findSubComp: A function that looks for either equality between two complexes or complete containment of one complex in another

Description

This function determines if either a complex C-i of bg1 is equal to some complex K-j of bg2 or if a complex C-i (or K-j) is a subcomplex to K-j (or C-i).

Usage

findSubComp(bg1, bg2, interSectMat, simMat)

Arguments

bg1

The first bipartite graph matrix

bg2

The second bipartite graph matrix; bg2 may be equal to bg1

interSectMat

A matrix whose rows and columns are indexed by protein complexes: the rows are indexed by complexes of bg1 (colnames of bg1) and the columns indexed by complexes of bg2 (colnames of bg2). The (i,j) entries is the cardinality of the intersection between the i-th complex of bg1 and the j-th complex of bg2.

simMat

A matrix of similarity measures (e.g. Jaccard Index) between two bipartite graphs where the rows are indexed by complexes of the first bipartite graph, bg1, and the columns are indexed by the complexes of the second bipartite graph, bg2. The (i,j) entry of this matrix would be the similarity between C-i of bg1 and K-j of bg2.

Value

record1: A list of lists. The value of each sublist is: 1. a complex of bg1, 2. a complex of bg2, 3. the cardinality of the complex of bg1, 4. the cardinality of the complex of bg2, 5. the cardinality of these two complexes mutual intersection.
record3: A list of lists. The value of each sublist is: 1. a complex of bg1, 2. a complex of bg2, 3. the cardinality of the complex of bg1, 4. the cardinality of the complex of bg2, 5. the cardinality of these two complexes mutual intersection.
toBeRm1: A character vector of the names of complexes in bg1 that equal some complex in bg2. These complexes should be deleted to avoid redundancy if these two bipartite graphs are merged.
toBeRm2: A character vector of the names of complexes from either bg1 or bg2 which are sub-complexes of another protein complex.

Details

This function uses interSectMat and simMat to determine which complexes C-i of bg1 is equal to which complexes K-j of bg2. When the function finds an equality, C-i = K-j, it produces 5 statistics:

1. The name of C-i 2. The name of K-j 3. The cardinality of C-i 4. The cardinality of K-j 5. The cardinality of (C-i intersect K-j)

When all the equality of complexes have been found, this function also uses interSectMat and simMat to find which complexes C-i (or K-j) completely contain complexes K-n (or C-m respectively), i.e. which complexes are subcomplexes. It also returns the 5 statistics listed above.

NB - from the 5 statistics above, it will be clear if the relationship between the complexes is that of equality or sub-ordination.

Examples

Run this code

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

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