rateModel: rateModel

In ndukler/epiAllele: Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles

Description

Contructs an object that holds a rate model for a set of alleles

Usage

rateModel(data, siteLabelCriteria = NULL, lineageTable = NULL,
  rate = NULL, pi = NULL)

Arguments

data	An alleleData object
siteLabelCriteria	A charecter vector of the columns in siteData contained in alleleData label genomic regions
lineageTable	A table with columns parent,child,edgeID, and rateGroup, where rateGroup is used to specify how the rates are tied between the branches
rate	Starting value for rate parameter. (Default: 0.1)
pi	Starting frequencies for allele stationary distribution. Must be the same length as the number of alleles. Default is a uniform probability.

Value

an rateModel object

ndukler/epiAllele documentation built on May 5, 2019, 4:50 p.m.