| getCodonSpecificPosteriorMeanForCodon {AnaCoDa} | R Documentation |
getCodonSpecificPosteriorMeanForCodon
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