based on a current project I have acquired RPPA data based on selected proteins (metabolism and signaling networks) based on around ~1k patients with breast cancer. The major goal is both to cluster the patients into distinct groups and inspect the association with available clinicopathological subtypes, as also prioritize "important" proteins or protein clusters that differentiate between different groups and have a pivotal role. The second part, is more dedicated to identify a robust PPI network, that then could be generalized in other datasets.
My main question is as I have not analyzed proteomics data in the past, is there any computational workflow or pipeline in R for analyzing RPPA data ? From a brief search, I have found the R package RPPanalyzer:
however, there is only a reference manual but not any vignette-
Thank you in advance,