infoValue: Function calculates the partial Shannon information of gene...

In CLippmann/ORA: Overrepresentation Analysis

Description

Function calculates the partial Shannon information of gene sets in GO terms explaining how informative a certain term in the context of all terms is.

Usage

infoValue(NrOfAnnotationsInTerm, NrOfGenesInUniverse = max(NrOfAnnotationsInTerm))

Arguments

NrOfAnnotationsInTerm	Numeric; Vector of numbers of genes annotated to corresponding GO terms.
NrOfGenesInUniverse	Numeric; Default: max(NrOfAnnotationsInTerm) Number of genes in universe. (If not restricted to reference set, NrOfGenesInUniverse is the same as the number of genes (directly + indirectly) annotated to the root.)

Value

InfoValue	Numeric; A value for each term that describes how informative that term is.
InfoValueP	Numeric; The ratio of NrOfAnnotationsInTerm/NrOfGenesInUniverse for each term which is the empirical probability of occurrence.

Author(s)

CL

See Also

certainty, importance, remarkableness.

CLippmann/ORA documentation built on Feb. 4, 2020, 9:38 p.m.