getUniquePairs: Find unique pairs from an genetic interaction matrix.

In SLGI: Synthetic Lethal Genetic Interaction

Description

getUniquePairs can find all the unique pairs from an interaction matrix and supplementary array genes, or finds only the unique pairs that shows positive interaction.

Usage

getUniquePairs(iMat, respV = character(0), only = FALSE)

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)
only	has default value FALSE, if TRUE, then only reports the positively interacted pairs.

Value

A data.frame with two or three columns. The first two columns are the query gene name and the array gene name, respectively. If only is TRUE, the third column shows the interaction status.

Author(s)

Z. Jiang

See Also

getSharedDomains

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
getUniquePairs(intM,respV,only=FALSE)
getUniquePairs(intM,respV,only=TRUE)
getUniquePairs(intM,only=FALSE)
getUniquePairs(intM,only=TRUE)

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