compareStructs: Compares two posets

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

Description

compareStructs compares two posets of same size, encoded as binary matrices. It returns various metrics comparing the two matrices.

Usage

compareStructs(oldStruct, newStruct)

Arguments

oldStruct	the first of the two structures to compare, corresponding to the previous optimization step.
newStruct	the second of the two structures to compare, corresponding to the current optimization step.

Details

For computing the false posive and false negative rates, it is assumed that the first argument (oldStruct) is the real structure. In this help page, fhe first structure is referred to as the old structure, while the new structure is referred to as the new structure. The number of all possible directed edges, often used to compute rates, equals twice the number of events choose 2. In case the two structures are equal, the accuracy measure is 1.

Value

list consisting of

• falseNeg number of edges which are in the old structure, but not in the new structure, divided by the number of all possible directed edges.

• falsePos number of edges which are in the new structure, but not in the old structure, divided by the number of all possible directed edges.

• accuracy measure of similarity of the two structures, equal to 1 - number of mismatches divided by the number of all possible directed edges. In case the two structures are equal, accuracy = 1.

• noMismatches the number of edges which are found in only one of either of the two structures

• densOld number of edges in the old structure.

• densNew number of edges in the new structure.

Author(s)

Simona Constantinescu, [e-mail]

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