drawSamples: Draws samples from a pathTiMEx model

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

Description

drawSamples generates samples form a pathTiMEx model

Usage

drawSamples(m, model)

Arguments

m	number of samples to be simulated
model	the pathTiMEx model, as a list, as returned by the functions which generate data: generateRandomModel, generateFixedModel and generateStructureModel

Details

This function generates a binary matrix on the level of genes from the pathTiMEx model, as well as various other features of the model, such as the waiting times to alteration, the observation times etc.

Value

list consisting of

• XGenes binary matrix with the simulated observations on the level of genes, including noise. Rows represent samples and columns represent genes.

• XGenesClean binary matrix with the simulated observations on the level of genes, before noise was added. Rows represent samples and columns represent genes.

• XPathwaysClean binary matrix with the simulated observations on the level of pathways, before noise was added. Rows represent samples and columns represent pathways.

• TGenes matrix with the waiting times of the genes. Rows represent samples and columns represent genes.

• TPathways matrix with the waiting times of the pathways. The waiting time of each pathway equals the minimum waiting time of its gene members. Rows represent samples and columns represent pathways.

• Tobs vector with the observation times. For each sample, an independent observation time is drawn exponentially.

• ZGenes matrix with the independent exponential components contributing to the waiting times of the genes. Rows represent samples and columns represent genes.

• m number of samples

• model structure with details about the model, s.a. waiting time rates, poset etc. This type of structure is returned by the functions whcih generate pathTiMEx models: generateRandomModel, generateFixedModel and generateStructureModel.

Author(s)

Simona Constantinescu, [e-mail]

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