generateRandomModel: Randomly generates a pathTiMEx model

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

Description

generateRandomModel generates randomly the structure and the parameters of a pathTiMEx model, including the exponential rates of the waiting times to mutations, the intensities of mutual exclusivity of the pathways, the error rate, the poset and the pathway assignments.

Usage

generateRandomModel(n, k, lamobs, minLam, maxLam, muInterval, ldensesInterval,
  epsilon)

Arguments

n	number of genes
k	number of pathways
lamobs	exponential rate of the observation time (usually fixed to 1)
minLam	lower limit for simulating the exponential rates of the waiting times to mutations of the genes
maxLam	upper limit for simulating the exponential rates of the waiting times to mutations of the genes
muInterval	vector of values from which the intensities of mutual exclusivity of the pathways are uniformly sampled
ldensesInterval	vector of values from which the density of edges in the poset is uniformly sampled
epsilon	the error rate at the level of genes, real number between 0 and 1

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 vector of exponential rates (lambda) of the waiting times to mutations of the genes

• lamobs the exponential rate of the observation time, usually fixed to 1

• mus vector of intensities of mutual exclusivity (mu) for 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 random

Author(s)

Simona Constantinescu, [e-mail]

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