utils.dist.ind.snp: Calculates a distance matrix for individuals defined in a...

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Calculates a distance matrix for individuals defined in a dartR genlight object using SNP data (DArTseq)

Description

This script calculates various distances between individuals based on SNP genotypes.

Usage

utils.dist.ind.snp(
  x,
  method = "Euclidean",
  scale = FALSE,
  output = "dist",
  verbose = NULL
)

Arguments

x	Name of the genlight containing the genotypes [required].
method	Specify distance measure [default Euclidean].
scale	If TRUE and method='Euclidean', the distance will be scaled to fall in the range [0,1] [default FALSE].
output	Specify the format and class of the object to be returned, dist for a object of class dist, matrix for an object of class matrix [default "dist"].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2].

Details

The distance measure can be one of:

• Euclidean – Euclidean Distance applied to Cartesian coordinates defined by the loci, scored as 0, 1 or 2.

• Simple – simple mismatch, 0 where no alleles are shared, 1 where one allele is shared, 2 where both alleles are shared.

• Absolute – absolute mismatch, 0 where no alleles are shared, 1 where one or both alleles are shared.

• Czekanowski (or Manhattan) calculates the city block metric distance by summing the scores on each axis (locus).

Value

An object of class 'dist' or 'matrix' giving distances between individuals

Author(s)

Author(s): Arthur Georges. Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

Examples

 
D <- utils.dist.ind.snp(testset.gl, method='Manhattan')
D <- utils.dist.ind.snp(testset.gl, method='Euclidean',scale=TRUE)

D <- utils.dist.ind.snp(testset.gl, method='Simple')

dartR documentation built on June 8, 2023, 6:48 a.m.