API for tidypopgen
Tidy Population Genetics
| Global functions | |
|---|---|
| $<-.gen_tbl | Man page |
| %>% | Man page |
| .gt_bigsnp_cols | Source code |
| .gt_bigsnp_rows | Source code |
| .gt_get_bigsnp | Source code |
| CutBySize | Source code |
| SNPHWE2_R | Source code |
| add_missing_cols | Source code |
| afs_to_f2_blocks | Source code |
| alt_freq_dip_pseudo_cpp | Source code |
| ambiguous | Source code |
| annotate_group_info | Source code |
| arrange.gen_tbl | Man page Source code |
| arrange.grouped_gen_tbl | Man page Source code |
| augment | Man page |
| augment.gt_dapc | Man page Source code |
| augment.gt_pca | Man page Source code |
| augment.q_matrix | Man page Source code |
| augment_gt_pca | Man page |
| augment_loci | Man page Source code |
| augment_loci.gt_pca | Man page Source code |
| augment_loci_gt_pca | Man page |
| augment_q_matrix | Man page |
| autoplot | Man page |
| autoplot.gt_admix | Man page Source code |
| autoplot.gt_cluster_pca | Man page Source code |
| autoplot.gt_dapc | Man page Source code |
| autoplot.gt_pca | Man page Source code |
| autoplot.gt_pcadapt | Man page Source code |
| autoplot.q_matrix | Man page Source code |
| autoplot.qc_report_indiv | Man page Source code |
| autoplot.qc_report_loci | Man page Source code |
| autoplot_gt_admix | Man page |
| autoplot_gt_pca | Man page |
| autoplot_gt_pcadapt | Man page |
| autoplot_l_qc_all | Source code |
| autoplot_l_qc_hwe | Source code |
| autoplot_l_qc_maf | Source code |
| autoplot_l_qc_missing | Source code |
| autoplot_l_qc_overview | Source code |
| autoplot_q_matrix | Man page |
| autoplot_qc_report_indiv | Source code |
| autoplot_qc_report_indiv_king | Source code |
| c.gt_admix | Man page Source code |
| cast_chromosome_to_int | Source code |
| cbind.gen_tbl | Man page Source code |
| change_duplicated_file_name | Source code |
| check_allele_alphabet | Source code |
| check_valid_loci | Source code |
| col_names_combinations | Source code |
| compute_np_mn | Source code |
| compute_wss | Source code |
| count_loci | Man page Source code |
| count_loci.tbl_df | Man page Source code |
| count_loci.vctrs_bigSNP | Man page Source code |
| count_vcf_individuals | Source code |
| count_vcf_variants | Source code |
| cpp_is_polymorphic | Source code |
| discard_from_aftable | Source code |
| distruct_colours | Man page |
| dplyr_col_modify.grouped_gen_tbl | Source code |
| dplyr_reconstruct.gen_tbl | Source code |
| dplyr_reconstruct.grouped_gen_tbl | Source code |
| dplyr_row_slice.grouped_gen_tbl | Source code |
| extract_cross_entropy | Source code |
| fbm256_part_prod | Source code |
| fbm256_prod_and_rowSumsSq | Source code |
| fct_inorder_base | Source code |
| file_ext | Source code |
| filter.gen_tbl | Man page Source code |
| filter.grouped_gen_tbl | Man page Source code |
| filter_high_relatedness | Man page Source code |
| find_duplicated_loci | Man page Source code |
| flip | Source code |
| format.vctrs_bigSNP | Source code |
| format_grouped_output | Source code |
| gen_tibble | Man page Source code |
| gen_tibble.character | Man page Source code |
| gen_tibble.matrix | Man page Source code |
| gen_tibble_bed_rds | Source code |
| gen_tibble_packedancestry | Source code |
| gen_tibble_ped | Source code |
| gen_tibble_vcf | Source code |
| get_p_matrix | Man page Source code |
| get_packedancestry_code | Source code |
| get_ploidy | Source code |
| get_q_matrix | Man page Source code |
| group_by.gen_tbl | Source code |
| grouped_alt_freq_dip_pseudo_cpp | Source code |
| grouped_missingness_cpp | Source code |
| grouped_summaries_dip_pseudo_cpp | Source code |
| gt_add_sf | Man page Source code |
| gt_admix_reorder_q | Man page Source code |
| gt_admixture | Man page Source code |
| gt_as_genind | Man page Source code |
| gt_as_genlight | Man page Source code |
| gt_as_geno_lea | Man page Source code |
| gt_as_hierfstat | Man page Source code |
| gt_as_plink | Man page Source code |
| gt_as_vcf | Man page Source code |
| gt_cluster_pca | Man page Source code |
| gt_cluster_pca_best_k | Man page Source code |
