Package: PopGenHelpR 1.3.2

PopGenHelpR: Streamline Population Genomic and Genetic Analyses

Estimate commonly used population genomic statistics and generate publication quality figures. 'PopGenHelpR' uses vcf, 'geno' (012), and csv files to generate output.

Authors:Keaka Farleigh [aut, cph, cre], Mason Murphy [aut, cph, ctb], Christopher Blair [aut, cph, ctb], Tereza Jezkova [aut, cph, ctb]

PopGenHelpR_1.3.2.tar.gz
PopGenHelpR_1.3.2.zip(r-4.5)PopGenHelpR_1.3.2.zip(r-4.4)PopGenHelpR_1.3.2.zip(r-4.3)
PopGenHelpR_1.3.2.tgz(r-4.4-any)PopGenHelpR_1.3.2.tgz(r-4.3-any)
PopGenHelpR_1.3.2.tar.gz(r-4.5-noble)PopGenHelpR_1.3.2.tar.gz(r-4.4-noble)
PopGenHelpR_1.3.2.tgz(r-4.4-emscripten)PopGenHelpR_1.3.2.tgz(r-4.3-emscripten)
PopGenHelpR.pdf |PopGenHelpR.html✨
PopGenHelpR/json (API)
NEWS

# Install 'PopGenHelpR' in R:

install.packages('PopGenHelpR', repos = c('https://kfarleigh.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kfarleigh/popgenhelpr/issues

Datasets:

Fst_dat - A genetic differentiation matrix and locality information for each population. This data was generated by subsetting data of Farleigh et al., 2021.
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'.
Q_dat - A list representing a q-matrix and the locality information associated with the qmatrix

On CRAN:

diversity fst heterozygosity interpolation neis population-genetics population-genomics private-alleles snmf structure vcf

5.36 score 3 stars 14 scripts 401 downloads 10 exports 71 dependencies

Last updated 4 months agofrom:74f53b7017. Checks:OK: 6 ERROR: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 29 2024
R-4.5-win	ERROR	Oct 29 2024
R-4.5-linux	OK	Oct 29 2024
R-4.4-win	OK	Oct 29 2024
R-4.4-mac	OK	Oct 29 2024
R-4.3-win	OK	Oct 29 2024
R-4.3-mac	OK	Oct 29 2024

Exports:Ancestry_barchart Differentiation Heterozygosity Network_map Pairwise_heatmap PCA Piechart_map Plot_coordinates Point_map Private.alleles

Dependencies:ape boot class classInt cli cluster colorspace cpp11 DBI deldir digest dplyr e1071 fansi farver fs generics ggforce ggfun ggplot2 glue gtable isoband KernSmooth labeling lattice lifecycle magrittr MASS Matrix memuse mgcv munsell nlme permute pillar pinfsc50 pkgconfig plyr polyclip proxy purrr R6 RColorBrewer Rcpp RcppEigen reshape2 rlang s2 scales scatterpie sf sp spData spdep stringi stringr systemfonts tibble tidyr tidyselect tweenr units utf8 vcfR vctrs vegan viridisLite withr wk yulab.utils

PopGenHelpR Vignette

Rendered fromPopGenHelpR_vignette.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2024-02-20
Started: 2023-02-03

Citation

Development and contributors

Readme and manuals

Help Manual

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