examples/mixOmics-examples.R

In mixOmicsTeam/mixOmics: Omics Data Integration Project

## -- directed towards PLS framework because X is a matrix and the study argument is missing
# ----------------------------------------------------
data(liver.toxicity)
X = liver.toxicity$gene
Y = liver.toxicity$clinic
Y.factor = as.factor(liver.toxicity$treatment[, 4])

# directed towards PLS
out = mixOmics(X, Y, ncomp = 2)

# directed towards sPLS because of keepX and/or keepY
out = mixOmics(X, Y, ncomp = 2, keepX = c(50, 50), keepY = c(10, 10))

# directed towards PLS-DA because Y is a factor
out = mixOmics(X, Y.factor, ncomp = 2)

# directed towards sPLS-DA because Y is a factor and there is a keepX
out = mixOmics(X, Y.factor, ncomp = 2, keepX = c(20, 20))


\dontrun{
## -- directed towards block.pls framework because X is a list
# ----------------------------------------------------
data(nutrimouse)
Y = unmap(nutrimouse$diet)
data = list(gene = nutrimouse$gene, lipid = nutrimouse$lipid, Y = Y)

# directed towards block PLS
out = mixOmics(X = data, Y = Y,ncomp = 3)

# directed towards block sPLS because of keepX and/or keepY
out = mixOmics(X = data, Y = Y,ncomp = 3,
keepX = list(gene = c(10,10), lipid = c(15,15)))

# directed towards block PLS-DA because Y is a factor
out = mixOmics(X = data, Y = nutrimouse$diet, ncomp = 3)

# directed towards block sPLS-DA because Y is a factor and there is a keepX
out = mixOmics(X = data, Y = nutrimouse$diet, ncomp = 3,
keepX = list(gene = c(10,10), lipid = c(15,15)))


## -- directed towards mint.pls framework because of the study factor
# ----------------------------------------------------
data(stemcells)
# directed towards PLS
out = mixOmics(X = stemcells$gene, Y = unmap(stemcells$celltype), ncomp = 2)

# directed towards mint.PLS
out = mixOmics(X = stemcells$gene, Y = unmap(stemcells$celltype),
ncomp = 2, study = stemcells$study)

# directed towards mint.sPLS because of keepX and/or keepY
out = mixOmics(X = stemcells$gene, Y = unmap(stemcells$celltype),
ncomp = 2, study = stemcells$study, keepX = c(10, 5, 15))

# directed towards mint.PLS-DA because Y is a factor
out = mixOmics(X = stemcells$gene, Y = stemcells$celltype, ncomp = 2,
study = stemcells$study)

# directed towards mint.sPLS-DA because Y is a factor and there is a keepX
out = mixOmics(X = stemcells$gene, Y = stemcells$celltype, ncomp = 2,
study = stemcells$study, keepX = c(10, 5, 15))
}