reduce.allele: Remove low variance alleles (dimensionality reduction)

In alexkychen/assignPOP: Population Assignment using Genetic, Non-Genetic or Integrated Data in a Machine Learning Framework

Remove low variance alleles (dimensionality reduction)

Description

This function helps remove alleles that have low variance in the data set such that it can speed up further analyses for a large data set (e.g., > 10K SNPs).

Usage

reduce.allele(x, p = 0.95)

Arguments

x	A returned object (a list) from the function read.genpop().
p	A threshold of variance for the alleles to be removed. For example, if p = 0.95 (default setting), an allele occupied more than 95 percents across all the samples will be removed.

Value

This function return the same object as the function read.genpop() except that the number of columns in the matrix [[1]] is reduced and so is the locus name [[3]].

alexkychen/assignPOP documentation built on March 18, 2024, 6:26 a.m.