countPerfSims: Assesses how well each group was reconstructed

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

Description

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

Usage

countPerfSims(pathwaysTable, groups)

Arguments

pathwaysTable	a binary matrix of all groups identified aross many repetitions, as returned by multiple runs of addPathBinary. rows represent indetified groups and columns represent genes. the element [i,j] is 1 if gene j was identified as part of pathway i and 0 otherwise.
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.

Details

This function summarizes multiple repetitions of the inference of pathways from a simulated dataset. Ideally, the groups with largest counts are the real groups.

Value

a binary matrix in which the first columns represent the unique pathways identified in the input matrix (columns named with Gr, followed by the group index, followed by ge, followed by the gene index). next column, counts, counts how many times each group was identified as mutually exclusive. next columns correspond to each of the unique pathways identified, and show either the total number of genes form each group which were part of the group (Tot), or how much this number represents, as a percentage, from the real number of genes in each group (Per).

Author(s)

Simona Constantinescu, [e-mail]

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