Package index • tidypopgen

All functions
`as_q_matrix()`	Convert a Q matrix into a `q_matrix` obejct
`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 object
`augment_loci(<gt_pca>)`	Augment the loci table with information from a gt_pca object
`autoplot(<q_matrix>)`	Autoplots for `q_matrix` objects
`autoplot(<qc_report_indiv>)`	Autoplots for `qc_report_indiv` objects
`autoplot(<qc_report_loci>)`	Autoplots for `qc_report_loci` 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
`count_loci()`	Count the number of loci in a `gen_tibble`
`distruct_colours`	Distruct colours
`filter_high_relatedness()`	Filter individuals based on a relationship threshold
`gen_tibble()`	Constructor for a `gen_tibble`
`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 package
`gt_as_hierfstat()`	Convert a `gen_tibble` to a data.frame compatible with `hierfstat`
`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 components
`gt_dapc()`	Discriminant Analysis of Principal Components for gen_tibble
`gt_extract_f2()`	Compute and store blocked f2 statistics for ADMIXTOOLS 2
`gt_get_file_names()`	Get the names of files storing the genotypes of a `gen_tibble`
`gt_has_imputed()`	Checks if a `gen_tibble` has been imputed
`gt_impute_simple()`	Simple imputation based on allele frequencies
`gt_king()`	Compute the KING-robust Matrix for a a `gen_tibble` object
`gt_load()`	Load a gen_tibble
`gt_pca`	Principal Component Analysis for `gen_tibble` objects
`gt_pca_autoSVD()`	PCA controlling for LD for `gen_tibble` objects
`gt_pca_partialSVD()`	PCA for `gen_tibble` objects by partial SVD
`gt_pca_randomSVD()`	PCA for `gen_tibble` objects by randomized partial SVD
`gt_pcadapt()`	pcadapt analysis on a `gen_tibble` object
`gt_roh_window()`	Detect runs of homozygosity using a sliding-window approach
`gt_save()`	Save a gen_tibble
`gt_set_imputed()`	Sets a `gen_tibble` to use imputed data
`gt_uses_imputed()`	Checks if a `gen_tibble` uses imputed data
`indiv_het_obs()`	Estimate individual observed heterozygosity
`indiv_missingness()`	Estimate individual missingness
`indiv_ploidy()`	Return individual ploidy
`loci_alt_freq()` `loci_maf()`	Estimate allele frequencies at each 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_transitions()`	Find transitions
`loci_transversions()`	Find transversions
`pairwise_allele_sharing()`	Compute the Pairwise Allele Sharing Matrix for a `gen_tibble` object
`pairwise_ibs()`	Compute the Identity by State Matrix for a `gen_tibble` object
`pairwise_pop_fst()`	Compute pairwise population Fst
`pop_fis()`	Compute population specific FIS
`pop_fst()`	Compute population specific Fst
`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
`rbind(<gen_tbl>)`	Combine two gen_tibbles
`rbind_dry_run()`	Generate a report of what would happen to each SNP in a merge
`read_q_matrix_list()`	Tidy ADMXITURE output files into plots
`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_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 object
`snp_ibs()`	Compute the Identity by State Matrix for a bigSNP object
`snp_king()`	Compute the KING-robust Matrix for a bigSNP object
`summary(<rbind_report>)`	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(<q_matrix>)`	Tidy a Q matrix
`tidy(<gt_pca>)`	Tidy a `gt_pca` object

Reference

All functions