generateRandomModel: Randomly generates a pathTiMEx model

Description Usage Arguments Details Value Author(s)

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

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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:

Author(s)

Simona Constantinescu, simona.constantinescu@bsse.ethz.ch


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