tests/test04-plasma.R

In plasma: Partial LeAst Squares for Multiomic Analysis

library(plasma)
fls <- try(loadESCAdata())
if (inherits(fls, "try-error")) {
  stop("Unable to load data from remote server.")
}
ls()
## prepare MultiOmics
MO <- with(plasmaEnv, prepareMultiOmics(assemble, Outcome))
MO <- MO[c("ClinicalBin", "ClinicalCont", "RPPA"),]
summary(MO)
## split into train and test
set.seed(12345)
train <- rep(FALSE, 185)
train[sample(185, 113)] <- TRUE
MO2 <- MO[, train]
summary(MO2)
## test complete cox models
bigfit <- fitCoxModels(MO2, "Days", "vital_status", "dead")
## extend across dataset pairs
mfm <- plasma(MO2, bigfit)
plot(mfm)
##heatmap(mfm@meanPredictions)

foo <- predict(mfm)
plot(foo, main="Train")

noo <- predict(mfm, MO[, !train])
plot(noo, main = "Test")