| gt_dapc | Man page Source code |
| gt_dapc_tidiers | Man page |
| gt_extract_f2 | Man page Source code |
| gt_get_file_names | Man page Source code |
| gt_grouped_hwe | Source code |
| gt_grouped_pi_diploid | Source code |
| gt_has_imputed | Man page Source code |
| gt_impute_simple | Man page Source code |
| gt_impute_xgboost | Man page Source code |
| gt_ind_hetero | Source code |
| gt_load | Man page Source code |
| gt_order_loci | Man page Source code |
| gt_pca | Man page |
| gt_pca_autoSVD | Man page Source code |
| gt_pca_partialSVD | Man page Source code |
| gt_pca_randomSVD | Man page Source code |
| gt_pca_tidiers | Man page |
| gt_pcadapt | Man page Source code |
| gt_pi_diploid | Source code |
| gt_pseudohaploid | Man page Source code |
| gt_roh_window | Man page Source code |
| gt_save | Man page Source code |
| gt_save_light | Source code |
| gt_set_imputed | Man page Source code |
| gt_snmf | Man page Source code |
| gt_to_aftable | Source code |
| gt_update_backingfile | Man page Source code |
| gt_uses_imputed | Man page Source code |
| gt_write_bed | Source code |
| gt_write_bigsnp_from_dfs | Source code |
| gt_write_ped_raw | Source code |
| harmonise_missing_values | Source code |
| hwe_on_matrix | Source code |
| identify_pseudohaploids | Source code |
| increment_as_counts | Source code |
| increment_ibs_counts | Source code |
| increment_king_numerator | Source code |
| indiv_het_obs | Man page Source code |
| indiv_het_obs.tbl_df | Man page Source code |
| indiv_het_obs.vctrs_bigSNP | Man page Source code |
| indiv_inbreeding | Man page Source code |
| indiv_inbreeding.grouped_df | Man page Source code |
| indiv_inbreeding.tbl_df | Man page Source code |
| indiv_inbreeding.vctrs_bigSNP | Man page Source code |
| indiv_missingness | Man page Source code |
| indiv_missingness.tbl_df | Man page Source code |
| indiv_missingness.vctrs_bigSNP | Man page Source code |
| indiv_ploidy | Man page Source code |
| indiv_ploidy.tbl_df | Man page Source code |
| indiv_ploidy.vctrs_bigSNP | Man page Source code |
| is_diploid_only | Source code |
| is_loci_table_ordered | Man page Source code |
| is_loci_table_ordered.tbl_df | Man page Source code |
| is_loci_table_ordered.vctrs_bigSNP | Man page Source code |
| is_pseudohaploid | Source code |
| king_hist_plot | Source code |
| load_example_gt | Man page Source code |
| loci_alt_freq | Man page Source code |
| loci_alt_freq.grouped_df | Man page Source code |
| loci_alt_freq.tbl_df | Man page Source code |
| loci_alt_freq.vctrs_bigSNP | Man page Source code |
| loci_alt_freq_dip_pseudo | Source code |
| loci_alt_freq_polyploid | Source code |
| loci_chromosomes | Man page Source code |
| loci_chromosomes.tbl_df | Man page Source code |
| loci_chromosomes.vctrs_bigSNP | Man page Source code |
| loci_hwe | Man page Source code |
| loci_hwe.grouped_df | Man page Source code |
| loci_hwe.tbl_df | Man page Source code |
| loci_hwe.vctrs_bigSNP | Man page Source code |
| loci_ld_clump | Man page Source code |
| loci_ld_clump.tbl_df | Man page Source code |
| loci_ld_clump.vctrs_bigSNP | Man page Source code |
| loci_maf | Man page Source code |
| loci_maf.grouped_df | Man page Source code |
| loci_maf.tbl_df | Man page Source code |
| loci_maf.vctrs_bigSNP | Man page Source code |
| loci_missingness | Man page Source code |
| loci_missingness.grouped_df | Man page Source code |
| loci_missingness.tbl_df | Man page Source code |
| loci_missingness.vctrs_bigSNP | Man page Source code |
| loci_names | Man page Source code |
| loci_names.tbl_df | Man page Source code |
| loci_names.vctrs_bigSNP | Man page Source code |
| loci_pi | Man page Source code |
| loci_pi.grouped_df | Man page Source code |
| loci_pi.tbl_df | Man page Source code |
| loci_pi.vctrs_bigSNP | Man page Source code |
| loci_transitions | Man page Source code |
| loci_transitions.tbl_df | Man page Source code |
| loci_transitions.vctrs_bigSNP | Man page Source code |
| loci_transversions | Man page Source code |
| loci_transversions.tbl_df | Man page Source code |
