Hello,

I need to perform a correlation analysis on a data frame constructed as follows: Rows: Features --> gene variants related with different levels of severity of the disease we are studying, in a format of a Boolean matrix Columns: Observations --> List of patients;

The discriminant of my analysis is, thus, the severity marked as follows: -A: less severe than expected -B: equal to what expected -C: more severe than expected

Suppose I have a lot more features than observations and I want to use the PTM function with a three-level annotation (i.e. A,B,C) as a match template. The function requires you to set the annotation.level.set.high parameter, but it's not clear to me how it works. For example, if I set annotation.level.set.high='A', does that mean I'm making a comparison between A vs B&C? So I can only do a comparison between two groups/classes even if I have multiple levels? Because my goal is to compare all levels with each other (i.e. A vs B vs C), but it is not clear to me how to achieve this comparison, if it is possible.

Thanks