Man pages for tidypopgen
Tidy Population Genetics
| arrange.gen_tbl | An arrange method for 'gen_tibble' objects |
| arrange.grouped_gen_tbl | An arrange method for grouped 'gen_tibble' objects |
| augment.gt_dapc | Augment data with information from a gt_dapc object |
| augment_gt_pca | Augment data with information from a gt_pca object |
| augment_loci | Augment the loci table with information from a analysis... |
| augment_loci_gt_pca | Augment the loci table with information from a gt_pca object |
| augment_q_matrix | Augment data with information from a q_matrix object |
| autoplot_gt_admix | Autoplots for 'gt_admix' objects |
| autoplot_gt_cluster_pca | Autoplots for 'gt_cluster_pca' objects |
| autoplot_gt_dapc | Autoplots for 'gt_dapc' objects |
| autoplot_gt_pca | Autoplots for 'gt_pca' objects |
| autoplot_gt_pcadapt | Autoplots for 'gt_pcadapt' objects |
| autoplot.qc_report_indiv | Autoplots for 'qc_report_indiv' objects |
| autoplot.qc_report_loci | Autoplots for 'qc_report_loci' objects |
| autoplot_q_matrix | Autoplots for 'q_matrix' objects |
| cash-set-.gen_tbl | A $ method for 'gen_tibble' objects |
| cbind.gen_tbl | Combine a gen_tibble to a data.frame or tibble by column |
| c.gt_admix | Combine method for gt_admix objects |
| count_loci | Count the number of loci in a 'gen_tibble' |
| distruct_colours | Distruct colours |
| filter.gen_tbl | Tidyverse methods for gt objects |
| filter.grouped_gen_tbl | A filter method for grouped 'gen_tibble' objects |
| filter_high_relatedness | Filter individuals based on a relationship threshold |
| find_duplicated_loci | Find duplicates in the loci table |
| gen_tibble | Constructor for a 'gen_tibble' |
| get_p_matrix | Return a single P matrix from a 'gt_admix' object |
| get_q_matrix | Return a single Q matrix from a 'gt_admix' object |
| gt_add_sf | Add an simple feature geometry to a 'gen_tibble' |
| gt_admix_reorder_q | Reorder the q matrices based on the grouping variable |
| gt_admixture | Run ADMIXTURE from R |
| gt_as_genind | Convert a 'gen_tibble' to a 'genind' object from 'adegenet' |
| gt_as_genlight | Convert a 'gen_tibble' to a 'genlight' object from 'adegenet' |
| gt_as_geno_lea | Convert a 'gentibble' to a .geno file for sNMF from the LEA... |
| gt_as_hierfstat | Convert a 'gen_tibble' to a data.frame compatible with... |
| gt_as_plink | Export a 'gen_tibble' object to PLINK bed format |
| gt_as_vcf | Convert a 'gen_tibble' to a VCF |
| gt_cluster_pca | Run K-clustering on principal components |
| gt_cluster_pca_best_k | Find the best number of clusters based on principal... |
| gt_dapc | Discriminant Analysis of Principal Components for gen_tibble |
| gt_extract_f2 | Compute and store blocked f2 statistics for ADMIXTOOLS 2 |
| gt_from_genlight | Convert a 'genlight' object from adegenet to a 'gen_tibble' |
| gt_get_file_names | Get the names of files storing the genotypes of a... |
| gt_has_imputed | Checks if a 'gen_tibble' has been imputed |
| gt_impute_simple | Simple imputation based on allele frequencies |
| gt_impute_xgboost | Imputation based XGBoost |
| gt_load | Load a gen_tibble |
| gt_order_loci | Order the loci table of a gen_tibble |
| gt_pca | Principal Component Analysis for 'gen_tibble' objects |
| gt_pca_autoSVD | PCA controlling for LD for 'gen_tibble' objects |
| gt_pcadapt | pcadapt analysis on a 'gen_tibble' object |
| gt_pca_partialSVD | PCA for 'gen_tibble' objects by partial SVD |
| gt_pca_randomSVD | PCA for 'gen_tibble' objects by randomized partial SVD |
| gt_pseudohaploid | Set the ploidy of a 'gen_tibble' to include pseudohaploids |
| gt_save | Save a gen_tibble |
| gt_set_imputed | Sets a 'gen_tibble' to use imputed data |
| gt_snmf | Run SNMF from R in tidypopgen |
