Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X A AdmixtureMappingVCFWriter (class in snputils) AdmixtureReader (class in snputils) AdmixtureWriter (class in snputils) allele_freq() (snputils.SNPObject method) allele_freq_stream() (in module snputils.stats) ancestries (snputils.GlobalAncestryObject property) ancestry (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) ancestry_file (snputils.AdmixtureReader property) (snputils.AdmixtureWriter property) ancestry_map (snputils.AdmixtureMappingVCFWriter property) (snputils.LocalAncestryObject property) (snputils.SNPObject property) AncIBDReader (class in snputils) are_strands_summed (snputils.SNPObject property) available_datasets_list() (in module snputils) average_strands (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) (snputils.processing.pca.PCA property) B backend (snputils.processing.pca.PCA property) BCFReader (class in snputils) BCFWriter (class in snputils) BEDReader (class in snputils) BEDWriter (class in snputils) BGENReader (class in snputils) BGENWriter (class in snputils) build_association_covariates() (in module snputils.phenotype) build_embedding_dataframe() (in module snputils.processing) build_synthetic_admixture_dataset() (in module snputils) build_synthetic_chromosome_painting_dataset() (in module snputils) build_synthetic_grg() (in module snputils) build_synthetic_maasmds_dataset() (in module snputils) build_synthetic_mdpca_dataset() (in module snputils) build_synthetic_phenotype_dataset() (in module snputils) build_synthetic_snp_dataset() (in module snputils) C calldata_gp (snputils.SNPObject property) calldata_gt (snputils.SNPObject property) calldata_lai (snputils.LocalAncestryObject property) (snputils.SNPObject property) centimorgan_pos (snputils.LocalAncestryObject property) chrom (snputils.IBDObject property) chromosome_painting() (in module snputils.visualization) chromosomes (snputils.LocalAncestryObject property) components_ (snputils.processing.pca.PCA property) (snputils.processing.pca.TorchPCA property) concat() (snputils.SNPObject method) concat_variants() (snputils.SNPObject class method) convert_chromosome_format() (snputils.SNPObject method) convert_to_snp_level() (snputils.LocalAncestryObject method) convert_to_window_level() (snputils.SNPObject method) copy() (snputils.GlobalAncestryObject method) (snputils.GRGObject method) (snputils.IBDObject method) (snputils.LocalAncestryObject method) (snputils.processing.maasmds.maasMDS method) (snputils.processing.mdpca.mdPCA method) (snputils.processing.pca.PCA method) (snputils.processing.pca.TorchPCA method) (snputils.SNPObject method) correct_flipped_variants() (snputils.SNPObject method) covariance_matrix_file (snputils.processing.mdpca.mdPCA property) CovariateObject (class in snputils) create_filemap() (in module snputils.visualization.admixture_viz) D d_stat() (in module snputils.stats) detect_chromosome_format() (snputils.SNPObject method) device (snputils.processing.pca.PCA property) distance_type (snputils.processing.maasmds.maasMDS property) dosage() (snputils.SNPObject method) E embedding_column_names() (in module snputils.processing) embedding_dataframe_from_model() (in module snputils.processing) embedding_table_path (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) (snputils.processing.pca.PCA property) end (snputils.IBDObject property) export_qp() (in module snputils.stats) F F (snputils.GlobalAncestryObject property) f2() (in module snputils.stats) f3() (in module snputils.stats) f4() (in module snputils.stats) f4_ratio() (in module snputils.stats) file (snputils.AdmixtureMappingVCFWriter property) (snputils.FLAREReader property) (snputils.FLAREWriter property) (snputils.MSPReader property) (snputils.MSPWriter property) (snputils.MultiPhenReader property) (snputils.PhenotypeReader property) file_prefix (snputils.AdmixtureWriter property) filename (snputils.GRGObject property) filter_biallelic_variants() (snputils.SNPObject method) filter_complete_genotypes() (snputils.SNPObject method) filter_polymorphic_variants() (snputils.SNPObject method) filter_samples() (snputils.LocalAncestryObject method) (snputils.MultiPhenotypeObject method) (snputils.SNPObject method) filter_segments() (snputils.IBDObject method) filter_variants() (snputils.SNPObject method) filter_windows() (snputils.LocalAncestryObject method) fit() (snputils.processing.pca.PCA method) (snputils.processing.pca.TorchPCA method) fit_transform() (snputils.processing.maasmds.maasMDS method) (snputils.processing.mdpca.mdPCA method) (snputils.processing.pca.PCA method) (snputils.processing.pca.TorchPCA method) fitting (snputils.processing.pca.PCA property) (snputils.processing.pca.TorchPCA property) FLAREReader (class in snputils) FLAREWriter (class in snputils) force_nan_incomplete_strands (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) fst() (in module snputils.stats) G genotypes (snputils.GRGObject property) (snputils.SNPObject property) get_common_markers_intersection() (snputils.SNPObject method) get_common_variants_intersection() (snputils.SNPObject method) GlobalAncestryObject (class in snputils) GRGObject (class in snputils) GRGReader (class in snputils) GRGWriter (class in snputils) group_snp_frequencies_only (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) groups_to_remove (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) H HapIBDReader (class in snputils) haplotype_id_1 (snputils.IBDObject property) haplotype_id_2 (snputils.IBDObject property) haplotype_pairs (snputils.IBDObject property) haplotypes (snputils.LocalAncestryObject property) haplotypes_ (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) (snputils.processing.pca.PCA property) I IBDObject (class in snputils) IBDReader (class in snputils) is_masked (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) is_weighted (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) iter_read() (snputils.BEDReader method) (snputils.PGENReader method) (snputils.snp.io.read.vcf.VCFReaderPolars method) K keys() (snputils.GlobalAncestryObject method) (snputils.GRGObject method) (snputils.IBDObject method) (snputils.LocalAncestryObject method) (snputils.SNPObject method) L labels_file (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) lai (snputils.LocalAncestryObject property) laiobj (snputils.AdmixtureMappingVCFWriter property) (snputils.FLAREWriter property) (snputils.MSPWriter property) (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) length_cm (snputils.IBDObject property) load_dataset() (in module snputils) load_masks (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) LocalAncestryObject (class in snputils) M maasMDS (class in snputils.processing.maasmds) main() (in module snputils.tools.cli) manhattan_plot() (in module snputils.visualization.manhattan_plot) masks_file (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) match_chromosome_format() (snputils.SNPObject method) mdPCA (class in snputils.processing.mdpca) mean_ (snputils.processing.pca.PCA property) (snputils.processing.pca.TorchPCA property) merge() (snputils.SNPObject method) method (snputils.processing.mdpca.mdPCA property) min_percent_snps (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) module snputils snputils.ancestry snputils.ancestry.io snputils.datasets snputils.ibd snputils.ibd.io snputils.phenotype snputils.phenotype.io snputils.processing snputils.simulation snputils.snp snputils.snp.io snputils.stats snputils.tools snputils.visualization MSPReader (class in snputils) MSPWriter (class in snputils) MultiPhenotypeObject (class in snputils) MultiPhenReader (class in snputils) N n_ancestries (snputils.GlobalAncestryObject property) (snputils.LocalAncestryObject property) (snputils.SNPObject property) n_chrom (snputils.SNPObject property) n_chromosomes (snputils.IBDObject property) n_components (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) (snputils.processing.pca.PCA property) (snputils.processing.pca.TorchPCA property) n_components_ (snputils.processing.pca.PCA property) (snputils.processing.pca.TorchPCA property) n_haplotypes (snputils.LocalAncestryObject property) (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) n_samples (snputils.GlobalAncestryObject property) (snputils.IBDObject property) (snputils.LocalAncestryObject property) (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) (snputils.SNPObject property) n_samples() (snputils.GRGObject method) n_segments (snputils.IBDObject property) n_snps (snputils.GlobalAncestryObject property) (snputils.SNPObject property) n_windows (snputils.LocalAncestryObject property) O OnlineSimulator (class in snputils.simulation.simulator.simulator) output_file (snputils.processing.mdpca.mdPCA property) P P (snputils.GlobalAncestryObject property) P_file (snputils.AdmixtureReader property) (snputils.AdmixtureWriter property) pairs (snputils.IBDObject property) PCA (class in snputils.processing.pca) pca_row_haplotype_ids() (in module snputils.processing) percent_vals_masked (snputils.processing.mdpca.mdPCA property) PGENReader (class in snputils) PGENWriter (class in snputils) PhenotypeObject (class in snputils) PhenotypeReader (class in snputils) physical_pos (snputils.LocalAncestryObject property) plot_admixture() (in module snputils.visualization.admixture) plot_lai() (in module snputils.visualization.lai) pong_viz() (in module snputils.visualization.admixture_viz) Python Enhancement Proposals PEP 562 Q Q (snputils.GlobalAncestryObject property) Q_file (snputils.AdmixtureReader property) (snputils.AdmixtureWriter property) qq_plot() (in module snputils.visualization.qq_plot) R read() (snputils.AdmixtureReader method) (snputils.AncIBDReader method) (snputils.BCFReader method) (snputils.BEDReader method) (snputils.BGENReader method) (snputils.FLAREReader method) (snputils.GRGReader method) (snputils.HapIBDReader method) (snputils.MSPReader method) (snputils.MultiPhenReader method) (snputils.PGENReader method) (snputils.PhenotypeReader method) (snputils.snp.io.read.vcf.VCFReaderPolars method) (snputils.VCFReader method) read_adm() (in module snputils) read_admixture() (in module snputils) read_bcf() (in module snputils) read_bed() (in module snputils) read_bgen() (in module snputils) read_covar_file() (in module snputils.phenotype) read_flare() (in module snputils) read_grg() (in