Package: tidypopgen 0.0.0.9021

Andrea Manica

tidypopgen: Tidy Population Genetics

We provide a tidy grammar of population genetics, facilitating the manipulation and analysis of data on biallelic single nucleotide polymorphisms (SNPs).

Authors:Evie Carter [aut], Andrea Manica [aut, cre]

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tidypopgen.pdf |tidypopgen.html✨
tidypopgen/json (API)

# Install 'tidypopgen' in R:
install.packages('tidypopgen', repos = c('https://evolecolgroup.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/evolecolgroup/tidypopgen/issues

Pkgdown site:https://evolecolgroup.github.io

Uses libs:
  • openblas– Optimized BLAS
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On CRAN:

openblaszlibcppopenmp

5.80 score 4 stars 8 scripts 78 exports 76 dependencies

Last updated 11 days agofrom:47e2dd266c (on main). Checks:6 OK, 3 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 21 2025
R-4.5-win-x86_64OKJan 21 2025
R-4.5-linux-x86_64OKJan 21 2025
R-4.4-win-x86_64OKJan 21 2025
R-4.4-mac-x86_64OKJan 21 2025
R-4.4-mac-aarch64OKJan 21 2025
R-4.3-win-x86_64ERRORJan 21 2025
R-4.3-mac-x86_64ERRORJan 21 2025
R-4.3-mac-aarch64ERRORJan 21 2025

Exports:%>%augmentaugment_lociautoplotcount_locifilter_high_relatednessgen_tibbleget_p_matrixget_q_matrixgt_admix_reorder_qgt_admixturegt_as_genindgt_as_genlightgt_as_geno_leagt_as_hierfstatgt_as_plinkgt_as_vcfgt_cluster_pcagt_cluster_pca_best_kgt_dapcgt_extract_f2gt_get_file_namesgt_has_imputedgt_impute_simplegt_loadgt_order_locigt_pca_autoSVDgt_pca_partialSVDgt_pca_randomSVDgt_pcadaptgt_roh_windowgt_savegt_set_imputedgt_snmfgt_update_backingfilegt_uses_imputedindiv_het_obsindiv_inbreedingindiv_missingnessindiv_ploidyis_loci_table_orderedloci_alt_freqloci_chromosomesloci_hweloci_ld_clumploci_mafloci_missingnessloci_namesloci_transitionsloci_transversionspairwise_allele_sharingpairwise_grmpairwise_ibspairwise_kingpairwise_pop_fstpop_fispop_fstpop_gene_divpop_global_statspop_het_exppop_het_obsq_matrixqc_report_indivqc_report_locirbind_dry_runread_q_filesscale_fill_distructselect_lociselect_loci_ifshow_genotypesshow_locishow_loci<-show_ploidysnp_allele_sharingsnp_ibssnp_kingtheme_distructtidy

Dependencies:BHbigassertrbigparallelrbigreadrbigsnprbigsparserbigstatsrbigutilsrbitclicodetoolscolorspacecowplotcpp11data.tableDEoptimRdigestdoParalleldoRNGdplyrfansifarverffflockforcatsforeachgenericsggplot2gluegridExtragtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnabornlmeparallellypatchworkpillarpkgconfigplyrpspurrrR6RColorBrewerRcppRcppArmadilloRcppEigenRhpcBLASctlrlangrmiorngtoolsrobustbaseroptimRSpectrarunoncescalesstringistringrtibbletidyrtidyselecttriebeardUpSetRurltoolsutf8vctrsviridisLitewithr

Example workflow with tidypopgen

Rendered froma03_example_clustering_and_dapc.Rmdusingknitr::rmarkdownon Jan 21 2025.

Last update: 2025-01-21
Started: 2024-06-11

Overview

Rendered froma01_overview.Rmdusingknitr::rmarkdownon Jan 21 2025.

Last update: 2024-11-04
Started: 2024-06-11

PLINK cheatsheet

Rendered froma99_plink_cheatsheet.Rmdusingknitr::rmarkdownon Jan 21 2025.

Last update: 2024-11-22
Started: 2024-06-11

Quality Control

Rendered froma02_qc.Rmdusingknitr::rmarkdownon Jan 21 2025.

