phyclust.em.step {phyclust}

One EM-step of phyclust

Description

This is a single EM-step of phyclust.

Usage

phyclust.em.step(X, 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)

Arguments

X

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

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.

Details

X should be a numerical matrix containing sequence data that can be transfered by code2nid or code2sid.

Either input ret.phyclust or all other arguments for this function. ret.phyclust can be obtained either from an EM iteration of phyclust or from a M step of phyclust.m.step.

If label is inputted, the label information will be used the EM-step, even the ret.phyclust is the result of unsupervised clustering.

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, phyclust.e.step, phyclust.m.step.

Examples

library(phyclust, quiet = TRUE)

set.seed(1234)
EMC.1 <- .EMC
EMC.1$EM.iter <- 1
# the same as EMC.1 <- .EMControl(EM.iter = 1)
X <- seq.data.toy$org

ret.1 <- phyclust(X, 2, EMC = EMC.1)
ret.2 <- phyclust.em.step(X, ret.phyclust = ret.1)
str(ret.2)

# For semi-supervised clustering.
semi.label <- rep(0, nrow(X))
semi.label[1:3] <- 1
ret.3 <- phyclust.em.step(X, ret.phyclust = ret.1, label = semi.label)
str(ret.3)