computeScore: Computes clustering score

In cbg-ethz/pathTiMEx: Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics

Description

computeScore computes the score of a given clustering, for a given structure.

Usage

computeScore(Datamat, groupys, adjmat)

Arguments

Datamat	binary alteration matrix where rows are samples and columns are genes and an 1 on position [i,j] means that gene j is altered in sample i.
groupys	list with as many elements as mutually exclusive groups, each element consists of the genes assigned to the respective pathway.
adjmat	binary matrix, representing the optimal structure which is kept fixed. The matrix contains one dummy column and row at the end, identically 0, hence its dimension is number of groups +1.

Details

The score equals the number of contradictions due to both mutual exclusivity and progression, or the number of ones that would need to be changed to zeroes to ensure consistency of the data with the clusters and structure.

Value

clustering score (integer)

Author(s)

Simona Constantinescu, [e-mail]

cbg-ethz/pathTiMEx documentation built on May 13, 2019, 2:03 p.m.