iterTiMExSims: Performs TiMEx iteratively on a simulated dataset

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

Description

iterTiMExSims performs TiMEx iteratively on a simulated dataset, by each time removing the highest ranking group of largest size and runnning TiMEx again.

Usage

iterTiMExSims(samplesModel, pairMu, pairPvalue, groupPvalue, corr, noRuns)

Arguments

samplesModel	structure as returned by the function drawSamples, containing the simulated pathTiMEx model, including the simulated binary matrices, the waiting times etc
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

The groups reported are always the most significant ones of largest size. Once a group is reported, it is removed from the dataset and TiMEx is ran again. The groups are reported decreasingly by size. This function is designed to be applied on data simulated by the functions in this package.

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.

• geneAssignments list consisting of the initial assignment to pathways of the genes in the identified groups. Each element is a vector of pathway indices corresponding to an identified mutually exclusive group. The names of each vector represent the indices of the genes in the binary input 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.