examples/tune-examples.R

In mixOmicsTeam/mixOmics: Omics Data Integration Project

## sPLS-DA
data(breast.tumors)
X <- breast.tumors$gene.exp
Y <- as.factor(breast.tumors$sample$treatment)
tune= tune(method = "splsda", X, Y, ncomp=1, nrepeat=10, logratio="none",
test.keepX = c(5, 10, 15), folds=10, dist="max.dist", progressBar = TRUE)

plot(tune)

\dontrun{
## mint.splsda

data(stemcells)
data = stemcells$gene
type.id = stemcells$celltype
exp = stemcells$study

out = tune(method="mint.splsda", X=data,Y=type.id, ncomp=2, study=exp, test.keepX=seq(1,10,1))
out$choice.keepX

plot(out)
}