Index A | C | E | F | G | H | I | L | M | N | O | P | R | S | V | X A allele_counts() (in module grapp.util.simple) allele_frequencies() (in module grapp.util.simple) C common_mut_dataframe() (in module grapp.util.simple) E eigs() (in module grapp.linalg) exact_hamming_dists() (grapp.nn.NearestNeighborContext method) exact_hamming_dists_by_mutation() (grapp.nn.NearestNeighborContext method) exact_hamming_dists_by_sample() (grapp.nn.NearestNeighborContext method) export_igd() (in module grapp.util.igd) export_vcf() (in module grapp.util.igd) F fast_pairwise_hamming() (grapp.nn.NearestNeighborContext method) G get_eig_pcs() (in module grapp.linalg) get_variant_type() (in module grapp.util.simple) get_zygosities() (in module grapp.util.simple) grapp module grapp.assoc module grapp.linalg module grapp.nn module grapp.util.filter module grapp.util.igd module grapp.util.parallel module grapp.util.simple module grg (grapp.nn.NearestNeighborContext property) grg_save_freq() (in module grapp.util.filter) grg_save_individuals() (in module grapp.util.filter) grg_save_mut_filter() (in module grapp.util.filter) grg_save_populations() (in module grapp.util.filter) grg_save_range() (in module grapp.util.filter) grg_save_samples() (in module grapp.util.filter) H hwe() (in module grapp.util.simple) hwe_df() (in module grapp.util.simple) hwe_from_counts() (in module grapp.util.simple) I igd_to_vcf() (in module grapp.util.igd) INDELS (grapp.util.simple.VariantType attribute) L linear_assoc_covar() (in module grapp.assoc) linear_assoc_no_covar() (in module grapp.assoc) M MatrixSelection (class in grapp.linalg) MNPS (grapp.util.simple.VariantType attribute) module grapp grapp.assoc grapp.linalg grapp.nn grapp.util.filter grapp.util.igd grapp.util.parallel grapp.util.simple multi_allelic_muts() (in module grapp.util.simple) multi_grg_save_mut_filter() (in module grapp.util.filter) MultiSciPyStdXOperator (class in grapp.linalg.ops_scipy) MultiSciPyStdXTXOperator (class in grapp.linalg.ops_scipy) MultiSciPyXOperator (class in grapp.linalg.ops_scipy) MultiSciPyXTXOperator (class in grapp.linalg.ops_scipy) muts_above (grapp.nn.NearestNeighborContext property) N NearestNeighborContext (class in grapp.nn) O OTHER (grapp.util.simple.VariantType attribute) P PCs() (in module grapp.linalg) R read_pheno() (in module grapp.assoc) read_plink_covariates() (in module grapp.assoc) ref_hwe() (in module grapp.util.simple) S samps_below (grapp.nn.NearestNeighborContext property) SciPyStdXOperator (class in grapp.linalg.ops_scipy) SciPyStdXTXOperator (class in grapp.linalg.ops_scipy) SciPyStdXXTOperator (class in grapp.linalg.ops_scipy) SciPyXOperator (class in grapp.linalg.ops_scipy) SciPyXTXOperator (class in grapp.linalg.ops_scipy) SciPyXXTOperator (class in grapp.linalg.ops_scipy) site_alleles() (in module grapp.util.simple) site_samples() (in module grapp.util.simple) SNPS (grapp.util.simple.VariantType attribute) sort_by_eigvalues() (in module grapp.linalg) split_and_run() (in module grapp.util.parallel) split_by_ranges() (in module grapp.util.filter) V variance() (in module grapp.util.simple) variants_of_types() (in module grapp.util.simple) VariantType (class in grapp.util.simple) X X (grapp.linalg.MatrixSelection attribute) XT (grapp.linalg.MatrixSelection attribute) XTX (grapp.linalg.MatrixSelection attribute)