inst/examples/predictNewClasses.R

In OmicsMarkeR: Classification and Feature Selection for 'Omics' Datasets

dat.discr <- create.discr.matrix(
    create.corr.matrix(
        create.random.matrix(nvar = 50, 
                             nsamp = 100, 
                             st.dev = 1, 
                             perturb = 0.2)),
    D = 10
)

vars <- dat.discr$discr.mat
groups <- dat.discr$classes

fits <- fs.stability(vars, 
                     groups, 
                     method = c("plsda", "rf"), 
                     f = 10, 
                     k = 3, 
                     k.folds = 10, 
                     verbose = 'none')

newdata <- create.discr.matrix(
    create.corr.matrix(
        create.random.matrix(nvar = 50, 
                             nsamp = 100, 
                             st.dev = 1, 
                             perturb = 0.2)),
    D = 10
)$discr.mat

orig.df <- data.frame(vars, groups)

# see what the PLSDA predicts for the new data
# NOTE, newdata does not require a .classes column
predictNewClasses(fits, "plsda", orig.df, newdata)