compareComplex: A function to compare two bipartite graph matrices

In ScISI: In Silico Interactome

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

ScISI documentation built on Nov. 8, 2020, 5:48 p.m.