tool.overlap: Calculate overlaps between groups of specified items
In Mergeomics: Integrative network analysis of omics data

Description Usage Arguments Value Author(s) Examples

tool.overlap checks each pair of blocks, finds number of shared items, and obtains significance values of the sharings for block pairs.

1	tool.overlap(items, groups, nbackground = NULL)

`items`	array of item identities
`groups`	array of group identities for items
`nbackground`	total number of items

a data list including following components

`A`	group name
`B`	group name
`POSa`	group name rank
`POSb`	group name rank
`Na`	group A size
`Nb`	group B size
`Nab`	shared items
`R`	overlap ratio
`F`	fold change to null expectation
`P`	overlap P-value (Fisher's test)

Ville-Petteri Makinen

## read the coexpr module file as an example:
moddata <- tool.read(system.file("extdata",
"modules.mousecoexpr.liver.human.txt", package="Mergeomics"))
## let us find the overlapping ratio between two modules:
## pick the first and last modules:
mod.names <- unique(moddata$MODULE)[c(1,length(unique(moddata$MODULE)))]
if(length(mod.names) > 0){
modA.members <- moddata[which(moddata$MODULE == mod.names[1]),]
modB.members <- moddata[which(moddata$MODULE == mod.names[2]),]
}
mod.pool <- rbind(modA.members, modB.members)
overlap.stats <- tool.overlap(mod.pool[,2], mod.pool[,1])