Index

A

add_bim_data() (genome_integration.utils.gcta_ma_utils.MaFile method) add_estimate() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) add_frequency_data() (genome_integration.variants.SNP method) add_frq_information() (genome_integration.variants.BimFile method) add_minor_allele_frequency() (genome_integration.variants.SNP method)

add_p_values_to_associations_dict() (in module genome_integration.association.binary_files) add_pos_chr() (genome_integration.variants.SNP method) add_snp_data() (genome_integration.association.association_classes.GeneticAssociation method) (genome_integration.variants.SNP method) Association (class in genome_integration.association.association_classes)

B

BaseAssociation (class in genome_integration.association.association_classes)

BimFile (class in genome_integration.variants)

C

choose_exposure_snps() (in module genome_integration.simulate_mr.simulation_functions) CojoCmaFile (class in genome_integration.utils.gcta_cojo_utils)

CojoCmaLine (class in genome_integration.utils.gcta_cojo_utils) convert_gene_list() (genome_integration.resources.enrichments.Enrich method)

D

do_and_add_single_term_mr_estimation() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) do_and_add_smr_estimation() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) do_chochrans_q_meta_analysis() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) do_egger_regression() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) do_egger_regression_single_variance_term() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) do_egger_regression_two_variance_term() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) do_enrichr_analysis() (genome_integration.resources.enrichments.Enrich method) do_gcta_cojo_conditional() (in module genome_integration.simulate_mr.geno_functions) do_gcta_cojo_joint() (in module genome_integration.utils.gcta_cojo_utils) do_gcta_cojo_joint_on_only_snps_genetic_associations() (in module genome_integration.utils.gcta_cojo_utils) do_gcta_cojo_on_genetic_associations() (in module genome_integration.utils.gcta_cojo_utils) do_gcta_cojo_slct() (in module genome_integration.utils.gcta_cojo_utils)

do_gcta_joint_on_specified_snps() (in module genome_integration.utils.gcta_cojo_utils) do_gwas_on_scaled_variants() (in module genome_integration.simulate_mr.geno_functions) do_gwas_on_scaled_variants_fast() (in module genome_integration.simulate_mr.geno_functions) do_ivw_estimation() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) do_ivw_estimation_on_estimate_vector() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) do_ivw_heterogeneity_estimation() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) do_ivw_heterogeneity_estimation_on_estimate_vector() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) do_lda_mr_egger() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) do_lda_mr_egger_on_estimates() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) do_single_term_mr_estimate() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) do_smr_estimate() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method) do_weighted_median_meta_analysis_on_estimate_vectors() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method)

E

Enrich (class in genome_integration.resources.enrichments)

enrich() (genome_integration.resources.enrichments.Enrich method)

F

FamFile (class in genome_integration.utils.plink_utils)

FamSample (class in genome_integration.utils.plink_utils)

G

GeneticAssociation (class in genome_integration.association.association_classes) geno_frq() (in module genome_integration.simulate_mr.geno_functions) genome_integration (module), [1], [2], [3], [4], [5], [6], [7] genome_integration.association.association_classes (module) genome_integration.association.binary_files (module) genome_integration.causal_inference.mendelian_randomization (module) genome_integration.causal_inference.mr_link (module) genome_integration.gene_regions (module) genome_integration.resources (module) genome_integration.resources.enrichments (module)

genome_integration.samples (module) genome_integration.simulate_mr (module) genome_integration.simulate_mr.geno_functions (module) genome_integration.simulate_mr.simulation_functions (module) genome_integration.utils (module) genome_integration.utils.file_utils (module) genome_integration.utils.gcta_cojo_utils (module) genome_integration.utils.gcta_ma_utils (module) genome_integration.utils.plink_utils (module) genome_integration.variants (module) get_ivw_estimates() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method)

H

harmonize_genotypes() (genome_integration.utils.plink_utils.PlinkFile method)

