summarizeSims: Assesses how well each group was reconstructed

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

Description

summarizeSims assesses the reconstruction performance of each group, inferred from any binary matrix.

Usage

summarizeSims(pathwaysTableSum, groups, noReps)

Arguments

pathwaysTableSum	a binary matrix of all unique groups identified across many repetitions, together with summary information about each of the identified groups, as returned by the function countPerfSims.
groups	a list with the real assignment of genes to pathways. each element of the list is a vector with the genes belonging to that pathway.
noReps	the number of repetitions of the simulation experiments

Details

This function further summarizes multiple repetitions of the inference of pathways from a simulated dataset, having as input a summary table with the unique groups inferred across many runs, as returned by the function countPerfSims. The summary returned by this function doesn't provide an assessment of the false positive rate.

Value

a list with as many elements as real pathways. each element is a matrix in which the first column is the reconstruction percentage of each pathway, and the second element is the number of times in which that reconstruction was attained.

Author(s)

Simona Constantinescu, [e-mail]

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