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 |
X.class |
class ids indicated for all sequences. |
Mu |
a center sequence with length |
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
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 0.1-34 Index]