Index

A | B | C | D | E | F | G | I | L | M | P | Q | R | S | V

A

additive_gwas()
- built-in function

apply_alpha() (EDGEAnalysis method)
attach_pcs_to_phenotype()
- built-in function

B

built-in function

C

calculate_alpha() (EDGEAnalysis method)
calculate_grm_gcta()
- built-in function
calculate_hwe_pvalues()
- built-in function
calculate_pca_pcair()
- built-in function
calculate_pca_plink()
- built-in function

calculate_pca_sklearn()
- built-in function
check_case_control_balance()
- built-in function
create_summary_report()
- built-in function
cross_validated_edge_analysis()
- built-in function

D

download_test_files()
- built-in function

E

EDGEAnalysis (built-in class)

F

filter_genotype_data()
- built-in function
filter_related_samples()
- built-in function
filter_samples_by_call_rate()
- built-in function
filter_variants_by_hwe()
- built-in function

filter_variants_by_maf()
- built-in function
filter_variants_by_missing()
- built-in function
format_gwas_output_for_locuszoom()
- built-in function

G

get_pc_covariate_list()
- built-in function

get_skipped_snps() (EDGEAnalysis method)

I

identify_related_samples()
- built-in function

impute_covariates()
- built-in function

L

load_alpha_values()
- built-in function
load_bgen_data()
- built-in function
load_grm_gcta()
- built-in function

load_pgen_data()
- built-in function
load_plink_data()
- built-in function
load_vcf_data()
- built-in function

M

manhattan_plot()
- built-in function

P

plot_alpha_distribution()
- built-in function

prepare_phenotype_data()
- built-in function

Q

qq_plot()
- built-in function

R

run_full_analysis() (EDGEAnalysis method)

S

save_for_locuszoom()
- built-in function
save_results()
- built-in function

standard_gwas()
- built-in function
stratified_train_test_split()
- built-in function

V

validate_and_align_data()
- built-in function
validate_and_fix_encoding()
- built-in function
validate_genotype_df()
- built-in function

validate_locuszoom_format()
- built-in function
validate_phenotype_df()
- built-in function