Package index
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CCT_internal_horizontal() - Cauchy Combination Test accelerated
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FindMarkersPACS() - Differential test with PACS on Seurat object
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compare_models() - Use gLRT to compare two models and obtain p values
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compute_infor_mat_tilda() - compute_information matrix tilda
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estimate_label_default() - Estimate cell type label for new data
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estimate_label_no_cap_rate_all_pks() - Estimate cell type label for new data using all peaks as input
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estimate_parameters() - Estimate parameters for the full model
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estimate_parameters_null() - Estimate parameters for the null model
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infor_mat() - Information matrix – original without Firth prior
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irls_iter() - Iteratively reweighted least squares function (main function)
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irls_iter_nt() - Iteratively reweighted least squares function – newton methods
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irls_iter_nt_null() - Iteratively reweighted least squares function for null – newton method for the null model
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irls_iter_null() - Iteratively reweighted least squares function (main function) for the null model
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loss_firth_from_wii() - Compute loss function with Firth regularization from Wii matrix
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loss_fun() - Calculate Loss Function without Firth prior
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loss_fun_star() - Regularized log loss function
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loss_grad_pen() - Gradient of penalized loss ( Invariant prior)
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loss_gradient() - Gradient of loss function without Firth prior
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our_method_no_firth() - Internal evaluation use only – PACS Without Firth
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pacs_test_cumu() - likelihood ratio test with PACS – cumulative logit
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pacs_test_logit() - Profile likelihood ratio test with PACS
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pacs_test_sparse() - Profile likelihood ratio test with PACS