getCodonSpecificPosteriorMeanForCodon: getCodonSpecificPosteriorMeanForCodon

In AnaCoDa: Analysis of Codon Data under Stationarity using a Bayesian Framework

Description

Method of Parameter class (access via parameter$<function name>, where parameter is an object initialized by initializeParameterObject). Calculate codon-specific parameter (CSP) posterior mean

Arguments

mixtureElement	mixture to calculate CSP posterior mean. Should be between 1 and n, where n is number of mixtures.
samples	number of samples to use for calculating posterior mean
codon	codon to calculate CSP
paramType	CSP to calculate posterior mean for. 0: Mutation (ROC,FONSE) or Alpha (PA, PANSE). 1: Selection (ROC,FONSE), Lambda (PANSE), Lambda^prime (PA). 2: NSERate (PANSE)
withoutReference	If model uses reference codon, then ignore this codon (fixed at 0). Should be TRUE for ROC and FONSE. Should be FALSE for PA and PANSE.
log_scale	If true, calculate posterior mean on log scale. Should only be used for PA and PANSE.

Value

posterior mean value for CSP

AnaCoDa documentation built on Jan. 8, 2021, 2:37 a.m.