Index

Symbols

--activation posthoc-pal command line option --additive posthoc-simulate-pheno command line option --attribution posthoc-attribute command line option --covar posthoc-attribute command line option posthoc-baseline command line option posthoc-pal command line option --data-dropout posthoc-pal command line option --device posthoc-attribute command line option posthoc-pal command line option --dominant posthoc-simulate-pheno command line option --dropout posthoc-attribute command line option posthoc-pal command line option --epochs posthoc-attribute command line option posthoc-pal command line option --geno posthoc-attribute command line option posthoc-baseline command line option posthoc-pal command line option --heritability posthoc-simulate-pheno command line option --hidden-dims posthoc-attribute command line option posthoc-pal command line option --ig-baseline posthoc-attribute command line option posthoc-pal command line option --indep-pairwise posthoc-attribute command line option posthoc-baseline command line option posthoc-pal command line option --interaction2 posthoc-simulate-pheno command line option --interaction3 posthoc-simulate-pheno command line option --ld-r-threshold posthoc-pal command line option --ld-window posthoc-pal command line option --linear posthoc-attribute command line option posthoc-pal command line option posthoc-simulate-pheno command line option --logistic posthoc-attribute command line option posthoc-pal command line option posthoc-simulate-pheno command line option --lr posthoc-attribute command line option posthoc-pal command line option

--maf posthoc-attribute command line option posthoc-baseline command line option posthoc-pal command line option --model posthoc-attribute command line option posthoc-pal command line option --n-bootstrap posthoc-pal command line option --n-models posthoc-pal command line option --n-null-models posthoc-pal command line option --n-steps posthoc-attribute command line option posthoc-pal command line option --out posthoc-attribute command line option posthoc-pal command line option posthoc-simulate-pheno command line option --patience posthoc-attribute command line option posthoc-pal command line option --pfile posthoc-attribute command line option posthoc-baseline command line option posthoc-pal command line option posthoc-simulate-pheno command line option --pheno posthoc-attribute command line option posthoc-baseline command line option posthoc-pal command line option --pheno-name posthoc-attribute command line option posthoc-baseline command line option posthoc-pal command line option posthoc-simulate-pheno command line option --prevalence posthoc-simulate-pheno command line option --recessive posthoc-simulate-pheno command line option --recode-centered posthoc-simulate-pheno command line option --seed posthoc-attribute command line option posthoc-baseline command line option posthoc-pal command line option posthoc-simulate-pheno command line option --theta-percentile posthoc-pal command line option --val-fraction posthoc-attribute command line option posthoc-baseline command line option posthoc-pal command line option --verbose posthoc command line option --weight-decay posthoc-pal command line option

A

activation (posthoc.models.base.MLPConfig attribute) additive_effects (posthoc.simulation.base.PhenotypeModel attribute) additive_indices (posthoc.simulation.base.PhenotypeModel attribute) align_samples() (in module posthoc.io.pheno_covar_reader)

all_causal_indices() (posthoc.simulation.base.PhenotypeModel method) amas (posthoc.attribution.pal.PALResult attribute) apply_ld_pruning() (in module posthoc.qc.filters) as_pheno_df() (posthoc.simulation.base.SimulationResult method) AttributionResult (class in posthoc.attribution.integrated_gradients)

B

baseline (posthoc.attribution.integrated_gradients.IntegratedGradientsConfig attribute) batch_norm (posthoc.models.base.MLPConfig attribute) batch_size (posthoc.attribution.integrated_gradients.IntegratedGradientsConfig attribute) (posthoc.models.base.TrainConfig attribute)

best_val_loss (posthoc.models.base.TrainResult attribute) build_mlp() (in module posthoc.models.mlp)

C

causal_indices (posthoc.simulation.base.SimulationResult attribute) causal_variant_ids() (posthoc.simulation.base.SimulationResult method) compute_maf() (in module posthoc.qc.filters)

compute_missing_rate() (in module posthoc.qc.filters) compute_pal() (in module posthoc.attribution.pal) compute_pal_pvalues() (in module posthoc.attribution.significance)

