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 property) (snputils.processing.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 property) (snputils.processing.mdPCA property) (snputils.processing.PCA property) B backend (snputils.processing.PCA property) BEDReader (class in snputils) BEDWriter (class in snputils) C calldata_gt (snputils.GRGObject property) (snputils.SNPObject property) calldata_lai (snputils.SNPObject property) centimorgan_pos (snputils.LocalAncestryObject property) chrom (snputils.IBDObject property) chromosomes (snputils.LocalAncestryObject property) components_ (snputils.processing.PCA property) (snputils.processing.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.MultiPhenotypeObject method) (snputils.processing.maasMDS method) (snputils.processing.mdPCA method) (snputils.processing.PCA method) (snputils.processing.TorchPCA method) (snputils.SNPObject method) correct_flipped_variants() (snputils.SNPObject method) covariance_matrix_file (snputils.processing.mdPCA property) 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 property) distance_type (snputils.processing.maasMDS property) E end (snputils.IBDObject property) 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.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 method) (snputils.processing.TorchPCA method) fit_transform() (snputils.processing.maasMDS method) (snputils.processing.mdPCA method) (snputils.processing.PCA method) (snputils.processing.TorchPCA method) fitting (snputils.processing.PCA property) (snputils.processing.TorchPCA property) force_nan_incomplete_strands (snputils.processing.maasMDS property) (snputils.processing.mdPCA property) fst() (in module snputils.stats) G 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 property) (snputils.processing.mdPCA property) groups_to_remove (snputils.processing.maasMDS property) (snputils.processing.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 property) (snputils.processing.mdPCA property) I IBDObject (class in snputils) IBDReader (class in snputils) is_masked (snputils.processing.maasMDS property) (snputils.processing.mdPCA property) is_weighted (snputils.processing.maasMDS property) (snputils.processing.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 property) (snputils.processing.mdPCA property) lai (snputils.LocalAncestryObject property) laiobj (snputils.AdmixtureMappingVCFWriter property) (snputils.MSPWriter property) (snputils.processing.maasMDS property) (snputils.processing.mdPCA property) length_cm (snputils.IBDObject property) load_dataset() (in module snputils) load_masks (snputils.processing.maasMDS property) (snputils.processing.mdPCA property) LocalAncestryObject (class in snputils) M maasMDS (class in snputils.processing) manhattan_plot() (in module snputils.visualization.admixture_manhattan_plot) masks_file (snputils.processing.maasMDS property) (snputils.processing.mdPCA property) match_chromosome_format() (snputils.SNPObject method) mdPCA (class in snputils.processing) mean_ (snputils.processing.PCA property) (snputils.processing.TorchPCA property) merge() (snputils.SNPObject method) method (snputils.processing.mdPCA property) min_percent_snps (snputils.processing.maasMDS property) (snputils.processing.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 property) (snputils.processing.mdPCA property) (snputils.processing.PCA property) (snputils.processing.TorchPCA property) n_components_ (snputils.processing.PCA property) (snputils.processing.TorchPCA property) n_haplotypes (snputils.LocalAncestryObject property) (snputils.processing.maasMDS property) (snputils.processing.mdPCA property) n_phenotypes (snputils.MultiPhenotypeObject property) n_samples (snputils.GlobalAncestryObject property) (snputils.IBDObject property) (snputils.LocalAncestryObject property) (snputils.MultiPhenotypeObject property) (snputils.processing.maasMDS property) (snputils.processing.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 output_file (snputils.processing.mdPCA property) P P (snputils.GlobalAncestryObject property) P_file (snputils.AdmixtureReader property) (snputils.AdmixtureWriter property) pairs (snputils.IBDObject property) PCA (class in snputils.processing) percent_vals_masked (snputils.processing.mdPCA property) PGENReader (class in snputils) PGENWriter (class in snputils) phen_df (snputils.MultiPhenotypeObject property) 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) Q Q (snputils.GlobalAncestryObject property) Q_file (snputils.AdmixtureReader property) (snputils.AdmixtureWriter property) R read() (snputils.AdmixtureReader method) (snputils.AncIBDReader method) (snputils.BEDReader 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_bed() (in module snputils) read_grg() (in module snputils) read_ibd() (in module snputils) read_lai() (in module snputils) read_msp() (in module snputils) read_pgen() (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 property) (snputils.processing.mdPCA property) 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 property) (snputils.processing.mdPCA property) samples_subset (snputils.processing.PCA property) save() (snputils.GlobalAncestryObject method) (snputils.LocalAncestryObject method) (snputils.SNPObject method) save_admixture() (snputils.GlobalAncestryObject method) save_bed() (snputils.SNPObject method) save_masks (snputils.processing.maasMDS property) (snputils.processing.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.MultiPhenotypeObject property) (snputils.SNPObject property) shuffle_variants() (snputils.SNPObject method) snp_file (snputils.AdmixtureReader property) (snputils.AdmixtureWriter property) snpobj (snputils.processing.maasMDS property) (snputils.processing.mdPCA property) (snputils.processing.PCA property) SNPObject (class in snputils) SNPReader (class in snputils) snps (snputils.GlobalAncestryObject property) snps_subset (snputils.processing.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_snpobject() (snputils.GRGObject method) TorchPCA (class in snputils.processing) transform() (snputils.processing.PCA method) (snputils.processing.TorchPCA method) 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 property) (snputils.processing.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.BEDWriter 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 property) X_new_ (snputils.processing.maasMDS property) (snputils.processing.mdPCA property) (snputils.processing.PCA property) (snputils.processing.TorchPCA property)