| summary {integrOmics} | R Documentation |
Produce summary methods for class "rcc",
"pls" and "spls".
## S3 method for class 'rcc':
summary(object, what = c("all", "communalities", "redundancy"),
ncomp, cutoff = NULL, digits = 4, ...)
## S3 method for class 'pls':
summary(object, what = c("all", "communalities", "redundancy",
"VIP"), digits = 4, keep.var = FALSE, ...)
## S3 method for class 'spls':
summary(object, what = c("all", "communalities", "redundancy",
"VIP"), digits = 4, keep.var = FALSE, ...)
object |
object of class inheriting from "rcc", "pls" or "spls". |
ncomp |
the number of components to include in the model. |
cutoff |
real between 0 and 1. Variables with all correlations components below this cutoff in absolute value are not showed (see Details). |
digits |
integer, the number of significant digits to use when printing.
Defaults to 4. |
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. |
keep.var |
boolean. If TRUE only the variables with loadings not zero
(as selected by spls) are showed. Defaults to FALSE. |
... |
not used currently. |
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 bisector 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.
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 algoritm 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. |
Sébastien Déjean Ignacio González and Kim-Anh Lę Cao.
## summary for objects of class 'rcc'
data(nutrimouse)
X <- nutrimouse$lipid
Y <- nutrimouse$gene
nutri.res <- rcc(X, Y, lambda1 = 0.064, lambda2 = 0.008)
more <- summary(nutri.res, ncomp = 3, cutoff = 0.65)
## 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)