test2Interact {SLGI} | R Documentation |
Summarize the genetic interactions within one cellular organizational unit or between 2 cellular organizational units.
test2Interact(iMat, tMat, interactome)
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. |
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 |
N. LeMeur
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)