From 409c94ad94ca075b9d66073e6afe08308c9d2af6 Mon Sep 17 00:00:00 2001 From: Ben Jeffery Date: Mon, 27 Nov 2023 02:48:55 +0000 Subject: [PATCH] Organise methods --- docs/api.rst | 68 ++++++++++++++++++++++++++++++++++++++++------------ 1 file changed, 53 insertions(+), 15 deletions(-) diff --git a/docs/api.rst b/docs/api.rst index 25f0b6d0e..77b5c629f 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -86,6 +86,9 @@ Dataset Methods ======= +Allele and Genotype Analysis +---------------------------- + .. autosummary:: :toctree: generated/ @@ -95,34 +98,69 @@ Methods count_cohort_alleles count_variant_alleles count_variant_genotypes + observed_heterozygosity + variant_stats + +Population and Cohort Genetics +------------------------------ + +.. autosummary:: + :toctree: generated/ + divergence diversity Fst + Tajimas_D + Weir_Goudet_beta Garud_H - genee + pbs + +Pedigree and Relationship +------------------------- + +.. autosummary:: + :toctree: generated/ + genomic_relationship - gwas_linear_regression - hardy_weinberg_test + pc_relate + pedigree_contribution + pedigree_inbreeding + pedigree_inverse_kinship + pedigree_kinship hybrid_inverse_relationship hybrid_relationship identity_by_state - individual_heterozygosity + +Linkage Disequilibrium and Heterozygosity +----------------------------------------- + +.. autosummary:: + :toctree: generated/ + ld_matrix ld_prune + individual_heterozygosity + +Genetic Association and Regression +---------------------------------- + +.. autosummary:: + :toctree: generated/ + + gwas_linear_regression + regenie + hardy_weinberg_test + genee + +Miscellaneous and Utilities +---------------------------- + +.. autosummary:: + :toctree: generated/ + maximal_independent_set - observed_heterozygosity pairwise_distance - pbs - pedigree_contribution - pedigree_inbreeding - pedigree_inverse_kinship - pedigree_kinship - pc_relate - regenie sample_stats - Tajimas_D - variant_stats - Weir_Goudet_beta Utilities =========