CalculateEmpiricalGenSemivariogram: Calculate empirical semi variance from genotype matrix.

In bcm-uga/TESS3_encho_sen: Inference of Spatial Population Genetic Structure

Calculate empirical semi variance from genotype matrix.

Description

Calculate empirical semi variance from genotype matrix.

Usage

CalculateEmpiricalGenSemivariogram(X, ploidy, coord, breaks = "FD",
  na.rm = TRUE)

Arguments

X	Genotype matrix.
ploidy	The number of chromosome.
coord	Coordinate matrix.
breaks	Same parameter that in hist R base function.
na.rm	A logical indicating whether missing values should be removed.

Value

Semi-variance

Examples

library(tess3r)

data("data.for.test", package = "tess3r")
em.vario <- CalculateEmpiricalGenSemivariogram(X = data.for.test$X,
                                ploidy = 1,
                                coord = data.for.test$coord,
                                breaks = "FD",
                                na.rm = TRUE)
ggplot2::ggplot(em.vario, ggplot2::aes(x = h, y = semi.variance, size = size)) +
               ggplot2::geom_point()

bcm-uga/TESS3_encho_sen documentation built on June 30, 2023, 3:08 a.m.