getTestedPairs: Find interacting and non-interacting tested pairs from an...

In SLGI: Synthetic Lethal Genetic Interaction

Description

getTestedPairs find all the pairs from an interaction matrix and a list of tested genes.

Usage

getTestedPairs(iMat, respV)

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.
respV	Character vector of all gene names that were tested (found to interact or not)

Value

A data.frame with 4 columns:

query	gene names of the query genes
array	gene names og the tested genes (e.g., array genes)
interact	numeric vector of the number of observed interactions (0: no interaction; 1: one interaction; 2: two interactions when the query genes were also on the array)
recip	logical to indicate whether the reported genes were both query and array genes (TRUE: both genes were query and array genes)

.

Author(s)

N. LeMeur

See Also

getSharedDomains getUniquePairs

Examples

intM <- c(0,1,0,0,1,1,0,0,1,0,0,1,1,0,1,0)
dim(intM) <- c(4,4)
dimnames(intM) <- list(c("p1","p2","p3","p4"),c("p1","p3","p5","p7") )
respV <- c("p6","p8")
intM
getTestedPairs(intM,respV)

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