API reference

This reference documents all public modules included in seak meant for general usage, except for plotting functionalities. It details their respective objects, functions, and methods.

• seak
  • The construct_background_kernel module
    • GRMLoaderSnpReader
      • GRMLoaderSnpReader.compute_background_kernel()
      • GRMLoaderSnpReader.get_iids()
      • GRMLoaderSnpReader.update_individuals()
      • GRMLoaderSnpReader.write_kernel()
    • GRMLoader_from_file
  • The data_loaders module
    • AnnotationLoader
      • AnnotationLoader.anno_by_id()
      • AnnotationLoader.get_vids()
      • AnnotationLoader.update_variants()
    • BEDRegionLoader
      • BEDRegionLoader.regions
    • CovariatesLoader
      • CovariatesLoader.get_iids()
      • CovariatesLoader.update_individuals()
    • CovariatesLoaderCSV
      • CovariatesLoaderCSV.cov
      • CovariatesLoaderCSV.covariate_column_names
      • CovariatesLoaderCSV.get_iids()
      • CovariatesLoaderCSV.get_one_hot_covariates_and_phenotype()
      • CovariatesLoaderCSV.phenotype_of_interest
      • CovariatesLoaderCSV.update_individuals()
    • EnsemblVEPLoader
      • EnsemblVEPLoader.anno_by_id()
      • EnsemblVEPLoader.anno_by_interval()
      • EnsemblVEPLoader.get_vids()
      • EnsemblVEPLoader.pos_df
      • EnsemblVEPLoader.update_variants()
      • EnsemblVEPLoader.vep_df
    • Hdf5Loader
      • Hdf5Loader.anno_by_id()
      • Hdf5Loader.from_janggu
      • Hdf5Loader.get_vids()
      • Hdf5Loader.set_mask()
      • Hdf5Loader.update_variants()
      • Hdf5Loader.veps
      • Hdf5Loader.veps_index_df
    • RegionLoader
    • VariantLoader
      • VariantLoader.center()
      • VariantLoader.genotypes_by_id()
      • VariantLoader.genotypes_by_region()
      • VariantLoader.get_iids()
      • VariantLoader.get_vids()
      • VariantLoader.mean_imputation()
      • VariantLoader.preprocess_genotypes()
      • VariantLoader.scale()
      • VariantLoader.standardize()
      • VariantLoader.update_individuals()
      • VariantLoader.update_variants()
    • VariantLoaderSnpReader
      • VariantLoaderSnpReader.bed
      • VariantLoaderSnpReader.genotypes_by_id()
      • VariantLoaderSnpReader.genotypes_by_region()
      • VariantLoaderSnpReader.get_iids()
      • VariantLoaderSnpReader.get_vids()
      • VariantLoaderSnpReader.iid_fid
      • VariantLoaderSnpReader.update_individuals()
      • VariantLoaderSnpReader.update_variants()
    • intersect_and_update_datasets()
    • intersect_ids()
  • The kernels module
    • LocalCollapsing
      • LocalCollapsing.collapse()
    • diffscore_max()
    • linear()
    • linear_weighted()
    • single_column_kernel()
  • The lrt module
    • LRTnoK
      • LRTnoK.altmodel()
      • LRTnoK.pv_5050()
      • LRTnoK.pv_sim()
      • LRTnoK.pv_sim_chi2()
    • RLRTSim()
    • chi2mixture
      • chi2mixture.abserr
      • chi2mixture.alteqnull
      • chi2mixture.dof
      • chi2mixture.dofmax
      • chi2mixture.dofmin
      • chi2mixture.fit_params_Qreg()
      • chi2mixture.fit_scale_logP()
      • chi2mixture.fitdof
      • chi2mixture.imax
      • chi2mixture.isortlrt
      • chi2mixture.lrt
      • chi2mixture.lrtsort
      • chi2mixture.mixture
      • chi2mixture.qmax
      • chi2mixture.qnulllrtsort
      • chi2mixture.scale
      • chi2mixture.scale_dof_obj()
      • chi2mixture.scalemax
      • chi2mixture.scalemin
      • chi2mixture.tol
    • estimate_pointmass0_null()
    • fit_chi2_maximum_likelihood()
    • fit_chi2_moment_matching()
    • fit_chi2mixture()
    • make_lambdagrid()
    • pv_chi2mixture()
    • rlrsim()
    • rlrsim_loop()
    • rlrsim_np()
  • The scoretest module
    • DaviesError
    • Scoretest
      • Scoretest.D
      • Scoretest.N
      • Scoretest.Neff
      • Scoretest.P
      • Scoretest.X
      • Scoretest.Y
      • Scoretest.has_bias()
      • Scoretest.pv_alt_model()
    • Scoretest2K
      • Scoretest2K.G0
      • Scoretest2K.K0
      • Scoretest2K.S
      • Scoretest2K.U
      • Scoretest2K.UUY
      • Scoretest2K.UY
      • Scoretest2K.Xdagger
      • Scoretest2K.YUUY
      • Scoretest2K.lowrank
      • Scoretest2K.optparams
      • Scoretest2K.sigma2e
      • Scoretest2K.sigma2g
    • ScoretestLogit
      • ScoretestLogit.VX
      • ScoretestLogit.pY
      • ScoretestLogit.pinvVX
      • ScoretestLogit.stdY
    • ScoretestNoK
      • ScoretestNoK.RxY
      • ScoretestNoK.Xdagger
      • ScoretestNoK.coef()
      • ScoretestNoK.sigma2