congruence {SLGI}R Documentation

Calculate congruence score between pairs of of genes sharing pattern of synthetic genetic interactions (Ye et al. (2005)).

Description

The congruence score represents the number of common synthetic genetic interacting partners between two genes. The higher is the score the more overlap there is between the synthetic genetic partners of those genes.

Usage

congruence(iMat, sharedInt, mode="query", universe, padjust=FALSE)

Arguments

iMat Adjacency matrix reporting genetic Interactions. Each entry has value 0 or 1, representing positive or negative interaction of corresponding pairs of row and column, respectively.
sharedInt numeric vector representing the number of common genetic interactions between a pair of query or target genes. See getSharedInteraction for more details
mode character vector of value "query" or "target"
universe total number of genes tested
padjust adjust by the number of genes tested that show at least one synthetic genetic interaction.

Value

A numeric vector of the congruence score values.

Author(s)

N. LeMeur

References

Ye P. et al. (2005). Gene function prediction from congruent synthetic lethal interactions in yeast. Molecular Systems Biology 1:2005.0026.

See Also

getSharedInteraction

Examples

intM <- matrix(c(0,1,0,0,1,1,1,0,1,1,1,1,1,0,1,1),
                nrow=4, ncol=4, 
                dimnames=list(c("p1","p2","p3","p4"),
                  c("p1","p3","p5","p7")))
sharedInt <- getSharedInteraction(intM)
score <- congruence(intM, sharedInt, mode="query", universe=15, padjust=FALSE)

[Package SLGI version 1.2.0 Index]