Index

A

abserr (seak.lrt.chi2mixture attribute) alteqnull (seak.lrt.chi2mixture attribute) altmodel() (seak.lrt.LRTnoK method) anno_by_id() (seak.data_loaders.AnnotationLoader method) (seak.data_loaders.EnsemblVEPLoader method) (seak.data_loaders.Hdf5Loader method)

anno_by_interval() (seak.data_loaders.EnsemblVEPLoader method) AnnotationLoader (class in seak.data_loaders)

B

bed (seak.data_loaders.VariantLoaderSnpReader attribute)

BEDRegionLoader (class in seak.data_loaders)

C

center() (seak.data_loaders.VariantLoader static method) chi2mixture (class in seak.lrt) coef() (seak.scoretest.ScoretestNoK method) collapse() (seak.kernels.LocalCollapsing method)

compute_background_kernel() (seak.construct_background_kernel.GRMLoaderSnpReader method) cov (seak.data_loaders.CovariatesLoaderCSV attribute) covariate_column_names (seak.data_loaders.CovariatesLoaderCSV attribute) CovariatesLoader (class in seak.data_loaders) CovariatesLoaderCSV (class in seak.data_loaders)

D

D (seak.scoretest.Scoretest attribute) DaviesError diffscore_max() (in module seak.kernels)

dof (seak.lrt.chi2mixture attribute) dofmax (seak.lrt.chi2mixture attribute) dofmin (seak.lrt.chi2mixture attribute)

E

EnsemblVEPLoader (class in seak.data_loaders)

estimate_pointmass0_null() (in module seak.lrt)

F

fit_chi2_maximum_likelihood() (in module seak.lrt) fit_chi2_moment_matching() (in module seak.lrt) fit_chi2mixture() (in module seak.lrt)

fit_params_Qreg() (seak.lrt.chi2mixture method) fit_scale_logP() (seak.lrt.chi2mixture method) fitdof (seak.lrt.chi2mixture attribute) from_janggu (seak.data_loaders.Hdf5Loader attribute)

G

G0 (seak.scoretest.Scoretest2K attribute) genotypes_by_id() (seak.data_loaders.VariantLoader method) (seak.data_loaders.VariantLoaderSnpReader method) genotypes_by_region() (seak.data_loaders.VariantLoader method) (seak.data_loaders.VariantLoaderSnpReader method) get_iids() (seak.construct_background_kernel.GRMLoaderSnpReader method) (seak.data_loaders.CovariatesLoader method) (seak.data_loaders.CovariatesLoaderCSV method) (seak.data_loaders.VariantLoader method) (seak.data_loaders.VariantLoaderSnpReader method)

get_one_hot_covariates_and_phenotype() (seak.data_loaders.CovariatesLoaderCSV method) get_vids() (seak.data_loaders.AnnotationLoader method) (seak.data_loaders.EnsemblVEPLoader method) (seak.data_loaders.Hdf5Loader method) (seak.data_loaders.VariantLoader method) (seak.data_loaders.VariantLoaderSnpReader method) GRMLoader_from_file (class in seak.construct_background_kernel) GRMLoaderSnpReader (class in seak.construct_background_kernel)

H

has_bias() (seak.scoretest.Scoretest static method)

Hdf5Loader (class in seak.data_loaders)

I

iid_fid (seak.data_loaders.VariantLoaderSnpReader attribute) imax (seak.lrt.chi2mixture attribute)

intersect_and_update_datasets() (in module seak.data_loaders) intersect_ids() (in module seak.data_loaders) isortlrt (seak.lrt.chi2mixture attribute)

K

K0 (seak.scoretest.Scoretest2K attribute)

L

linear() (in module seak.kernels) linear_weighted() (in module seak.kernels) LocalCollapsing (class in seak.kernels)

lowrank (seak.scoretest.Scoretest2K attribute) lrt (seak.lrt.chi2mixture attribute) LRTnoK (class in seak.lrt) lrtsort (seak.lrt.chi2mixture attribute)

M

make_lambdagrid() (in module seak.lrt) mean_imputation() (seak.data_loaders.VariantLoader static method) mixture (seak.lrt.chi2mixture attribute) module seak seak.construct_background_kernel seak.data_loaders seak.kernels seak.lrt seak.scoretest

