compareComplex {simulatorAPMS}R Documentation

Function to compare the ISI to the estimate

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 protein intersection set, (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(TSNMat, erMat)

Arguments

TSNMat ISI Bipartite Graph Matrix
erMat The Estimate 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 ISI and its estimate. The runCompareComplex() function must be called first since all the proteins present in the ISI must be present in the estimate and vice versa so a true comparison can be made.

Value

comp1 A matrix of pairwise intersections between C-i and K-j. Rows are indexed by C-i and columns by K-j
comp2 A matrix of pairwise set differences, C-i K-j. Rows indexed by C-i and columns by K-j
comp3 A matrix of pairwise set differences, K-j C-i. Rows indexed by C-i and columns by K-j

Author(s)

Tony Chiang

See Also

runCompareComplex

Examples


library(apComplex)
data(MBMEcHMSPCI)
data(MBMEcTAP)
runCompareComplex(MBMEcHMSPCI[,1:10], MBMEcTAP[,1:10])


[Package simulatorAPMS version 1.2.1 Index]