JaccardCoef: A function to calculate the Jaccard similarity index between...
In ScISI: In Silico Interactome

Description Usage Arguments Details Value Author(s) Examples

The JaccardCoef function takes the return values of compareComplex function and calculates, for each pair of complexes C-i and K-j (where C-i is in first bipartite graph matrix and K-j is second), the similarity coefficient of Jaccard.

1	JaccardCoef(dataMat)

dataMat

A list which is the output from compareComplex, which is a list of three matrices: intersect, cminusk, and kminusc which are explained in the details.

The argument of this function is a list of three matrices all of whom are indexed exactly in the same manner - the rows of each of the matrix is indexed by the complexes, {C-i}, of the first bipartite graph, bg1, and the colunms are indexed by the complexes, {K-j} of the second bipartite graph, bg2.

The first matrix of the list is the intersect matrix, I. The (i,j) entry of I is the cardinality of complex C-i of bg1 and K-j of bg2.

The second matrix of the list is the cminusk matrix, Q. The (i,j) entry of Q is the cardinality of the set difference between C-i and K-j.

The third matrix of the list is the kminusc matrix, P. The (i,j) entry of P is the cardinality of the set difference between K-j and C-i.

The Jaccard Coefficient between two sets (here between two complexes) C-i and K-j is given by the quotient of cardinality(C-i intersect K-j) and cardinality(C-i union K-j). Note that cardinality(C-i intersect K-j) is the (i,j) entry of I, and that cardinality(C-i union K-j) is the sum of the (i,j) entry of I, Q, P.

The return value is a matrix consisting of the Jaccaard coefficient for each pair of complexes C-i and K-j with rows in indexed by C-i and columns indexed by K-j.

Tony Chiang

#go = getGOInfo(wantAllComplexes=FALSE)
#mips = getMipsInfo(wantSubComplexes=FALSE)
#goM = createGOMatrix(go)
#mipsM = createMipsMatrix(mips)
#cc = runCompareComplex(mipsM, goM, byWhich = "ROW")
#cc$simInd

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