iterTiMExBinaryMats: Interative TiMEx on any binary dataset

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

Description

iterTiMExBinaryMats performs TiMEx iteratively on any binary dataset, by each time removing the most significant group of largest size and runnning TiMEx again.

Usage

iterTiMExBinaryMats(mat, pairMu, pairPvalue, groupPvalue, corr, noRuns)

Arguments

mat	binary input matrix, with rows representing samples and columns representing genes
pairMu	threshold on the pair-level mu (input to the function TiMEx). Default to 0.5.
pairPvalue	threshold on the pair-level pvalue (input to the function TiMEx). Default to 0.01.
groupPvalue	threshold on the group-level pvalue (input to the function TiMEx). Default to 0.1.
corr	type of correction employed by TiMEx. It has to either be "bonf" or "fdr". Default to "bonf".
noRuns	maximum number of times to run the iterative procedure. Default to 10.

Details

This function reports the most significant mutually exclusive groups of largest size inferred iteratively, on the basis of any binary input matrix. Once a group is reported, it is removed from the dataset and TiMEx is ran again. The groups are reported decreasingly by size.

Value

list consisting of

• geneNames list consisting of the names of the genes part of the identified mutually exclusive groups. each element is a vector of gene names corresponding to one group.

• geneIndices list consisting of the indices in the input binary matrix of the genes part of the identified mutually exclusive groups. each element is a vector of gene indices corresponding to one group.

• mat input binary matrix

• samplesModel input structure containing the simulated pathTiMEx model, including the binary matrix used as input to the function TiMEx.

• muEst vector with the estimated mu for the identified mutually exclusive groups, of length the number of groups identified.

• corr the input method for multiple testing correction used by TiMEx.

Author(s)

Simona Constantinescu, [e-mail]

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