congruence: 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.

References

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

Examples

Run this code

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)