genlight_creator: Creates a genlight object from a vcf file that can be used in...

In sorenDJ/R_package_Johnson: An R Package to help with genomic population structure analysis

Description

need packages ape, poppr, vcfR

Usage

genlight_creator(vcf_file = "c_ven_phy_50_pop.vcf", pop_data = "c_ven_pop_5.txt", genlight_name = "gl.test", sample_col = sample, pop_col = sub_species)

Arguments

vcf_file	the path to the vcf file that will be used to create the genlight object
pop_data	a text file with the samples and population data to be analyzed, should have a heading for each of the columns
genlight_name	the name of the output genelight object, needs to be in quotes
sample_col	the name of the column that contains the sample names
pop_col	the column from the population text file to be used as the population data

sorenDJ/R_package_Johnson documentation built on Dec. 23, 2021, 4:23 a.m.