Models for detecting positive selection
Usage
codonTest(tree, object, model = c("M0", "M1a", "M2a"),
frequencies = "F3x4", opt_freq = FALSE, codonstart = 1,
control = pml.control(maxit = 20), ...)Arguments
- tree
a phylogenetic tree.
- object
an object of class phyDat.
- model
a vector containing the substitution models to compare with each other or "all" to test all available models.
- frequencies
a character string or vector defining how to compute the codon frequencies
- opt_freq
optimize frequencies (so far ignored)
- codonstart
an integer giving where to start the translation. This should be 1, 2, or 3, but larger values are accepted and have for effect to start the translation further within the sequence.
- control
a list of parameters for controlling the fitting process.
- ...
further arguments passed to or from other methods.
Value
A list with an element called summary containing a data.frame with the log-likelihood, number of estimated parameters, etc. of all tested models. An object called posterior which contains the posterior probability for the rate class for each sites and the estimates of the defined models.
Details
codonTest allows to test for positive selection similar to programs
like PAML Yang (2007)
or HyPhy Pond, Frost, and Muse (2005)
.
There are several options for deriving the codon frequencies. Frequencies can be "equal" (1/61), derived from nucleotide frequencies "F1x4" and "F3x4" or "empirical" codon frequencies. The frequencies taken using the empirical frequencies or estimated via maximum likelihood.
So far the M0 model (Goldman and Yang 2002), M1a and M2a are implemented. The M0 model is always computed the other are optional. The convergence may be very slow and sometimes fails.
References
Nielsen R, Yang Z (1998). “Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene.” Genetics, 148(3), 929–936.
Pond SLK, Frost SD, Muse SV (2005). “HyPhy: hypothesis testing using phylogenies.” Bioinformatics, 21(5), 676–679.
Yang Z (2014). Molecular Evolution: A Statistical Approach. Oxford University Press, Oxford.
Yang Z (2007). “PAML 4: phylogenetic analysis by maximum likelihood.” Molecular biology and evolution, 24(8), 1586–1591. Genetics, 148: 929–936
Author
Klaus Schliep klaus.schliep@gmail.com
Examples
if (FALSE) { # \dontrun{
# load woodmouse data from ape
data(woodmouse)
dat_codon <- dna2codon(as.phyDat(woodmouse), code=2)
tree <- NJ(dist.ml(dat_codon))
# optimize the model the old way
fit <- pml(tree, dat_codon, bf="F3x4")
M0 <- optim.pml(fit, model="codon1")
# Now using the codonTest function
fit_codon <- codonTest(tree, dat_codon)
fit_codon
plot(fit_codon, "M1a")
} # }