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'))

Peer review:

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:

diversityfstheterozygosityinterpolationneispopulation-geneticspopulation-genomicsprivate-allelessnmfstructurevcf

10 exports 3 stars 1.84 score 71 dependencies 14 scripts 740 downloads

Last updated 2 months agofrom:74f53b7017. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 30 2024
R-4.5-winOKAug 30 2024
R-4.5-linuxOKAug 30 2024
R-4.4-winOKAug 30 2024
R-4.4-macOKAug 30 2024
R-4.3-winOKAug 30 2024
R-4.3-macOKAug 30 2024

Exports:Ancestry_barchartDifferentiationHeterozygosityNetwork_mapPairwise_heatmapPCAPiechart_mapPlot_coordinatesPoint_mapPrivate.alleles

Dependencies:apebootclassclassIntcliclustercolorspacecpp11DBIdeldirdigestdplyre1071fansifarverfsgenericsggforceggfunggplot2gluegtableisobandKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmemusemgcvmunsellnlmepermutepillarpinfsc50pkgconfigplyrpolyclipproxypurrrR6RColorBrewerRcppRcppEigenreshape2rlangs2scalesscatterpiesfspspDataspdepstringistringrsystemfontstibbletidyrtidyselecttweenrunitsutf8vcfRvctrsveganviridisLitewithrwkyulab.utils

PopGenHelpR Vignette

Rendered fromPopGenHelpR_vignette.Rmdusingknitr::rmarkdownon Aug 30 2024.

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

Readme and manuals

Help Manual

Help pageTopics
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 qmatrixQ_dat