examples/block.pls-examples.R

In mixOmicsTeam/mixOmics: Omics Data Integration Project

# Example with TCGA multi omics study
# -----------------------------------
data("breast.TCGA")
# this is the X data as a list of mRNA and miRNA; the Y data set is a single data set of proteins
data = list(mrna = breast.TCGA$data.train$mrna, mirna = breast.TCGA$data.train$mirna)
# set up a full design where every block is connected
design = matrix(1, ncol = length(data), nrow = length(data),
dimnames = list(names(data), names(data)))
diag(design) =  0
design
# set number of component per data set
ncomp = c(2)

TCGA.block.pls = block.pls(X = data, Y = breast.TCGA$data.train$protein, 
                           ncomp = ncomp, design = design)
TCGA.block.pls
## use design = 'full'
TCGA.block.pls = block.pls(X = data, Y = breast.TCGA$data.train$protein, 
                           ncomp = ncomp, design = 'full')
# in plotindiv we color the samples per breast subtype group but the method is unsupervised!
# here Y is the protein data set
plotIndiv(TCGA.block.pls, group =  breast.TCGA$data.train$subtype, ind.names = FALSE)