I am running GISTIC on some modified ASCAT copy number profiles. Part of the algorithm is a deconstruction/reconstruction of the copy number profile to find statistically likely underlying somatic copy number alterations. The output is a structure Q that is described as:
The Qs structure added to D has four fields for different kinds of events:
'amp' contains pure amplification (over amplification) events, 'del' pure
deletion events, 'aod' amplifications over deletions, and 'doa' deletions
over amplifications.
What are amplifications over deletions, what are deletions over amplifications, and how do they differ from pure amplification/deletion? The documentation doesn't describe it at all and I can't find it online.
I see; do you know how about in the context of GISTIC? That is where I see these labels.
Can you please show more information about where you are seeing this output? For example, which command produced it and in which output file did you see it?. Thanks!