compareComplex {ScISI} | R Documentation

## A function to compare two bipartite graph matrices

### Description

The `compareComplex` function takes two bipartite graph matrix representations and calculates three statistics between all pairs of complexes, C-i and K-j: (1) the intersection between C-i and K-j, (2) the proteins in C-i and not in K-j, (3) the proteins in K-j and not in C-i. These stats are later used to calculate Jaccard and Dice-Sorenson Coefficients as well as probability distributions of a protein p in a complex C.

### Usage

    compareComplex(BGMat1, BGMat2)

### Arguments

`BGMat1` | The first bipartite graph matrix
`BGMat2` | The second bipartite graph matrix

### Details

The main point to remember is that we don't compare complexes within the same matrix. We only compare pairs of complexes from the BGMat1 and BGMat2. The `runCompareComplex` function must be called first since all the labelled vertices present in BGMat1 must be present in the BGMat2 and vice versa so a true comparison can be made.

### Value

A list with the following entries:

`intersect` | A matrix of pairwise intersections of the complexes of BGMat1 and BGMat2
`cminusk` | A matrix of the setdiff of the complexes of BGMat1 and those of BGMat2
`kminusc` | A matric of the setdiff of the complexes of BGMat2 and those of BGMat1

### Author(s)

Tony Chiang

### Examples

    go = getGOInfo(wantAllComplexes = FALSE)
    mips = getMipsInfo(wantALLComplexes = FALSE)
    goM = createGOMatrix(go)
    mipsM = createMipsMatrix(mips)
    runCompareComplex(goM, mipsM)

[Package ScISI version 1.4.0 Index]