D

data (posthoc.qc.filters.QCResult attribute) data_dropout (posthoc.models.base.MLPConfig attribute) device (posthoc.attribution.integrated_gradients.IntegratedGradientsConfig attribute) (posthoc.models.base.TrainConfig attribute)

dominant_effects (posthoc.simulation.base.PhenotypeModel attribute) dominant_indices (posthoc.simulation.base.PhenotypeModel attribute) dropout (posthoc.models.base.MLPConfig attribute)

E

element_counts (posthoc.attribution.pal.PALResult attribute)

F

filter_geno() (in module posthoc.qc.filters) filter_maf() (in module posthoc.qc.filters)

fit_null_halfnorm() (in module posthoc.attribution.significance) forward() (posthoc.models.mlp.MLP method)

G

genotype_data (posthoc.simulation.base.SimulationResult attribute) GenotypeData (class in posthoc.io.genotype_reader)

GenotypeDataset (class in posthoc.models.base) genotypes (posthoc.io.genotype_reader.GenotypeData attribute), [1] get_loss_fn() (in module posthoc.models.utils)

H

halfnorm_scale (posthoc.attribution.significance.SignificanceResult attribute)

heritability (posthoc.simulation.base.PhenotypeModel attribute) hidden_dims (posthoc.models.base.MLPConfig attribute)

I

importances (posthoc.attribution.integrated_gradients.AttributionResult attribute) indep_pairwise() (in module posthoc.qc.filters) integrated_gradients_importance() (in module posthoc.attribution.integrated_gradients) IntegratedGradientsConfig (class in posthoc.attribution.integrated_gradients)

interaction_effects (posthoc.simulation.base.PhenotypeModel attribute) interaction_pairs (posthoc.simulation.base.PhenotypeModel attribute) interaction_triple_effects (posthoc.simulation.base.PhenotypeModel attribute) interaction_triples (posthoc.simulation.base.PhenotypeModel attribute)

L

ld_r2_threshold (posthoc.attribution.pal.PALConfig attribute) ld_window (posthoc.attribution.pal.PALConfig attribute) liability (posthoc.simulation.base.SimulationResult attribute)

load_covar() (in module posthoc.io.pheno_covar_reader) load_pheno() (in module posthoc.io.pheno_covar_reader) lr (posthoc.models.base.TrainConfig attribute)

M

make_split() (in module posthoc.models.utils) max_epochs (posthoc.models.base.TrainConfig attribute) metadata (posthoc.simulation.base.SimulationResult attribute) method (posthoc.attribution.integrated_gradients.AttributionResult attribute) min_model_occurence (posthoc.attribution.pal.PALConfig attribute) MISSING_CODE (posthoc.models.base.GenotypeDataset attribute) MLP (class in posthoc.models.mlp) MLPConfig (class in posthoc.models.base) model (posthoc.models.base.TrainResult attribute) module posthoc.attribution.integrated_gradients posthoc.attribution.pal posthoc.attribution.significance posthoc.io.genotype_reader posthoc.io.pheno_covar_reader posthoc.io.writer posthoc.models.base posthoc.models.mlp posthoc.models.utils posthoc.qc.filters posthoc.simulation.base

mu (posthoc.attribution.pal.PALResult attribute)

N

n_bootstrap (posthoc.attribution.significance.SignificanceConfig attribute) n_dropped_geno (posthoc.qc.filters.QCResult attribute) n_dropped_ld (posthoc.qc.filters.QCResult attribute) n_dropped_maf (posthoc.qc.filters.QCResult attribute)

n_models (posthoc.attribution.pal.PALResult attribute) n_repeats (posthoc.attribution.integrated_gradients.AttributionResult attribute) n_samples (posthoc.io.genotype_reader.GenotypeData property) n_steps (posthoc.attribution.integrated_gradients.IntegratedGradientsConfig attribute) n_variants (posthoc.io.genotype_reader.GenotypeData property)

