mixOmics (version 4.1-4)

select.var: Output of selected variables

Description

This function outputs the selected variables on each component for the sparse versions of the approaches.

Usage

## S3 method for class 'spls':
select.var(object, comp = 1, \ldots)
## S3 method for class 'splsda':
select.var(object, comp = 1, \ldots)
## S3 method for class 'spca':
select.var(object, comp = 1, \ldots)
## S3 method for class 'sipca':
select.var(object, comp = 1, \ldots)

Arguments

object

object of class inheriting from "spls", "splsda", "spca", "sipca".

comp

integer value indicating the component of interest.

...

other arguments.

encoding

latin1

Details

select.var provides the variables selected on a given component. \ [object Object],[object Object] These functions are only implemented for the sparse versions.

Examples

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

# example with sPCA
liver.spca <- spca(X, ncomp = 3, keepX = rep(10, 3))
select.var(liver.spca, comp = 1)$name
select.var(liver.spca, comp = 1)$value

#example with sIPCA
liver.sipca <- sipca(X, ncomp = 3, keepX = rep(10, 3))
select.var(liver.sipca, comp = 1)

# example with sPLS
liver.spls = spls(X, Y, ncomp = 2, keepX = c(20, 40),keepY = c(5, 5))
select.var(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 = select.var(srbct.splsda, comp = 2)
select
srbct$gene.name[substr(select$select, 2,5),]  # this is a very specific case where a data set has no rownames.