ScISI (version 1.40.0)

runCompareComplex: A function that calls all other types of comparison functions

Description

This function begins by acquiring the same vertex set for both BGMat1 and BGMat2. Then it calls the compareComplex function to calculate three statistics (see compareComplex man page for details). Next it calls calculates a similarity measure (default is Jaccard). Next it calls the runAlignment function to greedily calculate an alignment between BGMat1 and BGMat2.

Usage

runCompareComplex(BGMat1, BGMat2, index = "Jaccard", byWhich)

Arguments

BGMat1

The first bipartite graph matrix

BGMat2

The second bipartite graph matrix

index

The type of similarity index used

byWhich

A parameter for the maximizeSimilarity function. It can either be "ROW", "COL", or "BOTH"

Value

The return value of runCompareComplex is a list with the following statistics:

simInd

The matrix of similarity measures between two bipartite graphs.

maxIntersect

The output of maximizeSimilarity. A list. The first value is the largest similarity indices between complexes of the row and complexes of the columns if byWhich is "ROW" and vice versa if byWhich="COL". The second value returns the actual complex of highest similarity (column complexes if byWhich="ROW" and row complexes if byWhich="COL"

equal

A list of complexes of BGMat1 equal to complexes of BGMat2. The values of the list are the complex, C, of BGMat1, the complex, K, of BGMat2, the cardinality of C, the cardinality of K, and the cardinality of the intersection of C and K

toBeRm

A character vector of complexes that should be removed if two bipartite graphs are merged since they would represent redundant complexes. If the function is called on one bi-partite graph, then this vector looks for redundancies within one database and those complexes needs to be removed as well. These complexes are derived from BGMat1 only.

subcomplex

A list of complexes of BGMat1 which is contained in complexes of BGMat2 or vice versa. The values of the list are the complex, C, of BGMat1, the complex, K, of BGMat2, the cardinality of C, the cardinality of K, and the cardinality of the intersection of C and K

toBeRmSubC

A character vector. The same as toBeRm but instead of redundant protein complexes, this is a compilation of all the sub-complexes between two bi-partite graph matrices (bi-partite graph matrices need not be different)

Details

Examples

#go = getGOInfo()
#mips = getMipsInfo()
#goM = createGOMatrix(go)
#mipsM = createMipsMatrix(mips)
#cc = runCompareComplex(mipsM, goM, byWhich = "ROW")