| A $ method for 'gen_tibble' objects | $<-.gen_tbl |
| An arrange method for 'gen_tibble' objects | arrange.gen_tbl |
| An arrange method for grouped 'gen_tibble' objects | arrange.grouped_gen_tbl |
| Augment data with information from a gt_pca object | augment.gt_pca augment_gt_pca |
| Augment the loci table with information from a analysis object | augment_loci |
| Augment the loci table with information from a gt_pca object | augment_loci.gt_pca augment_loci_gt_pca |
| Augment data with information from a q_matrix object | augment.q_matrix augment_q_matrix |
| Augment data with information from a gt_dapc object | augment.gt_dapc |
| Autoplots for 'gt_admix' objects | autoplot.gt_admix autoplot_gt_admix |
| Autoplots for 'gt_pca' objects | autoplot.gt_pca autoplot_gt_pca |
| Autoplots for 'gt_pcadapt' objects | autoplot.gt_pcadapt autoplot_gt_pcadapt |
| Autoplots for 'q_matrix' objects | autoplot.q_matrix autoplot_q_matrix |
| Autoplots for 'gt_cluster_pca' objects | autoplot.gt_cluster_pca |
| Autoplots for 'gt_dapc' objects | autoplot.gt_dapc |
| Autoplots for 'qc_report_indiv' objects | autoplot.qc_report_indiv |
| Autoplots for 'qc_report_loci' objects | autoplot.qc_report_loci |
| Combine method for gt_admix objects | c.gt_admix |
| Combine a gen_tibble to a data.frame or tibble by column | cbind.gen_tbl |
| Count the number of loci in a 'gen_tibble' | count_loci count_loci.tbl_df count_loci.vctrs_bigSNP |
| Distruct colours | distruct_colours |
| Filter individuals based on a relationship threshold | filter_high_relatedness |
| Tidyverse methods for gt objects | filter.gen_tbl |
| A filter method for grouped 'gen_tibble' objects | filter.grouped_gen_tbl |
| Find duplicates in the loci table | find_duplicated_loci |
| Constructor for a 'gen_tibble' | gen_tibble gen_tibble.character gen_tibble.matrix |
| Return a single P matrix from a 'gt_admix' object | get_p_matrix |
| Return a single Q matrix from a 'gt_admix' object | get_q_matrix |
| Add an simple feature geometry to a 'gen_tibble' | gt_add_sf |
| Reorder the q matrices based on the grouping variable | gt_admix_reorder_q |
| Run ADMIXTURE from R | gt_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 package | gt_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 format | gt_as_plink |
| Convert a 'gen_tibble' to a VCF | gt_as_vcf |
| Run K-clustering on principal components | gt_cluster_pca |
| Find the best number of clusters based on principal components | gt_cluster_pca_best_k |
| Discriminant Analysis of Principal Components for gen_tibble | gt_dapc |
| Compute and store blocked f2 statistics for ADMIXTOOLS 2 | gt_extract_f2 |
| Convert a 'genlight' object from adegenet to a 'gen_tibble' | gt_from_genlight |
| Get the names of files storing the genotypes of a 'gen_tibble' | gt_get_file_names |
| Checks if a 'gen_tibble' has been imputed | gt_has_imputed |
| Simple imputation based on allele frequencies | gt_impute_simple |
| Imputation based XGBoost | gt_impute_xgboost |
| Load a gen_tibble | gt_load |
| Order the loci table of a gen_tibble | gt_order_loci |
| Principal Component Analysis for 'gen_tibble' objects | gt_pca |
| PCA controlling for LD for 'gen_tibble' objects | gt_pca_autoSVD |
| PCA for 'gen_tibble' objects by partial SVD | gt_pca_partialSVD |
| PCA for 'gen_tibble' objects by randomized partial SVD | gt_pca_randomSVD |
| pcadapt analysis on a 'gen_tibble' object | gt_pcadapt |
| Set the ploidy of a 'gen_tibble' to include pseudohaploids | gt_pseudohaploid |
| Save a gen_tibble | gt_save |
| Sets a 'gen_tibble' to use imputed data | gt_set_imputed |
| Run SNMF from R in tidypopgen | gt_snmf |
| Update the backing matrix | gt_update_backingfile |
| Checks if a 'gen_tibble' uses imputed data | gt_uses_imputed |
| Estimate individual observed heterozygosity | indiv_het_obs indiv_het_obs.tbl_df indiv_het_obs.vctrs_bigSNP |
