geNetClassifier (version 1.12.0)

genesDetails-methods: Details of the genes in the network.

Description

Information of the genes in the ranking (table format).

Arguments

object

a GenesRanking

nGenes

integer. Number of genes to show per class

numDecimals

integer. Number of decimals to show in the numeric values

classes

character. Classes of the genes to show

genes

character. Genes to show

Value

A list containing a dataframe with the details of the genes of each class. For each gene, the following information is provided:

ranking

Ranking of the gene.

gERankMean

Mean rank the gene obtained in the cross-validation loops. Only available if geNetClassifier() was called with option estimateGError=TRUE (False by default).

class

Class the gene was chosen for (the class the gene differentiates from the other classes).

postProb

Posterior probability which the gene was assigned by the expectation-maximization algorithm (emfit). Tied values are ranked based on the higher absolute value of exprsMeanDiff. Values are rounded. Several genes may look tied at posterior probability '1' but may actually be i.e. 0.999998 and 0.999997.

exprsMeanDiff

Difference betwen the mean expression of the gene within its class and its mean expression in the other classes.

exprsUpDw

Gene repressed (DOWN) or over-expressed(UP) for the current class (compared to the other classes).

discriminantPower

Measure calculated based on the coordinates of the support vectors. Represents the weight that the classifier gives to each gene to separate the classes.

discrPwClass

Class for which the Discriminant Power was calculated for.

isRedundant

Does the gene have a high correlation or mutual information with other genes in the list? The threshold to consider a gene redundant can be set through the arguments (by default: correlationsThreshold=0.8 and interactionsThreshold=0.5).

Methods

genesDetails(object, nGenes=NULL, numDecimals=4, classes=NULL, genes=NULL)

See Also

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

Examples

data(leukemiasClassifier) # Sample geNetClassifier() return
options(width=200) # Optional, use in case the table rows are wrapped

genesDetails(leukemiasClassifier@classificationGenes)$CML
genesDetails(leukemiasClassifier@genesRanking, nGenes=5, numDecimals=2, 
classes="AML")
genesDetails(leukemiasClassifier@genesRanking, genes=c("ENSG00000096006", 
"ENSG00000168081","ENSG00000105699"))$CLL