DIABLO.test: Significance test based on cross-validation

In RVAideMemoire: Testing and Plotting Procedures for Biostatistics

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.

Details

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

Author(s)

Maxime HERVE <[e-mail]>

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)

## End(Not run)

RVAideMemoire documentation built on Nov. 6, 2023, 5:07 p.m.