examples/selectVar-examples.R

In mixOmicsTeam/mixOmics: Omics Data Integration Project

data(liver.toxicity)
X = liver.toxicity$gene
Y = liver.toxicity$clinic

# example with sPCA
# ------------------
liver.spca <- spca(X, ncomp = 1, keepX = 10)
selectVar(liver.spca, comp = 1)$name
selectVar(liver.spca, comp = 1)$value

\dontrun{
#example with sIPCA
# -----------------

liver.sipca <- sipca(X, ncomp = 3, keepX = rep(10, 3))
selectVar(liver.sipca, comp = 1)

# example with sPLS
# -----------------

liver.spls = spls(X, Y, ncomp = 2, keepX = c(20, 40),keepY = c(5, 5))
selectVar(liver.spls, comp = 2)

# example with sPLS-DA
data(srbct)   # an example with no gene name in the data
X = srbct$gene
Y = srbct$class

srbct.splsda = splsda(X, Y, ncomp = 2, keepX = c(5, 10))
select = selectVar(srbct.splsda, comp = 2)
select
# this is a very specific case where a data set has no rownames.
srbct$gene.name[substr(select$select, 2,5),]


# example with sGCCA
# -----------------

data(nutrimouse)

# ! need to unmap the Y factor
Y = unmap(nutrimouse$diet)
data = list(gene = nutrimouse$gene, lipid = nutrimouse$lipid,Y)
# in this design, gene expression and lipids are connected to the diet factor
# and gene expression and lipids are also connected
design = matrix(c(0,1,1,
1,0,1,
1,1,0), ncol = 3, nrow = 3, byrow = TRUE)
#note: the penalty parameters need to be tuned
wrap.result.sgcca = wrapper.sgcca(X = data, design = design, penalty = c(.3,.3, 1),
ncomp = 2,
scheme = "horst")

#variables selected and loadings values on component 1 for the two blocs
selectVar(wrap.result.sgcca, comp = 1, block = c(1,2))

#variables selected on component 1 for each block
selectVar(wrap.result.sgcca, comp = 1, block = c(1,2))$'gene'$name
selectVar(wrap.result.sgcca, comp = 1, block = c(1,2))$'lipid'$name

#variables selected on component 2 for each block
selectVar(wrap.result.sgcca, comp = 2, block = c(1,2))$'gene'$name
selectVar(wrap.result.sgcca, comp = 2, block = c(1,2))$'lipid'$name

# loading value of the variables selected on the first block
selectVar(wrap.result.sgcca, comp = 1, block = 1)$'gene'$value
}