getCodonSpecificQuantilesForCodon: getCodonSpecificQuantilesForCodon

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 quantiles of CSP traces

Arguments

mixtureElement	mixture to calculate CSP variance. Should be between 1 and n, where n is number of mixtures.
samples	number of samples to use for calculating variance
codon	codon to calculate CSP
paramType	CSP to calculate variance for. 0: Mutation (ROC,FONSE) or Alpha (PA, PANSE). 1: Selection (ROC,FONSE), Lambda (PANSE), Lambda^prime (PA). 2: NSERate (PANSE)
probs	vector of two doubles between 0 and 1 indicating range over which to calculate quantiles. <0.0275, 0.975> would give 95% quantiles.
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

vector representing lower and upper bound of quantile

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