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 1.48.0 Index]