gi2Interactome: Reduce genetic interactions matrix

In SLGI: Synthetic Lethal Genetic Interaction

Description

Reduce genetic interactions matrix to the pairs that genetically interact and that are present in the interactome of interest.

Usage

gi2Interactome(iMat, interactome, threshold=0)

Arguments

iMat	Genetic interaction matrix. Each entry has usually a value of 0 or 1, representing positive or negative interaction of corresponding pairs of row and column, respectively.
interactome	Interactome matrix, e.g. ScISIC.
threshold	Integer

Value

The returned value is the genetic interaction matrix reduced to the row and column (genes) names that are present in the interactome and where the row and column sums are higher than the specified threshold.

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)

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