Last update: 2024-12-02
Started: 2024-06-11

Readme and manuals

Help Manual

Help pageTopics
Augment data with information from a gt_pca objectaugment.gt_pca augment_gt_pca
Augment the loci table with information from a analysis objectaugment_loci
Augment the loci table with information from a gt_pca objectaugment_loci.gt_pca augment_loci_gt_pca
Augment data with information from a q_matrix objectaugment.q_matrix augment_q_matrix
Augment data with information from a gt_dapc objectaugment.gt_dapc
Autoplots for 'gt_admix' objectsautoplot.gt_admix autoplot_gt_admix
Autoplots for 'gt_pca' objectsautoplot.gt_pca autoplot_gt_pca
Autoplots for 'gt_pcadapt' objectsautoplot.gt_pcadapt autoplot_gt_pcadapt
Autoplots for 'q_matrix' objectsautoplot.q_matrix autoplot_q_matrix
Autoplots for 'gt_cluster_pca' objectsautoplot.gt_cluster_pca
Autoplots for 'gt_dapc' objectsautoplot.gt_dapc
Autoplots for 'qc_report_indiv' objectsautoplot.qc_report_indiv
Autoplots for 'qc_report_loci' objectsautoplot.qc_report_loci
Combine method for gt_admix objectsc.gt_admix
Count the number of loci in a 'gen_tibble'count_loci count_loci.tbl_df count_loci.vctrs_bigSNP
Distruct coloursdistruct_colours
Filter individuals based on a relationship thresholdfilter_high_relatedness
Constructor for a 'gen_tibble'gen_tibble gen_tibble.character gen_tibble.matrix
Return a single P matrix from a 'gt_admix' objectget_p_matrix
Return a single Q matrix from a 'gt_admix' objectget_q_matrix
Reorder the q matrices based on the grouping variablegt_admix_reorder_q
Run ADMIXTURE from Rgt_admixture
Convert a 'gen_tibble' to a 'genind' object from 'adegenet'gt_as_genind
Convert a 'gen_tibble' to a 'genlight' object from 'adegenet'gt_as_genlight
Convert a 'gentibble' to a .geno file for sNMF from the LEA packagegt_as_geno_lea
Convert a 'gen_tibble' to a data.frame compatible with 'hierfstat'gt_as_hierfstat
Export a 'gen_tibble' object to PLINK bed formatgt_as_plink
Convert a 'gen_tibble' to a VCFgt_as_vcf
Run K-clustering on principal componentsgt_cluster_pca
Find the best number of clusters based on principal componentsgt_cluster_pca_best_k
Discriminant Analysis of Principal Components for gen_tibblegt_dapc
Compute and store blocked f2 statistics for ADMIXTOOLS 2gt_extract_f2
Get the names of files storing the genotypes of a 'gen_tibble'gt_get_file_names
Checks if a 'gen_tibble' has been imputedgt_has_imputed
Simple imputation based on allele frequenciesgt_impute_simple
Load a gen_tibblegt_load
Order the loci table of a gen_tibblegt_order_loci
Principal Component Analysis for 'gen_tibble' objectsgt_pca
PCA controlling for LD for 'gen_tibble' objectsgt_pca_autoSVD
PCA for 'gen_tibble' objects by partial SVDgt_pca_partialSVD
PCA for 'gen_tibble' objects by randomized partial SVDgt_pca_randomSVD
pcadapt analysis on a 'gen_tibble' objectgt_pcadapt
Detect runs of homozygosity using a sliding-window approachgt_roh_window
Save a gen_tibblegt_save
Sets a 'gen_tibble' to use imputed datagt_set_imputed
Run SNMF from R in tidypopgengt_snmf
Update the backing matrixgt_update_backingfile
Checks if a 'gen_tibble' uses imputed datagt_uses_imputed
Estimate individual observed heterozygosityindiv_het_obs indiv_het_obs.tbl_df indiv_het_obs.vctrs_bigSNP
Individual inbreeding coefficientindiv_inbreeding indiv_inbreeding.grouped_df indiv_inbreeding.tbl_df indiv_inbreeding.vctrs_bigSNP
Estimate individual missingnessindiv_missingness indiv_missingness.tbl_df indiv_missingness.vctrs_bigSNP
