Streamline Population Genomic and Genetic Analyses

Documentation for package ‘PopGenHelpR’ version 1.4.0

Ancestry_barchart	Plot an ancestry matrix for individuals and(or) populations.
Differentiation	A function to estimate three measures of genetic differentiation using geno files, vcf files, or vcfR objects. Data is assumed to be bi-allelic.
Fst_dat	A genetic differentiation matrix and locality information for each population. This data was generated by subsetting data of Farleigh et al., 2021.
Heterozygosity	A function to estimate seven measures of heterozygosity using geno files, vcf files, or vcfR objects. Data is assumed to be bi-allelic.
Het_dat	A data frame of hypothetical heterozygosity data produced by Heterozygosity.
HornedLizard_Pop	A population assignment data frame to be used in 'Heterozygosity' and 'Differentiation'.
HornedLizard_VCF	A vcfR object to be used in 'Heterozygosity' and 'Differentiation'.
Network_map	A function to map statistics (i.e., genetic differentiation) between points as a network on a map.
Pairwise_heatmap	A function to plot a heatmap from a symmetric matrix.
PCA	A function to perform principal component analysis (PCA) on genetic data. Loci with missing data will be removed prior to PCA.
Piechart_map	Plot a map of ancestry pie charts.
Plot_coordinates	A function to plot coordinates on a map.
Point_map	A function to map statistics as colored points on a map.
Private.alleles	A function to estimate the number of private alleles in each population.
Q_dat	A list representing a q-matrix and the locality information associated with the qmatrix