setEnrichmentFactors: Set the depth and densitiy enrichment factors for GO term...

Description Usage Arguments Value Note Author(s) References See Also Examples

View source: R/termSimilarity.R

Description

Sets the depth and density enrichment factors for the enriched FuSSiMeg GO term similarity measure by Couto et al.

Usage

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setEnrichmentFactors(alpha = 0.5, beta = 0.5)

Arguments

alpha

depth factor

beta

density factor

Value

none

Note

The enrichment factors are stored internally and are used by the function getTermSim, if one uses the method "CoutoEnriched" to calculate GO term similarities

Author(s)

Holger Froehlich

References

F.Couto,M. Silva, P. Coutinho, Implementation of a Functional Semantic Similarity Measure between Gene-Products, DI/FCUL TR 03-29, Department of Informatics, University of Lisbon, 2003

See Also

getTermSim

Examples

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#\donttest{ 
 	setEnrichmentFactors(alpha=0.1,beta=0.5)
 	getTermSim(c("GO:0006955","GO:0007584"),method="CoutoEnriched")
#}

GOSim documentation built on Nov. 1, 2018, 2:26 a.m.