mostRepresentativeSequences: Representative Sequences

In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

Representative Sequences

Description

Finds the set of sequences that represent the requested number of clusters.

Usage

mostRepresentativeSequences(
  x,
  num.seqs = NULL,
  model = "raw",
  pairwise.deletion = TRUE,
  as.haplotypes = TRUE,
  simplify = TRUE
)

Arguments

x	a DNAbin object.
num.seqs	number of sequences to return. If NULL (default), all sequences are returned.
model	a character string specifying the evolutionary model to be used. See dist.dna for more information.
pairwise.deletion	a logical indicating whether to delete sites with missing data. See dist.dna for more information.
as.haplotypes	treat sequences as haplotypes (TRUE) or expand haplotypes to one sequence per individual (FALSE). If the latter, individual frequencies are used in cluster formation.
simplify	if there is a single locus, return result in a simplified form? If FALSE a list will be returned wth one element per locus.

Value

a vector of the sequence names.

Author(s)

Eric Archer [e-mail]

Examples

data(dolph.seqs)

mostRepresentativeSequences(dolph.seqs, 5)

mostRepresentativeSequences(dolph.seqs, 3)

EricArcher/strataG documentation built on Feb. 12, 2023, 4:11 a.m.