mostDistantSequences: Most Distant Sequences

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

Most Distant Sequences

Description

Finds the set of sequences that are on the edges of the cloud of distances. These are the ones that have the greatest mean pairwise distance and greatest variance in distances.

Usage

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

Arguments

x	a set of sequences or a gtypes object with sequences.
num.seqs	number of sequences to return. If NULL (default), all sequences are returned from most to least distant.
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 num.seqs sequence names that are the most divergent sorted from greatest to least distant.

Author(s)

Eric Archer [e-mail]

Examples

data(dolph.haps)

mostDistantSequences(dolph.haps, 5)

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