summary: Summary Methods for CCA and PLS objects

In mixOmicsTeam/mixOmics: Omics Data Integration Project

Summary Methods for CCA and PLS objects

Description

Produce summary methods for class "rcc", "pls" and "spls".

Usage

## S3 method for class 'mixo_pls'
summary(
  object,
  what = c("all", "communalities", "redundancy", "VIP"),
  digits = 4,
  keep.var = FALSE,
  ...
)

## S3 method for class 'mixo_spls'
summary(
  object,
  what = c("all", "communalities", "redundancy", "VIP"),
  digits = 4,
  keep.var = FALSE,
  ...
)

## S3 method for class 'rcc'
summary(
  object,
  what = c("all", "communalities", "redundancy"),
  cutoff = NULL,
  digits = 4,
  ...
)

## S3 method for class 'pca'
summary(object, ...)

Arguments

object	object of class inherited from "rcc", "pls" or "spls".
what	character string or vector. Should be a subset of c("all", "summarised", "communalities", "redundancy", "VIP"). "VIP" is only available for (s)PLS. See Details.
digits	integer, the number of significant digits to use when printing. Defaults to 4.
keep.var	Logical. If TRUE only the variables with loadings not zero (as selected by spls) are showed. Defaults to FALSE.
...	not used currently.
cutoff	real between 0 and 1. Variables with all correlations components below this cut-off in absolute value are not showed (see Details).

Details

The information in the rcc, pls or spls object is summarised, it includes: the dimensions of X and Y data, the number of variates considered, the canonical correlations (if object of class "rcc") and the (s)PLS algorithm used (if object of class "pls" or "spls") and the number of variables selected on each of the sPLS components (if x of class "spls").

"communalities" in what gives Communalities Analysis. "redundancy" display Redundancy Analysis. "VIP" gives the Variable Importance in the Projection (VIP) coefficients fit by pls or spls. If what is "all", all are given.

For class "rcc", when a value to cutoff is specified, the correlations between each variable and the equiangular vector between X- and Y-variates are computed. Variables with at least one correlation componente bigger than cutoff are showed. The defaults is cutoff=NULL all the variables are given.

Value

The function summary returns a list with components:

ncomp	the number of components in the model.
cor	the canonical correlations.
cutoff	the cutoff used.
keep.var	list containing the name of the variables selected.
mode	the algorithm used in pls or spls.
Cm	list containing the communalities.
Rd	list containing the redundancy.
VIP	matrix of VIP coefficients.
what	subset of c("all", "communalities", "redundancy", "VIP").
digits	the number of significant digits to use when printing.
method	method used: rcc, pls or spls.

Author(s)

Sébastien Déjean, Ignacio González, Kim-Anh Lê Cao, Al J Abadi

See Also

rcc, pls, spls, vip.

Examples

## summary for objects of class 'rcc'
data(nutrimouse)
X <- nutrimouse$lipid
Y <- nutrimouse$gene
nutri.res <- rcc(X, Y, ncomp = 3, lambda1 = 0.064, lambda2 = 0.008)
more <- summary(nutri.res, cutoff = 0.65)

## Not run: 
## summary for objects of class 'pls'
data(linnerud)
X <- linnerud$exercise
Y <- linnerud$physiological
linn.pls <- pls(X, Y)
more <- summary(linn.pls)

## summary for objects of class 'spls'
data(liver.toxicity)
X <- liver.toxicity$gene
Y <- liver.toxicity$clinic
toxicity.spls <- spls(X, Y, ncomp = 3, keepX = c(50, 50, 50),
keepY = c(10, 10, 10))
more <- summary(toxicity.spls, what = "redundancy", keep.var = TRUE)

## End(Not run)

mixOmicsTeam/mixOmics documentation built on Dec. 3, 2024, 11:15 p.m.