get.pca {MoBPS}

Principle components analysis

Description

Function to perform a principle component analysis

Usage

get.pca(
  population,
  path = NULL,
  database = NULL,
  gen = NULL,
  cohorts = NULL,
  coloring = "group",
  components = c(1, 2),
  plot = TRUE,
  pch = 1,
  export.color = FALSE
)

Arguments

population

Population list

path

Location were to save the PCA-plot

database

Groups of individuals to consider for the export

gen

Quick-insert for database (vector of all generations to export)

cohorts

Quick-insert for database (vector of names of cohorts to export)

coloring

Coloring by "group", "sex", "plain"

components

Default: c(1,2) for the first two principle components

plot

Set to FALSE to not generate a plot

pch

Point type in the PCA plot

export.color

Set to TRUE to export the per point coloring

Value

Genotype data for in gen/database/cohorts selected individuals

Examples

data(ex_pop)
get.pca(ex_pop, gen=2)