phyclust.se.update {phyclust}

Update phyclust Results by the Sequencing Error Model

Description

Since phyclust.se is difficult to optimize on a constrained high dimension parameter space, the phyclust is relatively easier to find a better result, as well as the find.best function.

This function will use the phyclust result as initial parameters and perform a sequencing error model. All parameters (Eta, Mu, Q, ...) in this function will be updated through the EM algorithm as phyclust.se.

Typically, this function run on the find.best results will yield a better result than on the phyclust.se.

Usage

phyclust.se.update(X, EMC = .EMC, ret.phyclust = NULL,
    K = NULL, Eta = NULL, Mu = NULL, pi = NULL, kappa = NULL,
    Tt = NULL, byrow = TRUE)

Arguments

X

nid/sid matrix with N rows/sequences and L columns/sites.

EMC

EM control.

ret.phyclust

an object with the class phyclust.

K

number of clusters.

Eta

proportion of subpopulations, \eta_k, length = K, sum to 1.

Mu

centers of subpopulations, dim = K\times L, each row is a center.

pi

equilibrium probabilities, each row sums to 1.

kappa

transition and transversion bias.

Tt

total evolution time, t.

byrow

advanced option for X, default = TRUE.

Details

All the input arguments are the same as the inputs of the function phyclust.em.step and phyclust.update.

Value

This function returns an object with class phyclust.

Author(s)

Wei-Chen Chen [e-mail]

References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

See Also

phyclust.se, phyclust.update, phyclust, find.best.

Examples

## Not run: 
library(phyclust, quiet = TRUE)

set.seed(1234)
X <- seq.data.toy$org

(ret.1 <- find.best(X, 4))
(ret.2 <- phyclust.se.update(X, ret.phyclust = ret.1))
.EMC$se.constant <- 1e-3
(ret.3 <- phyclust.se.update(X, ret.phyclust = ret.2))

### Search optimal error
func <- function(C){
  .EMC$se.constant <<- C
  -phyclust.se.update(X, ret.phyclust = ret.1)$logL
}
(ret.opt <- optimize(f = func, lower = 1e-3, upper = 1e-1))
.EMC$se.constant <- ret.opt$minimum
(ret.se.opt <- phyclust.se.update(X, ret.phyclust = ret.1))

## End(Not run)