tool.overlap {Mergeomics} | R Documentation

## 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 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)

### Author(s)

Ville-Petteri Makinen

### 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])

[Package Mergeomics version 1.20.0 Index]