getInteraction {SLGI} | R Documentation |
Count the number of genetic interactions within and between the elements of the interactome.
getInteraction(iMat, universe, interactome)
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. |
The returned value is a list of 2 matrices:
bwMat |
|
CDs |
Subset of the input interactome that shares interactions. |
N. LeMeur
##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)