| gt_update_backingfile | Update the backing matrix |
| gt_uses_imputed | Checks if a 'gen_tibble' uses imputed data |
| indiv_het_obs | Estimate individual observed heterozygosity |
| indiv_inbreeding | Individual inbreeding coefficient |
| indiv_missingness | Estimate individual missingness |
| indiv_ploidy | Return individual ploidy |
| is_loci_table_ordered | Test if the loci table is ordered |
| load_example_gt | Load example gen_tibble |
| loci_alt_freq | Estimate allele frequencies at each locus |
| loci_chromosomes | Get the chromosomes of loci in a 'gen_tibble' |
| loci_hwe | Test Hardy-Weinberg equilibrium at each locus |
| loci_ld_clump | Clump loci based on a Linkage Disequilibrium threshold |
| loci_missingness | Estimate missingness at each locus |
| loci_names | Get the names of loci in a 'gen_tibble' |
| loci_pi | Estimate nucleotide diversity (pi) at each locus |
| loci_transitions | Find transitions |
| loci_transversions | Find transversions |
| mutate.gen_tbl | A mutate method for 'gen_tibble' objects |
| mutate.grouped_gen_tbl | A mutate method for grouped 'gen_tibble' objects |
| nwise_pop_pbs | Compute the Population Branch Statistics for each combination... |
| pairwise_allele_sharing | Compute the Pairwise Allele Sharing Matrix for a 'gen_tibble'... |
| pairwise_grm | Compute the Genomic Relationship Matrix for a 'gen_tibble'... |
| pairwise_ibs | Compute the Identity by State Matrix for a 'gen_tibble'... |
| pairwise_king | Compute the KING-robust Matrix for a 'gen_tibble' object |
| pairwise_pop_fst | Compute pairwise population Fst |
| pipe | Pipe operator |
| pop_fis | Compute population specific FIS |
| pop_fst | Compute population specific Fst |
| pop_global_stats | Compute basic population global statistics |
| pop_het_exp | Compute the population expected heterozygosity |
| pop_het_obs | Compute the population observed heterozygosity |
| pop_tajimas_d | Estimate Tajima's D for the whole genome |
| predict_gt_pca | Predict scores of a PCA |
| qc_report_indiv | Create a Quality Control report for individuals |
| qc_report_loci | Create a Quality Control report for loci |
| q_matrix | Convert a standard matrix to a 'q_matrix' object |
| rbind_dry_run | Generate a report of what would happen to each SNP in a merge |
| rbind.gen_tbl | Combine two gen_tibbles |
| read_q_files | Read and structure .Q files or existing matrices as... |
| reexports | Objects exported from other packages |
| scale_fill_distruct | Scale constructor using the distruct colours |
| select_loci | The 'select' verb for 'loci' |
| select_loci_if | The 'select_if' verb for 'loci' |
| show_genotypes | Show the genotypes of a 'gen_tibble' |
| show_loci | Show the loci information of a 'gen_tibble' |
| show_ploidy | Show the ploidy information of a 'gen_tibble' |
| snp_allele_sharing | Compute the Pairwise Allele Sharing Matrix for a bigSNP... |
| snp_ibs | Compute the Identity by State Matrix for a bigSNP object |
| snp_king | Compute the KING-robust Matrix for a bigSNP object |
| summary.gt_admix | Summary method for gt_admix objects |
| summary_rbind_dry_run | Print a summary of a merge report |
| theme_distruct | A theme to match the output of distruct |
| tidy.gt_dapc | Tidy a 'gt_dapc' object |
| tidy_gt_pca | Tidy a 'gt_pca' object |
| tidypopgen-package | tidypopgen: Tidy Population Genetics |
| tidy.q_matrix | Tidy a Q matrix |
| windows_indiv_roh | Detect runs of homozygosity using a sliding-window approach |
| windows_nwise_pop_pbs | Compute the Population Branch Statistics over a sliding... |
| windows_pairwise_pop_fst | Compute pairwise Fst for a sliding window |
| windows_pop_tajimas_d | Compute Tajima's D for a sliding window |
| windows_stats_generic | Estimate window statistics from per locus estimates |
