geNetClassifier (version 1.12.0)

getRanking-methods: Shows the genes ranking.

Description

Shows the ranking as matrix: Ranked genes by classes.

Arguments

object

a GenesRanking

showGeneID

boolean. If TRUE, the genes will be shown with the gene IDs used in the expressionSet. This matrix will be ...$geneID in the returned list.

showGeneLabels

boolean. If TRUE, and if the ranking contains gene labels, the ranking matrix will use them. This matrix will be ...$geneLabels in the returned list.

Value

The method returns a list with one or two matrices: ...$geneLabels and ...$geneID.

See Also

Main package function and classifier training: geNetClassifier This method's class (GenesRanking) help page.

Examples

data(leukemiasClassifier)
getRanking(leukemiasClassifier@classificationGenes)

# Top 7 genes (two ways):
getRanking(leukemiasClassifier@genesRanking)$geneLabels[1:7,]
getRanking(getTopRanking(leukemiasClassifier@genesRanking, 7))

# Show gene ID and select a class:
getRanking(leukemiasClassifier@classificationGenes, showGeneID=TRUE
)$geneID[,"CML", drop=FALSE]