SLGI (version 1.32.0)

modelSLGI: Permutation model for assessing synthetic genetic interactions in cellular organizational units.

Description

Permutation model for assessing synthetic genetic interactions within and between cellular organizational units such as multi-protein complexes.

Usage

modelSLGI(iMat, universe, interactome,  type="intM", perm=50)

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.

universe

character vector of the names of the tested genes, e.g., names of the genes on the synthetic genetic array (SGA) used by Tong et al.

interactome

Adjacency matrix where row are genes and columns are cellular organizational units. Each entry has value 0 or 1, for absence or presence of a gene in a complex.

type

Character vector of value "intM" (Default) or "interactome" to either perform the test based on to the genetic interaction matrix or the interactome, respectively.

perm

Number of permutations to apply. Default is 50.

Value

Interaction matrix between cellular organizational units.

See Also

getInteraction

Examples

 data(ScISIC)
 data(Atong)
 data(SGA)
 model <-  modelSLGI(Atong, universe= SGA, interactome=ScISIC,
type="intM", perm=2)