module snputils) read_ibd() (in module snputils) read_labels() (in module snputils) read_lai() (in module snputils) read_msp() (in module snputils) read_pgen() (in module snputils) read_pheno() (in module snputils) read_snp() (in module snputils) read_vcf() (in module snputils) remove_mismatching_variants() (snputils.SNPObject method) remove_strand_ambiguous_variants() (snputils.SNPObject method) rename_chrom() (snputils.SNPObject method) rename_missings() (snputils.SNPObject method) reorder_admixture() (in module snputils.visualization.admixture) restrict_to_ancestry() (snputils.IBDObject method) rsid_or_chrompos (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) run_admixture_mapping() (in module snputils) run_gwas() (in module snputils) S sample_fid (snputils.SNPObject property) sample_file (snputils.AdmixtureReader property) (snputils.AdmixtureWriter property) sample_id_1 (snputils.IBDObject property) sample_id_2 (snputils.IBDObject property) sample_sex (snputils.SNPObject property) samples (snputils.GlobalAncestryObject property) (snputils.LocalAncestryObject property) (snputils.SNPObject property) samples_ (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) (snputils.processing.pca.PCA property) samples_subset (snputils.processing.pca.PCA property) save() (snputils.GlobalAncestryObject method) (snputils.GRGObject method) (snputils.LocalAncestryObject method) (snputils.SNPObject method) save_admixture() (snputils.GlobalAncestryObject method) save_bcf() (snputils.SNPObject method) save_bed() (snputils.SNPObject method) save_bgen() (snputils.SNPObject method) save_embedding_table() (in module snputils.processing) save_embedding_table_from_model() (in module snputils.processing) save_flare() (snputils.LocalAncestryObject method) save_masks (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) save_msp() (snputils.LocalAncestryObject method) save_pgen() (snputils.SNPObject method) save_pickle() (snputils.GlobalAncestryObject method) (snputils.LocalAncestryObject method) (snputils.SNPObject method) save_vcf() (snputils.SNPObject method) scatter() (in module snputils.visualization) segment_type (snputils.IBDObject property) set_empty_to_missing() (snputils.SNPObject method) shape (snputils.GlobalAncestryObject property) (snputils.GRGObject property) (snputils.IBDObject property) (snputils.LocalAncestryObject property) (snputils.SNPObject property) shuffle_variants() (snputils.SNPObject method) simulate() (snputils.simulation.simulator.simulator.OnlineSimulator method) simulate_diploid_population() (snputils.simulation.simulator.simulator.OnlineSimulator method) snp_file (snputils.AdmixtureReader property) (snputils.AdmixtureWriter property) snpobj (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) (snputils.processing.pca.PCA property) SNPObject (class in snputils) SNPReader (class in snputils) snps (snputils.GlobalAncestryObject property) snps_subset (snputils.processing.pca.PCA property) snputils module snputils.ancestry module snputils.ancestry.io module snputils.datasets module snputils.ibd module snputils.ibd.io module snputils.phenotype module snputils.phenotype.io module snputils.processing module snputils.simulation module snputils.snp module snputils.snp.io module snputils.stats module snputils.tools module snputils.visualization module start (snputils.IBDObject property) subset_to_common_markers() (snputils.SNPObject method) subset_to_common_variants() (snputils.SNPObject method) sum_strands() (snputils.SNPObject method) T to_dosage() (snputils.SNPObject method) to_snpobject() (snputils.GRGObject method) TorchPCA (class in snputils.processing.pca) transform() (snputils.processing.pca.PCA method) (snputils.processing.pca.TorchPCA method) try_save_embedding_table() (in module snputils.processing) U unique_chrom (snputils.SNPObject property) V variants_alt (snputils.SNPObject property) variants_chrom (snputils.SNPObject property) variants_cm (snputils.SNPObject property) variants_filter_pass (snputils.SNPObject property) variants_id (snputils.SNPObject property) variants_id_ (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) variants_info (snputils.SNPObject property) variants_pos (snputils.SNPObject property) variants_qual (snputils.SNPObject property) variants_ref (snputils.SNPObject property) VCFReader (class in snputils) VCFReaderPolars (class in snputils.snp.io.read.vcf) VCFWriter (class in snputils) W wideobj (snputils.AdmixtureWriter property) window_sizes (snputils.LocalAncestryObject property) write() (snputils.AdmixtureMappingVCFWriter method) (snputils.AdmixtureWriter method) (snputils.BCFWriter method) (snputils.BEDWriter method) (snputils.BGENWriter method) (snputils.FLAREWriter method) (snputils.GRGWriter method) (snputils.MSPWriter method) (snputils.PGENWriter method) (snputils.VCFWriter method) write_pgen() (snputils.PGENWriter method) write_psam() (snputils.PGENWriter method) write_pvar() (snputils.PGENWriter method) X X_ (snputils.processing.pca.PCA property) X_new_ (snputils.processing.maasmds.maasMDS property) (snputils.processing.mdpca.mdPCA property) (snputils.processing.pca.PCA property) (snputils.processing.pca.TorchPCA property)