R: Streamline Population Genomic and Genetic Analyses

# Streamline Population Genomic and Genetic Analyses

## Documentation for package ‘PopGenHelpR’ version 1.3.0

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

## 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.
Dif_stats | *WARNING! This function has been deprecated and is no longer supported. Please use the Differentiation function.* A function to calculate differentiation statistics and perform significance testing with a vcf file.
Dif_Stats_Map | *WARNING! This function has been deprecated and is no longer supported. Please use the Network_map function.* A function to map differentiation statistics.
Div_stats | *WARNING! This function has been deprecated and is no longer supported. Please use the Heterozygosity and Private.alleles functions.* A function to estimate heterozygosity and the number of private alleles from a vcf file.
Div_Stats_Map | *WARNING! This function has been deprecated and is no longer supported. Please use the Point_map function instead.* A function to map diversity statistics.
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 Div_Stats.
HornedLizard_Pop | A population assignment data frame to be used in 'Div_stats' and 'Dif_stats'.
HornedLizard_VCF | A vcfR object to be used in 'Div_stats' and 'Dif_stats'.
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_ancestry | *WARNING! This function has been deprecated and is no longer supported. Please use the Ancestry_barchart and Piechart_map functions.* Plot an ancestry matrix and 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