sharedInt {SLGI} | R Documentation

## 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).

### Author(s)

N. LeMeur

### 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)

[Package SLGI version 1.0.0 Index]