phyclust (version 0.1-11)

phyclust.se.update: 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.

Usage

phyclust.se.update(X, se.model = .EMC$se.model, se.constant = .EMC$se.constant,
    ret.phyclust = NULL, K = NULL, Eta = NULL,
    Mu = NULL, pi = NULL, kappa = NULL, Tt = NULL,
    substitution.model = NULL, identifier = NULL, code.type = NULL,
    label = NULL, byrow = TRUE)

Arguments

X

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

se.model

sequencing error model, default = "CONVOLUTION".

se.constant

constrained constant, default = 1e-2.

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, $t$.

substitution.model

substitution model.

identifier

identifier.

code.type

code type.

label

label of sequences for semi-supervised clustering.

byrow

advanced option for X, default = TRUE.

Value

• This function return an object with class phyclust.

Details

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

References

Phylogenetic Clustering Website: http://thirteen-01.stat.iastate.edu/snoweye/phyclust/

See Also

phyclust.se, phyclust, find.best.

Examples

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

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