generateStructureModel: Generates a pathTiMEx model for given parameters

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

Description

generateStructureModel randomly generates the structure for a pathTiMEx model under given parameters, i.e. the poset and the pathway assignments are generated, while the exponential rates of the waiting times to mutations and of the observation time, the intensities of mutual exclusivity and the error rate are known.

Usage

generateStructureModel(lams, lamobs, mus, epsilon)

Arguments

lams	vector of exponential rates of the waiting times to mutations, equal in size to the number of genes
lamobs	the exponential rate of the observation time (usually fixed to 1)
mus	vector of intensities of mutual exclusivity, equal in size to the number of pathways
epsilon	the error rate at the level of genes, real number between 0 and 1
ldensesInterval	vector of values from which the density of edges in the poset is uniformly sampled

Details

The exponential rate of the observation time is kept fixed (usually to 1) when generating parameters for the model.

Value

lists of parameters and structure for a pathTiMEx model, as follows:

• lams input vector of exponential rates of the waiting times to mutation of each gene

• lamobs input exponential rate of the observation time

• mus input vector of mutual exclusivity intensities of each pathway

• ldense the density of edges in the poset

• poset the poset of the model

• assignment the assignment of genes to pathways

• epsilon the error rate at the level of genes, real number between 0 and 1

• type way in which the model was simulated, in this case structure

Author(s)

Simona Constantinescu, [e-mail]

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