BUSTED_S
Usage
BUSTED_S(submodel: Double
-> CTMC<Codons<a>>, omegaDist: DiscreteDist<Double>, posP: Double, posW: Double, posSelection: Int, alpha: Double, nGammaBins: Int, n: Int) →
DiscreteDist<CTMC<Codons<a>>>
Arguments
Underlined names in default expressions refer to other arguments. A
default beginning with ~ specifies a prior
distribution.
-
submodel: -
The model as a function of dN/dS
-
Default:
|w:GTR+>x3+>dNdS(omega=w)| -
posP: -
The fraction of positively selected sites
-
Default:
~Beta(1,10) -
posW: -
The dN/dS value for positively selected sites
-
Default:
~LogGamma(4,0.25) -
posSelection: -
The model selector: 1 if positive selection, 0 if not
-
Default:
~Bernoulli(0.5) -
alpha: -
The shape parameter for the Gamma distribution
-
Default:
~LogLaplace(6,2) -
nGammaBins: -
The number of bins for discretizing the Gamma distribution
-
Default:
3 -
n: -
The number of conserved omega categories, if not specified
-
Default:
2
Original default expressions
-
omegaDist -
~DirichletMixture(Uniform(0,1), 2, @n)
Description
A Bayesian test of positive selection using the BUSTED-S model. The BUSTED-S model handles synonymous rate variation by adding Gamma-distributed across-site rate variation (ASRV) to the BUSTED model using n=3 bins.
The posterior mean of PrPosSelection can provide a more accurate estimate of the posterior probability of positive selection than the posterior mean of posSelection. The statreport tool uses LogOddsPosSelection to report the corresponding posterior log odds accurately, even when the probability is extremely close to 0 or 1. (Do not average LogOddsPosSelection directly.)
Examples
|w: TN93 +> x3 +> dNdS(omega=w)| +> BUSTED_S|w: TN93 +> MNM +> dNdS(omega=w)| +> BUSTED_SCitation
Wisotsky, Sadie R.; Kosakovsky Pond, Sergei L.; Shank, Stephen D.; Muse, Spencer V. (2020). Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril. Mol. Biol. Evol. 37(8): 2430--2439. Article