Return individual ploidyindiv_ploidy indiv_ploidy.tbl_df indiv_ploidy.vctrs_bigSNP
Test if the loci table is orderedis_loci_table_ordered is_loci_table_ordered.tbl_df is_loci_table_ordered.vctrs_bigSNP
Estimate allele frequencies at each each locusloci_alt_freq loci_alt_freq.grouped_df loci_alt_freq.tbl_df loci_alt_freq.vctrs_bigSNP loci_maf loci_maf.grouped_df loci_maf.tbl_df loci_maf.vctrs_bigSNP
Get the chromosomes of loci in a 'gen_tibble'loci_chromosomes loci_chromosomes.tbl_df loci_chromosomes.vctrs_bigSNP
Test Hardy-Weinberg equilibrium at each locusloci_hwe loci_hwe.grouped_df loci_hwe.tbl_df loci_hwe.vctrs_bigSNP
Clump loci based on a Linkage Disequilibrium thresholdloci_ld_clump loci_ld_clump.grouped_df loci_ld_clump.tbl_df loci_ld_clump.vctrs_bigSNP
Estimate missingness at each locusloci_missingness loci_missingness.grouped_df loci_missingness.tbl_df loci_missingness.vctrs_bigSNP
Get the names of loci in a 'gen_tibble'loci_names loci_names.tbl_df loci_names.vctrs_bigSNP
Find transitionsloci_transitions loci_transitions.grouped_df loci_transitions.tbl_df loci_transitions.vctrs_bigSNP
Find transversionsloci_transversions loci_transversions.grouped_df loci_transversions.tbl_df loci_transversions.vctrs_bigSNP
Compute the Pairwise Allele Sharing Matrix for a 'gen_tibble' objectpairwise_allele_sharing
Compute the Genomic Relationship Matrix for a 'gen_tibble' objectpairwise_grm
Compute the Identity by State Matrix for a 'gen_tibble' objectpairwise_ibs
Compute the KING-robust Matrix for a a 'gen_tibble' objectpairwise_king
Compute pairwise population Fstpairwise_pop_fst
Compute population specific FISpop_fis
Compute population specific Fstpop_fst
Compute basic population global statisticspop_global_stats
Compute the population expected heterozygositypop_gene_div pop_het_exp
Compute the population observed heterozygositypop_het_obs
Predict scores of a PCApredict.gt_pca
Convert a standard matrix to a 'q_matrix' objectq_matrix
Create a Quality Control report for individualsqc_report_indiv qc_report_indiv.grouped_df qc_report_indiv.tbl_df
Create a Quality Control report for lociqc_report_loci qc_report_loci.grouped_df qc_report_loci.tbl_df
Generate a report of what would happen to each SNP in a mergerbind_dry_run
Combine two gen_tibblesrbind.gen_tbl
Read and structure .Q files or existing matrices as 'q_matrix' or 'gt_admix' objects.read_q_files
Scale constructor using the distruct coloursscale_fill_distruct
The 'select' verb for 'loci'select_loci
The 'select_if' verb for 'loci'select_loci_if
Show the genotypes of a 'gen_tibble'show_genotypes show_genotypes.tbl_df show_genotypes.vctrs_bigSNP
Show the loci information of a 'gen_tibble'show_loci show_loci.tbl_df show_loci.vctrs_bigSNP show_loci<- show_loci<-.tbl_df show_loci<-.vctrs_bigSNP
Show the ploidy information of a 'gen_tibble'show_ploidy show_ploidy.tbl_df show_ploidy.vctrs_bigSNP
Compute the Pairwise Allele Sharing Matrix for a bigSNP objectsnp_allele_sharing
Compute the Identity by State Matrix for a bigSNP objectsnp_ibs
Compute the KING-robust Matrix for a bigSNP objectsnp_king
Summary method for gt_admix objectssummary.gt_admix
Print a summary of a merge reportsummary.rbind_report summary_rbind_report
A theme to match the output of distructtheme_distruct
Tidy a 'gt_dapc' objectgt_dapc_tidiers tidy.gt_dapc
Tidy a 'gt_pca' objectgt_pca_tidiers tidy.gt_pca
Tidy a Q matrixtidy.q_matrix