RVAideMemoire (version 0.9-79)

DIABLO.test: Significance test based on cross-validation

Description

Performs a permutation significance test based on cross-validation with DIABLO (block.plsda or block.splsda).

Usage

DIABLO.test(x, method = c("mahalanobis.dist", "max.dist", "centroids.dist"),
  validation = c("Mfold", "loo"), k = 7, nperm = 999, progress = TRUE, ...)

Arguments

x

an object of class "sgccda".

method

criterion used to predict class membership. See perf.

validation

a character giving the kind of (internal) validation to use. See perf.

k

an integer giving the number of folds (can be re-set internally if needed).

nperm

number of permutations.

progress

logical indicating if the progress bar should be displayed.

…

other arguments to pass to perf.

Value

method

a character string indicating the name of the test.

data.name

a character string giving the name of the data, plus additional information.

statistic

the value of the test statistics (classification error rate).

permutations

the number of permutations.

p.value

the p-value of the test.

Details

The function uses the weighted predicted classification error rate (see perf).

See Also

block.plsda, block.splsda, perf

Examples

# NOT RUN {
require(mixOmics)
data(nutrimouse)
data <- list(gene=nutrimouse$gene,lipid=nutrimouse$lipid,Y=nutrimouse$diet)
DIABLO <- block.plsda(X=data,indY=3)
DIABLO.test(DIABLO)
# }