue subject says, it might be useful to subset samples in GISTIC objects, similar to what it is done for MAFs. A use case I have is a global analysis I made with GISTIC, but I want to display the individual alterations in two different oncoplots basing on some clinical data.

[PoisonAlien]

I have been trying to implement it but it seems it does not make sense to subset GISTIC object because the statistics such as p-values, amplitude, g-scores, etc are all estimated on the original cohort and can not be subsetted (or recalculated in R). Even you subset for specific samples you will end up with faulty values.

[ShixiangWang]

If it is truly important, maybe we can consider providing GisticCompare for two or more gistic objects. It should make sense.

[PoisonAlien]

Yeah something like GisticCompare should be a better option. Also you can just add clinical parameter as one of the annotation row which should be suffice and show the differences between groups.

[github-actions[bot]]

This issue is stale because it has been open for 60 days with no activity.

[github-actions[bot]]

This issue was closed because it has been inactive for 14 days since being marked as stale.