test2Interact: Summarize genetic interactions within or between cellular...

In SLGI: Synthetic Lethal Genetic Interaction

Description

Summarize the genetic interactions within one cellular organizational unit or between 2 cellular organizational units.

Usage

test2Interact(iMat, tMat, interactome)

Arguments

iMat	Genetic interaction matrix. Each entry has value 0 or 1, representing positive or negative interaction of corresponding pairs of row and column, respectively.
tMat	Adjacency matrix of tested object. Each entry has value 0 or 1, representing the fact that the corresponding pairs of row and column have been tested for interaction or not.
interactome	Adjacency matrix where row are gene names and columns are cellular organizational units names. Each entry has value 0 or 1, for absence or presence of a gene in the complex.

Value

the return value is a data.frame with 6 columns.

unit1, unit2	cellular organizational units tested and interacting
tested	Number of interactions tested between unit1 and unit2
interact	Number of interactions found between unit1 and unit2
sizeC1, sizeC2	Number of genes in unit1 and unit2

Author(s)

N. LeMeur

Examples

set.seed(123)
##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]))

## Create cellular organizational units interaction matrix
gInt <- sample(c(1:8), 25, TRUE)
gInt  <- matrix(gInt, nrow=5, ncol=5, dimnames=list(LETTERS[1:5],LETTERS[1:5]))

## All interactome tested
gTest <- matrix(sample(c(0:3), 25, TRUE), nrow=5, ncol=5)
gTested <- gInt+gTest

val <- test2Interact(iMat=gInt, tMat=gTested, interactome=interactome)

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