R: Prune the Center Sequences Mu

prune.Mu {phyclust} | R Documentation

## 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 wccsnow@gmail.com

### 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)

[Package phyclust version 0.1-30 Index]