congruence: Calculate congruence score between pairs of of genes sharing...
In SLGI: Synthetic Lethal Genetic Interaction

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

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.

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

`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.

A numeric vector of the congruence score values.

N. LeMeur

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

getSharedInteraction

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)

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