numSignificantGenes-methods: Number of ranked genes over the posterior probability...

In geNetClassifier: Classify diseases and build associated gene networks using gene expression profiles

Description

Provides the number of ranked genes over the posterior probability threshold

Arguments

object	a GenesRanking
lpThreshold	Posterior probability threshold
numSignificantGenesType	"ranked" or "global". Ranked will show the count of genes on the ranking of each class. Each gene will be counted only once, since it is only kept in the class for which it had better ranking. Global counts the genes over the threshold before assigning them to a class. i.e. a gene might have 0.3 for one class, and 0.25 for another, if we are taking a thershold of 0.20, it will be counted on both classes.

Methods

numSignificantGenes(object, lpThreshold=0.95, numSignificantGenesType="ranked")

See Also

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

Examples

data(leukemiasClassifier)
# Total number of genes in the ranking:
numGenes(leukemiasClassifier@genesRanking)
# Number of genes ovher the posterior probability threshold
# Default:  lpThreshold=0.95, numSignificantGenesType="ranked"
numSignificantGenes(leukemiasClassifier@genesRanking)
numSignificantGenes(leukemiasClassifier@genesRanking, numSignificantGenesType="global")
numSignificantGenes(leukemiasClassifier@genesRanking, lpThreshold=0.90)

geNetClassifier documentation built on Nov. 8, 2020, 4:53 p.m.