| Individual inbreeding coefficient | indiv_inbreeding indiv_inbreeding.grouped_df indiv_inbreeding.tbl_df indiv_inbreeding.vctrs_bigSNP |
| Estimate individual missingness | indiv_missingness indiv_missingness.tbl_df indiv_missingness.vctrs_bigSNP |
| Return individual ploidy | indiv_ploidy indiv_ploidy.tbl_df indiv_ploidy.vctrs_bigSNP |
| Test if the loci table is ordered | is_loci_table_ordered is_loci_table_ordered.tbl_df is_loci_table_ordered.vctrs_bigSNP |
| Load example gen_tibble | load_example_gt |
| Estimate allele frequencies at each locus | loci_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 locus | loci_hwe loci_hwe.grouped_df loci_hwe.tbl_df loci_hwe.vctrs_bigSNP |
| Clump loci based on a Linkage Disequilibrium threshold | loci_ld_clump loci_ld_clump.tbl_df loci_ld_clump.vctrs_bigSNP |
| Estimate missingness at each locus | loci_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 |
| Estimate nucleotide diversity (pi) at each locus | loci_pi loci_pi.grouped_df loci_pi.tbl_df loci_pi.vctrs_bigSNP |
| Find transitions | loci_transitions loci_transitions.tbl_df loci_transitions.vctrs_bigSNP |
| Find transversions | loci_transversions loci_transversions.tbl_df loci_transversions.vctrs_bigSNP |
| A mutate method for 'gen_tibble' objects | mutate.gen_tbl |
| A mutate method for grouped 'gen_tibble' objects | mutate.grouped_gen_tbl |
| Compute the Population Branch Statistics for each combination of populations | nwise_pop_pbs |
| Compute the Pairwise Allele Sharing Matrix for a 'gen_tibble' object | pairwise_allele_sharing |
| Compute the Genomic Relationship Matrix for a 'gen_tibble' object | pairwise_grm |
| Compute the Identity by State Matrix for a 'gen_tibble' object | pairwise_ibs |
| Compute the KING-robust Matrix for a 'gen_tibble' object | pairwise_king |
| Compute pairwise population Fst | pairwise_pop_fst |
| Compute population specific FIS | pop_fis |
| Compute population specific Fst | pop_fst |
| Compute basic population global statistics | pop_global_stats |
| Compute the population expected heterozygosity | pop_gene_div pop_het_exp |
| Compute the population observed heterozygosity | pop_het_obs |
| Estimate Tajima's D for the whole genome | pop_tajimas_d pop_tajimas_d.grouped_df pop_tajimas_d.tbl_df pop_tajimas_d.vctrs_bigSNP |
| Predict scores of a PCA | predict.gt_pca |
| Convert a standard matrix to a 'q_matrix' object | q_matrix |
| Create a Quality Control report for individuals | qc_report_indiv qc_report_indiv.grouped_df qc_report_indiv.tbl_df |
| Create a Quality Control report for loci | qc_report_loci qc_report_loci.grouped_df qc_report_loci.tbl_df |
| Generate a report of what would happen to each SNP in a merge | rbind_dry_run |
| Combine two gen_tibbles | rbind.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 colours | scale_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 object | snp_allele_sharing |
| Compute the Identity by State Matrix for a bigSNP object | snp_ibs |
| Compute the KING-robust Matrix for a bigSNP object | snp_king |
| Summary method for gt_admix objects | summary.gt_admix |
| Print a summary of a merge report | summary.rbind_report summary_rbind_report |
| A theme to match the output of distruct | theme_distruct |
| Tidy a 'gt_dapc' object | gt_dapc_tidiers tidy.gt_dapc |
| Tidy a 'gt_pca' object | gt_pca_tidiers tidy.gt_pca |
| Tidy a Q matrix | tidy.q_matrix |
| Draw an UpSet plot from a data frame of logical columns | upset_plot |
| Detect runs of homozygosity using a sliding-window approach | gt_roh_window windows_indiv_roh |
| Compute the Population Branch Statistics over a sliding window | windows_nwise_pop_pbs |
| Compute pairwise Fst for a sliding window | windows_pairwise_pop_fst |
| Compute Tajima's D for a sliding window | windows_pop_tajimas_d |
| Estimate window statistics from per locus estimates | windows_stats_generic |
