dksSelectGenes: Extract gene signatures from a DKSGeneScores object.

In dualKS: Dual KS Discriminant Analysis and Classification

Description

The DKSGeneScores returned by dksTrain holds the rank data for all the genes in the original ExpressioSet. However, generally only the top n genes for each class are desired for classification. Rather than needing to re-run dksTrain every time a signature of different size (n) is desired, you simply extract that top n genes from this object using dksSelectGenes.

Usage

dksSelectGenes(data, n)

Arguments

data	An object of class DKSGeneScores, typically generated by dksTrain
n	The number of genes, per class, to include in the classification signature.

Value

An object of class DKSGeneScores

Author(s)

Eric J. Kort, Yarong Yang

See Also

dksTrain, dksSelectGenes, dksClassify, DKSGeneScores, DKSPredicted, DKSClassifier

Examples

	data("dks")
	tr <- dksTrain(eset, 1, "up")
	cl <- dksSelectGenes(tr, 100)
	pr <- dksClassify(eset, cl)
	summary(pr, pData(eset)[,1])
	show(pr)
	plot(pr, actual=pData(eset)[,1])	

dualKS documentation built on Nov. 8, 2020, 8:30 p.m.