M3_test
Usage
M3_test(submodel: Double
-> CTMC<Codons<a>>, omegaDist: DiscreteDist<Double>, posP: Double, posW: Double, posSelection: 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: -
Codon model as a function of omega
-
Default:
|w:GTR +> MNM +> MutSelAA +> dNdS(omega=w)| -
posP: -
The fraction of positively selected sites
-
Default:
~Beta(1,10) -
posW: -
The omega 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) -
n: -
The number of omega categories, if not specified
-
Default:
4
Original default expressions
-
omegaDist -
~DirichletMixture(Uniform(0,1), 2, @n)
Description
This model performs a Bayesian test of positive selection using a modified M3 model. The M3 model is extended with an extra category of sites that is either neutral (posSelection=0) or positively-selected (posSelection=1). The posterior probability that posSelection=1 is the posterior probability of positive selection.
The default background uses GTR, MNM, and MutSelAA. Here omega scales nonsynonymous rates after accounting for amino-acid fitnesses. Thus omega=1 retains these fitness effects; neutrality and positive selection are assessed relative to this background.
The posterior mean of PrPosSelection can provide a more accurate estimate of this probability 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.)