P

p_corrected (posthoc.attribution.integrated_gradients.AttributionResult attribute) p_values (posthoc.attribution.integrated_gradients.AttributionResult attribute) (posthoc.attribution.significance.SignificanceResult attribute) pal_amas (posthoc.attribution.pal.PALResult attribute) pal_common (posthoc.attribution.pal.PALResult attribute) PALConfig (class in posthoc.attribution.pal) PALResult (class in posthoc.attribution.pal) patience (posthoc.models.base.TrainConfig attribute) per_model_thetas (posthoc.attribution.pal.PALResult attribute) phenotype (posthoc.simulation.base.SimulationResult attribute) PhenotypeModel (class in posthoc.simulation.base) positions (posthoc.attribution.significance.SignificanceResult attribute) posthoc command line option --verbose posthoc-attribute command line option --attribution --covar --device --dropout --epochs --geno --hidden-dims --ig-baseline --indep-pairwise --linear --logistic --lr --maf --model --n-steps --out --patience --pfile --pheno --pheno-name --seed --val-fraction posthoc-baseline command line option --covar --geno --indep-pairwise --maf --pfile --pheno --pheno-name --seed --val-fraction posthoc-pal command line option --activation --covar --data-dropout --device --dropout --epochs --geno --hidden-dims --ig-baseline --indep-pairwise --ld-r-threshold --ld-window --linear --logistic --lr --maf --model --n-bootstrap --n-models --n-null-models --n-steps --out --patience --pfile --pheno --pheno-name --seed --theta-percentile --val-fraction --weight-decay

posthoc-simulate-pheno command line option --additive --dominant --heritability --interaction2 --interaction3 --linear --logistic --out --pfile --pheno-name --prevalence --recessive --recode-centered --seed posthoc.attribution.integrated_gradients module posthoc.attribution.pal module posthoc.attribution.significance module posthoc.io.genotype_reader module posthoc.io.pheno_covar_reader module posthoc.io.writer module posthoc.models.base module posthoc.models.mlp module posthoc.models.utils module posthoc.qc.filters module posthoc.simulation.base module prevalence (posthoc.simulation.base.PhenotypeModel attribute)

Q

QCResult (class in posthoc.qc.filters)

R

read_pgen() (in module posthoc.io.genotype_reader) recessive_effects (posthoc.simulation.base.PhenotypeModel attribute)

recessive_indices (posthoc.simulation.base.PhenotypeModel attribute) run_qc() (in module posthoc.qc.filters)

S

sample_ids (posthoc.io.genotype_reader.GenotypeData attribute), [1] (posthoc.simulation.base.SimulationResult property) seed (posthoc.attribution.integrated_gradients.IntegratedGradientsConfig attribute) (posthoc.attribution.significance.SignificanceConfig attribute) (posthoc.models.base.TrainConfig attribute) (posthoc.simulation.base.PhenotypeModel attribute) SignificanceConfig (class in posthoc.attribution.significance)

SignificanceResult (class in posthoc.attribution.significance) simulate() (in module posthoc.simulation.base) simulate_phenotype() (in module posthoc.simulation.base) SimulationResult (class in posthoc.simulation.base) stack_mas() (in module posthoc.attribution.pal) stopped_epoch (posthoc.models.base.TrainResult attribute) summary() (posthoc.qc.filters.QCResult method)

T

task (posthoc.attribution.integrated_gradients.IntegratedGradientsConfig attribute) (posthoc.models.base.TrainConfig attribute) (posthoc.simulation.base.PhenotypeModel attribute) theta (posthoc.attribution.pal.PALResult attribute) theta_percentile (posthoc.attribution.pal.PALConfig attribute)

train_idx (posthoc.models.base.TrainResult attribute) train_losses (posthoc.models.base.TrainResult attribute) train_model() (in module posthoc.models.utils) TrainConfig (class in posthoc.models.base) TrainResult (class in posthoc.models.base)

V

val_fraction (posthoc.models.base.TrainConfig attribute) val_idx (posthoc.models.base.TrainResult attribute)

val_losses (posthoc.models.base.TrainResult attribute) variant_df (posthoc.simulation.base.SimulationResult property) variant_ids (posthoc.io.genotype_reader.GenotypeData attribute), [1]

W

weight_decay (posthoc.models.base.TrainConfig attribute)

write_glm() (in module posthoc.io.writer) write_pal() (in module posthoc.io.writer)