R: Streamline Population Genomic and Genetic Analyses

# Streamline Population Genomic and Genetic Analyses

## Documentation for package ‘PopGenHelpR’ version 1.4.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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