getInteraction: Count genetic interactions within and between cellular...

In SLGI: Synthetic Lethal Genetic Interaction

Description

Count the number of genetic interactions within and between the elements of the interactome.

Usage

getInteraction(iMat, universe, interactome)

Arguments

iMat	Interaction matrix. Each entry has value 0 or 1, representing positive or negative interaction of corresponding pairs of row and column, respectively.
universe	Character vector of gene names, e.g., array genes used in synthetic genetic array experiments (SGA)
interactome	Adjacency matrix where row are gene names and columns are cellular organizational units.

Value

The returned value is a list of 2 matrices:

bwMat	A interaction matrix that corresponds to the cellular organizational units interaction matrix where row and columns a organizational units names and the value inside the matrix are the number of genetic interactions they share.
CDs	Subset of the input interactome that shares interactions.

Author(s)

N. LeMeur

Examples

##Create the genetic interaction matrix
gInt <- sample(c(0, 1), 25, TRUE)
iMat  <- matrix(gInt, nrow=5, ncol=5, dimnames=list(letters[1:5],letters[4:8]))

##Create the interactome
cInt <- sample(c(0,1),30, TRUE)
interactome  <- matrix(cInt, nrow=6, ncol=5,dimnames=list(letters[2:7],LETTERS[1:5]))

## Reduce the genetic interaction matrix to match the gene present in
## the interactome
reducediMat <- gi2Interactome(iMat, interactome)

## Get the interaction
prey <- letters[1:20]
myInteraction <- getInteraction(reducediMat, prey, interactome)

SLGI documentation built on Nov. 8, 2020, 11 p.m.