N

N (seak.scoretest.Scoretest attribute)

Neff (seak.scoretest.Scoretest attribute)

O

optparams (seak.scoretest.Scoretest2K attribute)

P

P (seak.scoretest.Scoretest attribute) phenotype_of_interest (seak.data_loaders.CovariatesLoaderCSV attribute) pinvVX (seak.scoretest.ScoretestLogit attribute) pos_df (seak.data_loaders.EnsemblVEPLoader attribute) preprocess_genotypes() (seak.data_loaders.VariantLoader static method)

pv_5050() (seak.lrt.LRTnoK method) pv_alt_model() (seak.scoretest.Scoretest method) pv_chi2mixture() (in module seak.lrt) pv_sim() (seak.lrt.LRTnoK method) pv_sim_chi2() (seak.lrt.LRTnoK method) pY (seak.scoretest.ScoretestLogit attribute)

Q

qmax (seak.lrt.chi2mixture attribute)

qnulllrtsort (seak.lrt.chi2mixture attribute)

R

RegionLoader (class in seak.data_loaders) regions (seak.data_loaders.BEDRegionLoader attribute) rlrsim() (in module seak.lrt)

rlrsim_loop() (in module seak.lrt) rlrsim_np() (in module seak.lrt) RLRTSim() (in module seak.lrt) RxY (seak.scoretest.ScoretestNoK attribute)

S

S (seak.scoretest.Scoretest2K attribute) scale (seak.lrt.chi2mixture attribute) scale() (seak.data_loaders.VariantLoader static method) scale_dof_obj() (seak.lrt.chi2mixture method) scalemax (seak.lrt.chi2mixture attribute) scalemin (seak.lrt.chi2mixture attribute) Scoretest (class in seak.scoretest) Scoretest2K (class in seak.scoretest) ScoretestLogit (class in seak.scoretest) ScoretestNoK (class in seak.scoretest) seak module seak.construct_background_kernel module

seak.data_loaders module seak.kernels module seak.lrt module seak.scoretest module set_mask() (seak.data_loaders.Hdf5Loader method) sigma2 (seak.scoretest.ScoretestNoK attribute) sigma2e (seak.scoretest.Scoretest2K attribute) sigma2g (seak.scoretest.Scoretest2K attribute) single_column_kernel() (in module seak.kernels) standardize() (seak.data_loaders.VariantLoader static method) stdY (seak.scoretest.ScoretestLogit attribute)

T

tol (seak.lrt.chi2mixture attribute)

U

U (seak.scoretest.Scoretest2K attribute) update_individuals() (seak.construct_background_kernel.GRMLoaderSnpReader method) (seak.data_loaders.CovariatesLoader method) (seak.data_loaders.CovariatesLoaderCSV method) (seak.data_loaders.VariantLoader method) (seak.data_loaders.VariantLoaderSnpReader method)

update_variants() (seak.data_loaders.AnnotationLoader method) (seak.data_loaders.EnsemblVEPLoader method) (seak.data_loaders.Hdf5Loader method) (seak.data_loaders.VariantLoader method) (seak.data_loaders.VariantLoaderSnpReader method) UUY (seak.scoretest.Scoretest2K attribute) UY (seak.scoretest.Scoretest2K attribute)

V

VariantLoader (class in seak.data_loaders) VariantLoaderSnpReader (class in seak.data_loaders) vep_df (seak.data_loaders.EnsemblVEPLoader attribute)

veps (seak.data_loaders.Hdf5Loader attribute) veps_index_df (seak.data_loaders.Hdf5Loader attribute) VX (seak.scoretest.ScoretestLogit attribute)

W

write_kernel() (seak.construct_background_kernel.GRMLoaderSnpReader method)

X

X (seak.scoretest.Scoretest attribute)

Xdagger (seak.scoretest.Scoretest2K attribute) (seak.scoretest.ScoretestNoK attribute)

Y

Y (seak.scoretest.Scoretest attribute)

YUUY (seak.scoretest.Scoretest2K attribute)