SLGI (version 1.32.0)

sharedInt: List shared genetic interactions between genes

Description

List shared interactions and cellular organizational units names between genes.

Usage

sharedInt(pairL, interactome, threshold=0)

Arguments

pairL

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 AtongPair dataset as example)

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.

threshold

Numeric. Indicate the minimum number of interactions that 2 genes must share

Value

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).

Examples

## 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)