Index

A

adjust_column_names() (in module genal.geno_tools) apply_action_2() (in module genal.MR_tools)

apply_proxies() (in module genal.proxy) association_test() (genal.GENO.GENO method), [1] association_test_func() (in module genal.association)

C

check_allele_column() (in module genal.geno_tools) check_arguments() (in module genal.geno_tools) check_beta_column() (in module genal.geno_tools) check_bfiles() (in module genal.tools) check_int_column() (in module genal.geno_tools) check_p_column() (in module genal.geno_tools) check_required_columns() (in module genal.MR_tools)

check_snp_column() (in module genal.geno_tools) checks (genal.GENO.GENO attribute) clump() (genal.GENO.GENO method), [1] clump_data() (in module genal.clump) Combine_GENO() (in module genal.geno_tools) copy() (genal.GENO.GENO method) cpus (genal.GENO.GENO attribute), [1] create_bedlist() (in module genal.extract_prs)

D

data (genal.GENO.GENO attribute) data_clumped (genal.GENO.GENO attribute), [1]

default_config() (in module genal.tools) delete_tmp() (in module genal.geno_tools)

E

extract_command_parallel() (in module genal.extract_prs) extract_snps() (genal.GENO.GENO method)

extract_snps_from_combined_data() (in module genal.extract_prs) extract_snps_func() (in module genal.extract_prs)

F

fill_coordinates_func() (in module genal.geno_tools) fill_ea_nea() (in module genal.geno_tools) fill_nea() (in module genal.geno_tools)

fill_se_p() (in module genal.geno_tools) fill_snpids_func() (in module genal.geno_tools) find_proxies() (in module genal.proxy) flip_alleles() (in module genal.MR_tools)

G

genal module genal.association module genal.clump module genal.extract_prs module genal.GENO module genal.geno_tools module genal.lift module genal.MR module

genal.MR_tools module genal.MRpresso module genal.proxy module genal.tools module GENO (class in genal.GENO) get_plink19_path() (in module genal.tools) get_reference_panel() (genal.GENO.GENO method) get_reference_panel_path() (in module genal.tools) getRandomData() (in module genal.MRpresso) getRSS_LOO() (in module genal.MRpresso)

H

handle_multiallelic_variants() (in module genal.extract_prs)

harmonize_MR() (in module genal.MR_tools)

I

init_attributes() (genal.GENO.GENO method)

L

lift() (genal.GENO.GENO method), [1] lift_coordinates() (in module genal.lift) lift_data() (in module genal.lift) lift_data_liftover() (in module genal.lift)

linreg() (in module genal.MR) load_outcome_from_filepath() (in module genal.MR_tools) load_outcome_from_geno_object() (in module genal.MR_tools) load_reference_panel() (in module genal.tools)

M

merge_extracted_snps() (in module genal.extract_prs) module genal genal.association genal.clump genal.extract_prs genal.GENO genal.geno_tools genal.lift genal.MR genal.MR_tools genal.MRpresso genal.proxy genal.tools MR() (genal.GENO.GENO method), [1]

MR_data (genal.GENO.GENO attribute) mr_egger_regression() (in module genal.MR) mr_egger_regression_bootstrap() (in module genal.MR) MR_func() (in module genal.MR_tools) mr_ivw() (in module genal.MR) mr_ivw_fe() (in module genal.MR) mr_ivw_re() (in module genal.MR) mr_pen_wm() (in module genal.MR) mr_presso() (in module genal.MRpresso) mr_sign() (in module genal.MR) mr_simple_median() (in module genal.MR) mr_uwr() (in module genal.MR) mr_weighted_median() (in module genal.MR) MRpresso() (genal.GENO.GENO method), [1] mrpresso_func() (in module genal.MR_tools)

N

name (genal.GENO.GENO attribute), [1]

O

outcome (genal.GENO.GENO attribute)

P

parallel_bootstrap_func() (in module genal.MR) parallel_RSS_LOO() (in module genal.MRpresso) phenotype (genal.GENO.GENO attribute) post_lift_operations() (in module genal.lift) power_eigen() (in module genal.MRpresso)

prepare_chain_file() (in module genal.lift) prepare_snp_list() (in module genal.extract_prs) process_split_data() (in module genal.extract_prs) prs() (genal.GENO.GENO method), [1] prs_func() (in module genal.extract_prs)

Q

query_outcome() (genal.GENO.GENO method), [1]

query_outcome_func() (in module genal.MR_tools) query_outcome_proxy() (in module genal.proxy)

R

ram (genal.GENO.GENO attribute), [1] read_config() (in module genal.tools)

reference_panel (genal.GENO.GENO attribute) remove_na() (in module genal.geno_tools) report_snps_not_found() (in module genal.extract_prs)

S

save() (genal.GENO.GENO method) save_data() (in module genal.geno_tools) set_phenotype() (genal.GENO.GENO method), [1] set_phenotype_func() (in module genal.association)

set_plink() (in module genal.tools) set_reference_folder() (in module genal.tools) setup_path() (in module genal.extract_prs) sort_group() (genal.GENO.GENO method) standardize() (genal.GENO.GENO method)

W

weighted_median() (in module genal.MR)

weighted_median_bootstrap() (in module genal.MR) write_config() (in module genal.tools)