Files in tidypopgen

Tidy Population Genetics

NEWS.md README.md R/RcppExports.R R/subset_bigSNP.R R/cbind_gen_tibble.R R/count_loci.R R/show_genotypes.R R/gt_order_loci.R R/gt_load.R R/load_example_gt.R R/gt_pca_randomSVD.R R/show_loci.R R/pop_fis.R R/gt_as_genlight.R R/scale_fill_distruct.R R/gt_has_imputed.R R/windows_pop_tajimas_d.R R/autoplot_gt_pcadapt.R R/count_vcf_variants.R R/vcf_to_fbm_vcfR.R R/gt_helper_functions.R R/utils-pipe.R R/gt_save.R R/loci_missingness.R R/predict_gt_pca.R R/pop_fst.R R/select_loci_if.R R/loci_chromosomes.R R/gt_admix_methods.R R/is_loci_table_ordered.R R/format_vctrs_bigSNP.R R/loci_ld_clump.R R/windows_stats_generic.R R/theme_distruct.R R/pop_het_exp.R R/gt_pca.R R/gt_add_sf.R R/gt_as_hierfstat.R R/pairwise_allele_sharing.R R/gt_dapc.R R/pop_tajimas_d.R R/loci_alt_freq.R R/gen_tibble.R R/snp_allele_sharing.R R/autoplot_gt_admix.R R/loci_transitions.R R/select_loci.R R/pairwise_king.R R/gt_snmf.R R/summary_rbind_report.R R/tidypopgen-package.R R/square_frobenius.R R/get_packedancestry_code.R R/loci_pi.R R/filter_high_relatedness.R R/gt_pca_autoSVD.R R/vcf_to_fbm_cpp_fast.R R/gt_cluster_pca.R R/tidyverse.R R/gt_as_plink.R R/gt_update_backingfile.R R/augment_loci.R R/pairwise_ibs.R R/indiv_het_obs.R R/gt_impute_simple.R R/rbind_gen_tibble.R R/loci_transversions.R R/gt_extract_f2.R R/q_matrix.R R/indiv_ploidy.R R/snp_ibs.R R/windows_pairwise_pop_fst.R R/loci_hwe.R R/autoplot_gt_pca.R R/nwise_pop_pbs.R R/gt_pcadapt.R R/gt_admixture.R R/rbind_dry_run.R R/snp_king.R R/flip.R R/gt_pseudohaploid.R R/gt_impute_xgboost.R R/gt_pca_tidiers.R R/dataset_docs.R R/windows_nwise_pop_pbs.R R/pop_global_stats.R R/indiv_missingness.R R/pairwise_pop_fst.R R/gen_tibble_vcf.R R/indiv_inbreeding.R R/gt_as_genind.R R/qc_report_indiv.R R/gt_cluster_pca_best_k.R R/pop_het_obs.R R/autoplot_gt_dapc.R R/loci_names.R R/gt_as_vcf.R R/gen_tibble_ped.R R/qc_report_loci.R R/annotate_group_info.R R/windows_indiv_roh.R R/show_ploidy.R R/gt_dapc_tidiers.R R/gen_tibble_packedancestry.R R/gt_as_geno_lea.R R/pairwise_grm.R R/utils.R R/gt_pca_partialSVD.R inst/doc/a01_overview.R inst/doc/tidypopgen.R inst/doc/a03_example_clustering_and_dapc.Rmd inst/doc/a99_plink_cheatsheet.R inst/doc/a03_example_clustering_and_dapc.R inst/doc/a99_plink_cheatsheet.Rmd inst/doc/a02_qc.Rmd inst/doc/a02_qc.R inst/doc/a01_overview.Rmd inst/doc/tidypopgen.Rmd inst/extdata/anolis/anolis_ld_run1.4.Q inst/extdata/anolis/anolis_ld_run1.3.Q tests/testthat.R tests/spelling.R tests/testthat/test_indiv_missingness.R tests/testthat/test_filter_high_relatedness.R tests/testthat/test_gt_extract_f2.R tests/testthat/test_window_indiv_roh.R tests/testthat/test_show_loci.R tests/testthat/test_window_pairwise_pop_fst.R tests/testthat/test_gt_as_plink.R tests/testthat/test_qc_report_indiv.R tests/testthat/test_qc_report_loci.R tests/testthat/test_subset_bigSNP.R tests/testthat/test_gen_tibble_save_load.R tests/testthat/test_gt_pseudohaploid.R tests/testthat/test_indiv_het_obs.R tests/testthat/test_example_gt.R tests/testthat/test_gt_as_.R tests/testthat/test_gt_pca_tidiers.R tests/testthat/test_gt_tibble_vcf.R tests/testthat/test_snp_king.R tests/testthat/test_select_loci_if.R tests/testthat/test_pop_fis_fst.R tests/testthat/test_loci_transversions_transitions.R tests/testthat/test_pairwise_pop_fst.R tests/testthat/test_gt_impute_simple.R tests/testthat/test_gt_add_sf.R tests/testthat/test_cbind_gen_tbl.R tests/testthat/test_gt_admixture.R tests/testthat/test_loci_freq.R tests/testthat/test_pairwise_allele_sharing.R tests/testthat/test_count_vcf_individuals.R tests/testthat/test_rbind_dry_run.R tests/testthat/test_window_stats_generic.R tests/testthat/test_gt_dapc_and_tidiers.R tests/testthat/test_gt_pcadapt.R tests/testthat/test_rbind_gen_tibble.R