generateFixedModel: Generates a pathTiMEx model for given structure and...

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

Description

generateFixedModel generates a pathTiMEx model for given structure (poset and pathway assignment) and parameters

Usage

generateFixedModel(lams, lamobs, mus, listEdges, assignment, epsilon)

Arguments

lams	the exponential rates of the waiting times to mutations
lamobs	the exponential rate of the observation time (usually fixed to 1)
mus	the intensities of mutual exclusivity
listEdges	list of pairs [i,j] such that the element [i,j] in the poset equals 1
assignment	vector of assignments of genes to pathways
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 input vector of exponential rates of the waiting times to mutation of each gene

• mus input vector of mutual exclusivity intensities of each pathway

• 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 fixed

Author(s)

Simona Constantinescu, [e-mail]

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