prune.Mu: Prune the Center Sequences Mu

In snoweye/phyclust: Phylogenetic Clustering (Phyloclustering)

Prune the Center Sequences Mu

Description

This function prune the center sequences Mu where the sites will be reset as GAPs if all members within the same cluster are all GAPs.

Usage

prune.Mu(X, X.class, Mu, code.type = .code.type[1])

Arguments

X	numerical data matrix with N rows/sequences and L columns/sites.
X.class	class ids indicated for all sequences.
Mu	a center sequence with length L.
code.type	either "NUCLEOTIDE" (default) or "SNP".

Details

For each cluster indicated by X.class, this function will prune Mu and reset the sites as GAPs if all members within cluster are all GAPs. Mu are usually the returning values of phyclust().

Value

A pruned Mu will be returned.

Author(s)

Wei-Chen Chen [e-mail]

References

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

See Also

phyclust.

Examples

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

X <- seq.data.toy$org
X[, 5] <- .nucleotide$nid[.nucleotide$code == "-"]
ret <- phyclust(X, 2)
Mu.GAPs <- prune.Mu(X, ret$class.id, ret$Mu)

ret$Mu[, 5]
Mu.GAPs[, 5]  # Replace by GAPs.

## End(Not run)

snoweye/phyclust documentation built on Sept. 12, 2023, 5 a.m.