| loci_transversions.vctrs_bigSNP | Man page Source code |
| mutate.gen_tbl | Man page Source code |
| mutate.grouped_gen_tbl | Man page Source code |
| new_vctrs_bigsnp | Source code |
| nwise_pop_pbs | Man page Source code |
| output_type | Source code |
| pairwise_allele_sharing | Man page Source code |
| pairwise_fst_hudson_loop | Source code |
| pairwise_fst_nei87_loop | Source code |
| pairwise_fst_wc84_loop | Source code |
| pairwise_grm | Man page Source code |
| pairwise_ibs | Man page Source code |
| pairwise_king | Man page Source code |
| pairwise_pop_fst | Man page Source code |
| parse_2bit_groups | Source code |
| pbs_one_triplet | Source code |
| poly_genotype_dosage | Source code |
| poly_indiv_dosage | Source code |
| pop_fis | Man page Source code |
| pop_fis_nei87 | Source code |
| pop_fis_wg17 | Source code |
| pop_fst | Man page Source code |
| pop_gene_div | Man page Source code |
| pop_global_stats | Man page Source code |
| pop_het_exp | Man page Source code |
| pop_het_obs | Man page Source code |
| pop_tajimas_d | Man page Source code |
| pop_tajimas_d.grouped_df | Man page Source code |
| pop_tajimas_d.tbl_df | Man page Source code |
| pop_tajimas_d.vctrs_bigSNP | Man page Source code |
| predict.gt_pca | Man page Source code |
| print.gt_cluster_pca | Source code |
| print.gt_dapc | Source code |
| print.gt_pca | Source code |
| pull_na | Source code |
| q_matrix | Man page Source code |
| qc_report_indiv | Man page Source code |
| qc_report_indiv.grouped_df | Man page Source code |
| qc_report_indiv.tbl_df | Man page Source code |
| qc_report_loci | Man page Source code |
| qc_report_loci.grouped_df | Man page Source code |
| qc_report_loci.tbl_df | Man page Source code |
| rbind.gen_tbl | Man page Source code |
| rbind_dry_run | Man page Source code |
| rbind_dry_run_df | Source code |
| read_packedancestry | Source code |
| read_pedfile | Source code |
| read_q_files | Man page Source code |
| recode_genotype | Source code |
| reexports | Man page |
| resolve_missing_alleles | Source code |
| scale_fill_distruct | Man page Source code |
| select_loci | Man page Source code |
| select_loci_if | Man page Source code |
| seq2 | Source code |
| show_genotypes | Man page Source code |
| show_genotypes.tbl_df | Man page Source code |
| show_genotypes.vctrs_bigSNP | Man page Source code |
| show_loci | Man page Source code |
| show_loci.tbl_df | Man page Source code |
| show_loci.vctrs_bigSNP | Man page Source code |
| show_loci<- | Man page |
| show_loci<-.tbl_df | Man page |
| show_loci<-.vctrs_bigSNP | Man page |
| show_ploidy | Man page Source code |
| show_ploidy.tbl_df | Man page Source code |
| show_ploidy.vctrs_bigSNP | Man page Source code |
| snp_allele_sharing | Man page Source code |
| snp_ibs | Man page Source code |
| snp_king | Man page Source code |
| square_frobenius | Source code |
| stopifnot_dip_pseudo | Source code |
| stopifnot_diploid | Source code |
| stopifnot_gen_tibble | Source code |
| str_replace_base | Source code |
| sub_gt | Source code |
| sub_rds | Source code |
| subset_bigSNP | Source code |
| summary.gt_admix | Man page Source code |
| summary.rbind_report | Man page Source code |
| summary.vctrs_bigSNP | Source code |
| summary_rbind_report | Man page |
| tajimas_d_from_pi_vec | Source code |
| tbl_sum.gen_tbl | Source code |
| theme_distruct | Man page Source code |
| tidy | Man page |
| tidy.gt_dapc | Man page Source code |
| tidy.gt_pca | Man page Source code |
| tidy.q_matrix | Man page Source code |
| tidy_dist_matrix | Source code |
| tidy_to_matrix | Source code |
| tidypopgen | Man page |
| tidypopgen-package | Man page |
| ungroup.grouped_gen_tbl | Source code |
| vcf_genotypes_to_fbm | Source code |
| vcf_loci_table | Source code |
| vcf_to_fbm_cpp | Source code |
| vcf_to_fbm_vcfR | Source code |
| windows_indiv_roh | Man page Source code |
| windows_nwise_pop_pbs | Man page Source code |
| windows_pairwise_pop_fst | Man page Source code |
| windows_pop_tajimas_d | Man page Source code |
| windows_stats_generic | Man page Source code |
| write_to_FBM | Source code |