I

in_gene_regions() (genome_integration.gene_regions.StartEndRegions method)

isolate_snps_of_interest_make_bed() (in module genome_integration.utils.plink_utils)

L

ld_from_geno_mat() (in module genome_integration.simulate_mr.geno_functions)

M

MaFile (class in genome_integration.utils.gcta_ma_utils) make_gcta_ma_header() (in module genome_integration.utils.gcta_cojo_utils) make_gcta_ma_line() (in module genome_integration.utils.gcta_cojo_utils) make_mr_link_design_matrix() (in module genome_integration.causal_inference.mr_link) make_non_overlapping_regions() (genome_integration.gene_regions.StartEndRegions method)

MaLine (class in genome_integration.utils.gcta_ma_utils) mask_instruments_in_ld() (in module genome_integration.causal_inference.mr_link) MendelianRandomization (class in genome_integration.causal_inference.mendelian_randomization) mr_link_ols() (in module genome_integration.causal_inference.mr_link) mr_link_ridge() (in module genome_integration.causal_inference.mr_link) mr_presso() (genome_integration.causal_inference.mendelian_randomization.MendelianRandomization method)

O

output_genotypes_to_bed_file() (genome_integration.utils.plink_utils.PlinkFile method)

P

plink_isolate_clump() (in module genome_integration.utils.plink_utils) PlinkFile (class in genome_integration.utils.plink_utils)

position_in_region() (genome_integration.gene_regions.StartEndRegion method) prune_for_a_list_of_snps() (genome_integration.utils.plink_utils.PlinkFile method) prune_for_a_region() (genome_integration.utils.plink_utils.PlinkFile method)

R

read_bed_file_into_numpy_array() (genome_integration.utils.plink_utils.PlinkFile method) read_bin_file() (in module genome_integration.association.binary_files) read_bin_file_region() (in module genome_integration.association.binary_files) read_geno_mat_plinkio() (in module genome_integration.simulate_mr.geno_functions)

read_newline_separated_file_into_list() (in module genome_integration.utils.file_utils) read_newline_separated_gz_file_into_list() (in module genome_integration.utils.file_utils) read_region_from_plink() (in module genome_integration.utils.plink_utils) remove_highly_correlated_snps() (in module genome_integration.causal_inference.mr_link) reset() (genome_integration.resources.enrichments.Enrich method)

S

Sample (class in genome_integration.samples) scale_geno_vec() (in module genome_integration.simulate_mr.geno_functions) score_and_assess_auc() (in module genome_integration.utils.plink_utils) score_individuals() (in module genome_integration.utils.plink_utils) set_p_val() (genome_integration.association.association_classes.Association method) set_pos_name() (genome_integration.variants.SNP method) set_wald_p_val() (genome_integration.association.association_classes.Association method) simulate_phenotypes() (in module genome_integration.simulate_mr.simulation_functions)

simulate_phenotypes_binary_outcome() (in module genome_integration.simulate_mr.simulation_functions) simulate_phenotypes_extended() (in module genome_integration.simulate_mr.simulation_functions) SNP (class in genome_integration.variants) snp_in_region() (genome_integration.gene_regions.StartEndRegion method) snp_names() (genome_integration.utils.gcta_ma_utils.MaFile method) snp_object_in_region() (genome_integration.gene_regions.StartEndRegion method) StartEndRegion (class in genome_integration.gene_regions) StartEndRegions (class in genome_integration.gene_regions)

T

turn_bin_into_plink_assoc() (in module genome_integration.association.binary_files)

turn_plink_assoc_into_bin() (in module genome_integration.association.binary_files) turn_plink_assoc_line_into_bin() (in module genome_integration.association.binary_files)

U

update_alleles() (genome_integration.variants.SNP method)

W

write_fdr_one_in_twenty_go_enrichments() (genome_integration.resources.enrichments.Enrich method)

write_list_to_newline_separated_file() (in module genome_integration.utils.file_utils) write_result() (genome_integration.utils.gcta_ma_utils.MaFile method)