RNA only model permutations

Normal Tissue Panel

library(angelare)
library(Biobase)
data(normal.prot.eset)
data(normal.mrna.eset)

Scaling, imputation etc

prepDat <- function(eset){
  exprs(eset) <- t(scale(t(exprs(eset))))
  eset
}
normal.prot.eset=prepDat(normal.prot.eset)
normal.mrna.eset=prepDat(normal.mrna.eset)

R2 for mRNA-only models

getR2 <- function(obj1, obj2){
  pearson.normal = diag(cor(obj1, obj2, use="complete.obs"))
  pearson.normal^2
}
r2.normal=getR2(exprs(normal.prot.eset), exprs(normal.mrna.eset))

R2 for permuted models

r2.normal.perm = replicate(100, getR2(exprs(normal.prot.eset), exprs(normal.mrna.eset)[, sample(1:ncol(normal.mrna.eset))]))