genal
Introduction
Installation
Tutorial
The Geno class
Clumping function
Extract and PRS functions
genal
Index
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
L
|
M
|
N
|
P
|
Q
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R
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S
|
U
|
W
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 method)
,
[1]
(genal.Geno.Geno method)
,
[1]
association_test_func() (in module genal.association)
B
beta_mode() (in module genal.MR)
bootstrap_mode() (in module genal.MR)
bootstrap_mode_iteration() (in module genal.MR)
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 attribute)
(genal.Geno.Geno attribute)
clump() (genal.Geno method)
,
[1]
(genal.Geno.Geno method)
,
[1]
clump_data() (in module genal.clump)
,
[1]
Combine_Geno() (in module genal.geno_tools)
copy() (genal.Geno method)
(genal.Geno.Geno method)
cpus (genal.Geno attribute)
(genal.Geno.Geno attribute)
create_bedlist() (in module genal.extract_prs)
create_tmp() (in module genal.tools)
D
data (genal.Geno attribute)
(genal.Geno.Geno attribute)
default_config() (in module genal.tools)
delete_tmp() (in module genal.tools)
df_mr_formatting() (in module genal.MR_tools)
E
extract_command_parallel() (in module genal.extract_prs)
extract_snps() (genal.Geno method)
(genal.Geno.Geno method)
extract_snps_from_combined_data() (in module genal.extract_prs)
extract_snps_from_split_data() (in module genal.extract_prs)
extract_snps_func() (in module genal.extract_prs)
,
[1]
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)
(class in genal.Geno)
get_plink19_path() (in module genal.tools)
get_reference_panel() (genal.Geno method)
(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)
L
lift() (genal.Geno method)
,
[1]
(genal.Geno.Geno method)
,
[1]
lift_coordinates_liftover() (in module genal.lift)
lift_coordinates_python() (in module genal.lift)
lift_data() (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_command_parallel() (in module genal.Geno)
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 method)
,
[1]
(genal.Geno.Geno method)
,
[1]
MR_data (genal.Geno attribute)
(genal.Geno.Geno attribute)
mr_egger_regression() (in module genal.MR)
mr_egger_regression_bootstrap() (in module genal.MR)
MR_forest() (genal.Geno method)
(genal.Geno.Geno method)
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_plot() (genal.Geno method)
(genal.Geno.Geno method)
mr_presso() (in module genal.MRpresso)
MR_results (genal.Geno attribute)
(genal.Geno.Geno attribute)
mr_sign() (in module genal.MR)
mr_simple_median() (in module genal.MR)
mr_simple_mode() (in module genal.MR)
mr_uwr() (in module genal.MR)
mr_weighted_median() (in module genal.MR)
mr_weighted_mode() (in module genal.MR)
MRpresso() (genal.Geno method)
,
[1]
(genal.Geno.Geno method)
,
[1]
mrpresso_func() (in module genal.MR_tools)
N
name (genal.Geno attribute)
(genal.Geno.Geno attribute)
P
parallel_bootstrap_func() (in module genal.MR)
parallel_RSS_LOO() (in module genal.MRpresso)
phenotype (genal.Geno attribute)
(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)
preprocess_data() (genal.Geno method)
,
[1]
(genal.Geno.Geno method)
,
[1]
prs() (genal.Geno method)
,
[1]
(genal.Geno.Geno method)
,
[1]
prs_func() (in module genal.extract_prs)
Q
query_outcome() (genal.Geno method)
,
[1]
(genal.Geno.Geno method)
,
[1]
query_outcome_func() (in module genal.MR_tools)
query_outcome_proxy() (in module genal.proxy)
R
ram (genal.Geno attribute)
(genal.Geno.Geno attribute)
read_config() (in module genal.tools)
reference_panel (genal.Geno attribute)
(genal.Geno.Geno attribute)
remove_na() (in module genal.geno_tools)
report_snps_not_found() (in module genal.extract_prs)
S
save() (genal.Geno method)
(genal.Geno.Geno method)
save_data() (in module genal.geno_tools)
set_phenotype() (genal.Geno method)
,
[1]
(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_genetic_path() (in module genal.tools)
sort_group() (genal.Geno method)
(genal.Geno.Geno method)
standardize() (genal.Geno method)
(genal.Geno.Geno method)
U
update_snpids() (genal.Geno method)
(genal.Geno.Geno method)
W
weighted_median() (in module genal.MR)
weighted_median_bootstrap() (in module genal.MR)
write_config() (in module genal.tools)