Mergeomics (version 1.0.0)

tool.overlap: Calculate overlaps between groups of specified items

Description

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

Usage

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

Arguments

items

array of item identities

groups

array of group identities for items

nbackground

total number of items

Value

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)

Examples

## 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])