tests/testthat/test_q_matrix.R tests/testthat/test_count_vcf_variants.R tests/testthat/test_show_ploidy.R tests/testthat/test_gen_tibble.R tests/testthat/test_indiv_inbreeding.R tests/testthat/test_select_loci.R tests/testthat/test_pop_basic_stats.R tests/testthat/test_gen_tibble_versioning.R tests/testthat/test_window_nwise_pop_pbs.R tests/testthat/test_snp_ibs.R tests/testthat/test_nwise_pop_pbs.R tests/testthat/test_loci_pi.R tests/testthat/test_gt_pca.R tests/testthat/test_loci_ld_clump.R tests/testthat/test_tidyverse.R tests/testthat/test_gt_admix_methods.R tests/testthat/test_loci_missingness.R tests/testthat/test_gt_order_loci.R tests/testthat/test_pairwise_grm.R tests/testthat/test_autoplot_loci_report.R tests/testthat/test_gt_snmf.R tests/testthat/test_ploidy_vcf.R tests/testthat/test_loci_hwe.R tests/testthat/test_window_pop_tajimas_d.R tests/testthat/test_gt_as_vcf.R tests/testthat/test_gt_impute_xgboost.R tests/testthat/test_pop_tajimas_d.R tests/testthat/test_augment_loci.R vignettes/a03_example_clustering_and_dapc.Rmd vignettes/a99_plink_cheatsheet.Rmd vignettes/a02_qc.Rmd vignettes/a01_overview.Rmd vignettes/tidypopgen.Rmd man/loci_alt_freq.Rd man/count_loci.Rd man/autoplot_gt_cluster_pca.Rd man/qc_report_indiv.Rd man/pairwise_grm.Rd man/indiv_ploidy.Rd man/snp_king.Rd man/cbind.gen_tbl.Rd man/gt_pseudohaploid.Rd man/gt_impute_xgboost.Rd man/theme_distruct.Rd man/autoplot.qc_report_loci.Rd man/reexports.Rd man/autoplot_gt_pcadapt.Rd man/windows_indiv_roh.Rd man/loci_missingness.Rd man/gt_as_genind.Rd man/nwise_pop_pbs.Rd man/show_ploidy.Rd man/pop_global_stats.Rd man/autoplot.qc_report_indiv.Rd man/gt_load.Rd man/loci_names.Rd man/augment.gt_dapc.Rd man/gt_add_sf.Rd man/get_p_matrix.Rd man/gt_as_plink.Rd man/windows_stats_generic.Rd man/snp_ibs.Rd man/indiv_missingness.Rd man/gt_as_geno_lea.Rd man/gt_as_genlight.Rd man/pairwise_pop_fst.Rd man/loci_pi.Rd man/arrange.gen_tbl.Rd man/tidy.gt_dapc.Rd man/tidypopgen-package.Rd man/c.gt_admix.Rd man/loci_hwe.Rd man/pop_het_obs.Rd man/gt_dapc.Rd man/autoplot_q_matrix.Rd man/select_loci.Rd man/indiv_het_obs.Rd man/gen_tibble.Rd man/read_q_files.Rd man/gt_uses_imputed.Rd man/is_loci_table_ordered.Rd man/augment_loci.Rd man/q_matrix.Rd man/load_example_gt.Rd man/summary_rbind_dry_run.Rd man/pop_het_exp.Rd man/pairwise_allele_sharing.Rd man/filter.gen_tbl.Rd man/find_duplicated_loci.Rd man/gt_set_imputed.Rd man/windows_pop_tajimas_d.Rd man/autoplot_gt_pca.Rd man/rbind.gen_tbl.Rd man/pop_fis.Rd man/autoplot_gt_dapc.Rd man/loci_transitions.Rd man/gt_cluster_pca.Rd man/gt_snmf.Rd man/select_loci_if.Rd man/gt_as_hierfstat.Rd man/gt_extract_f2.Rd man/tidy.q_matrix.Rd man/pop_tajimas_d.Rd man/pipe.Rd man/augment_loci_gt_pca.Rd man/get_q_matrix.Rd man/gt_has_imputed.Rd man/gt_admixture.Rd man/filter_high_relatedness.Rd man/gt_pca_autoSVD.Rd man/gt_as_vcf.Rd man/windows_pairwise_pop_fst.Rd man/gt_pcadapt.Rd man/loci_transversions.Rd man/gt_update_backingfile.Rd man/windows_nwise_pop_pbs.Rd man/pop_fst.Rd man/show_genotypes.Rd man/indiv_inbreeding.Rd man/gt_cluster_pca_best_k.Rd man/mutate.gen_tbl.Rd man/filter.grouped_gen_tbl.Rd man/gt_pca.Rd man/qc_report_loci.Rd man/loci_chromosomes.Rd man/summary.gt_admix.Rd man/mutate.grouped_gen_tbl.Rd man/loci_ld_clump.Rd man/pairwise_ibs.Rd man/snp_allele_sharing.Rd man/pairwise_king.Rd man/rbind_dry_run.Rd man/scale_fill_distruct.Rd man/gt_pca_randomSVD.Rd man/augment_gt_pca.Rd man/gt_get_file_names.Rd man/gt_pca_partialSVD.Rd man/tidy_gt_pca.Rd man/augment_q_matrix.Rd man/gt_admix_reorder_q.Rd man/distruct_colours.Rd man/arrange.grouped_gen_tbl.Rd man/autoplot_gt_admix.Rd man/show_loci.Rd man/predict_gt_pca.Rd man/gt_impute_simple.Rd man/cash-set-.gen_tbl.Rd man/gt_save.Rd man/gt_order_loci.Rd