cvPAMR: Main wrapper to call PAMR crossvalidation.

In bootfs: Derive Robust Feature Sets for Two or Multiclass Classification Problems

Description

Main wrapper to call PAMR crossvalidation.

Usage

cvPAMR(logX, groupings, DIR, params = 
	list(seed = 123, ncv = 5, repeats = 10,
	max_allowed_feat = 500, n.threshold = 50))

Arguments

logX	The data matrix. Samples in rows, features in columns.
groupings	A list. Each list element is a named vector (length equals the number of samples), holding group assignments for each sample (either 1 for group A and -1 for group B).
DIR	The output base directory.
params	A parameter list with the following elements. seed: a random seed. ncv: the number of folds in the crossvalidation. repeats: number of repeats of the CV. max_allowed_feat: maximum number of returned features. n.threshold: PAMR threshold parameter.

Details

Do a ncv-fold crossvalidation (CV) with repeats repeats. Each grouping assignment from groupings will be used as classification task. If more than one grouping is present, the package uses parallelisation in the package multicore.

This function is usually called by doCV.

Value

CV result. A list with three elements res, featlist and performance, holding the crossvalidation data, an extracted features list in each cv-iteration and an overall performance object, holding information on the performance (AUC values and a roc curve object that can be plotted). See resultCV for making a summary plot for the CV.

Author(s)

Christian Bender ([e-mail])

References

Robert Tibshirani, Trevor Hastie, Balasubramanian Narasimhan, and Gilbert Chu. "Diagnosis of multiple cancer types by shrunken centroids of gene expression" PNAS 2002 99:6567-6572 (May 14)

See Also

doCV Help of PAMR package.

Examples

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bootfs documentation built on May 2, 2019, 5:50 p.m.