List shared interactions and cellular organizational units names between genes.
sharedInt(pairL, interactome, threshold=0)
Dataframe with 3 columns. The first columns are the pair
of genes tested i.e., the query and array genes. The third columns
in a logical: TRUE when the 2 genes genetically interact and FALSE
when they do not.(see
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.
Numeric. Indicate the minimum number of interactions that 2 genes must share
The return value is a list. Each element of the list has for name 2 genes that genetically interact. Each element of the list corresponds to the list of cellular organizational units where the interacting genes are found (independently or together).
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## Synthetic genetic interactions dat <- data.frame("query" = LETTERS[1:5], "array" = LETTERS[2:6], "interact" = as.logical(sample(c(TRUE, FALSE), 5, TRUE))) ## interactome interA <- matrix(sample(c(0, 1), 30,TRUE), nrow=6, ncol=5,dimnames = list(LETTERS[1:6], letters[1:5])) sharedInt(dat, interA, threshold=1)
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