Package: tidypopgen 0.0.0.9016

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

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

On CRAN:

64 exports 1 stars 1.58 score 76 dependencies 8 scripts

Last updated 4 days agofrom:7c5ef31f70 (on main). Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 13 2024
R-4.5-win-x86_64OKSep 13 2024
R-4.5-linux-x86_64OKSep 13 2024
R-4.4-win-x86_64OKSep 13 2024
R-4.4-mac-x86_64OKSep 13 2024
R-4.4-mac-aarch64OKSep 13 2024
R-4.3-win-x86_64OKSep 13 2024
R-4.3-mac-x86_64OKSep 13 2024
R-4.3-mac-aarch64OKSep 13 2024

Exports:%>%as_q_matrixaugmentaugment_lociautoplotcount_locifilter_high_relatednessgen_tibblegt_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_kinggt_loadgt_pca_autoSVDgt_pca_partialSVDgt_pca_randomSVDgt_pcadaptgt_roh_windowgt_savegt_set_imputedgt_uses_imputedindiv_het_obsindiv_missingnessindiv_ploidyloci_alt_freqloci_chromosomesloci_hweloci_ld_clumploci_mafloci_missingnessloci_namesloci_transitionsloci_transversionspairwise_allele_sharingpairwise_ibspairwise_pop_fstpop_fispop_fstqc_report_indivqc_report_locirbind_dry_runread_q_matrix_listscale_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 Sep 13 2024.

Last update: 2024-07-19
Started: 2024-06-11

Overview

Rendered froma01_overview.Rmdusingknitr::rmarkdownon Sep 13 2024.

Last update: 2024-06-27
Started: 2024-06-11

PLINK cheatsheet

Rendered froma99_plink_cheatsheet.Rmdusingknitr::rmarkdownon Sep 13 2024.

Last update: 2024-06-16
Started: 2024-06-11

Quality Control

Rendered froma02_qc.Rmdusingknitr::rmarkdownon Sep 13 2024.

Last update: 2024-06-15
Started: 2024-06-11

Readme and manuals

Help Manual

Help pageTopics
Convert a Q matrix into a 'q_matrix' obejctas_q_matrix
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 gt_dapc objectaugment.gt_dapc
Autoplots for 'gt_pca' objectsautoplot.gt_pca autoplot_gt_pca
Autoplots for 'gt_pcadapt' objectsautoplot.gt_pcadapt autoplot_gt_pcadapt
Autoplots for 'gt_cluster_pca' objectsautoplot.gt_cluster_pca
Autoplots for 'gt_dapc' objectsautoplot.gt_dapc
Autoplots for 'q_matrix' objectsautoplot.q_matrix
Autoplots for 'qc_report_indiv' objectsautoplot.qc_report_indiv
Autoplots for 'qc_report_loci' objectsautoplot.qc_report_loci
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
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
Compute the KING-robust Matrix for a a 'gen_tibble' objectgt_king
Load a gen_tibblegt_load
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
Checks if a 'gen_tibble' uses imputed datagt_uses_imputed
Estimate individual observed heterozygosityindiv_het_obs indiv_het_obs.grouped_df indiv_het_obs.tbl_df indiv_het_obs.vctrs_bigSNP
Estimate individual missingnessindiv_missingness indiv_missingness.grouped_df indiv_missingness.tbl_df indiv_missingness.vctrs_bigSNP
Return individual ploidyindiv_ploidy indiv_ploidy.grouped_df indiv_ploidy.tbl_df indiv_ploidy.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 Identity by State Matrix for a 'gen_tibble' objectpairwise_ibs
Compute pairwise population Fstpairwise_pop_fst
Compute population specific FISpop_fis
Compute population specific Fstpop_fst
Predict scores of a PCApredict.gt_pca
Create a Quality Control report for individualsqc_report_indiv
Create a Quality Control report for lociqc_report_loci
Generate a report of what would happen to each SNP in a mergerbind_dry_run
Combine two gen_tibblesrbind.gen_tbl
Tidy ADMXITURE output files into plotsread_q_matrix_list
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
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