API for BPRMeth
Model higher-order methylation profiles
| Global functions | |
|---|---|
| .add_func | Source code |
| .bpr_EM | Source code |
| .bpr_EM_fast | Source code |
| .bpr_optim_fast | Source code |
| .calculate_errors | Source code |
| .cluster_profiles_mle_beta | Source code |
| .cluster_profiles_mle_bpr | Source code |
| .cluster_profiles_mle_gaussian | Source code |
| .cluster_profiles_vb_bpr | Source code |
| .cluster_profiles_vb_gaussian | Source code |
| .datatable.aware | Man page |
| .discard_bs_noise_reads | Source code |
| .discard_chr | Source code |
| .do_EM_checks | Source code |
| .do_centre_loc | Source code |
| .do_checks | Source code |
| .em_checks | Source code |
| .extract_fpkm | Source code |
| .extract_gene_name | Source code |
| .fourier_basis | Source code |
| .gg_theme | Source code |
| .gibbs_bpr | Source code |
| .infer_profiles_gibbs_bpr | Source code |
| .infer_profiles_gibbs_bpr.default | Source code |
| .infer_profiles_gibbs_bpr.list | Source code |
| .infer_profiles_gibbs_bpr.matrix | Source code |
| .infer_profiles_mle_beta | Source code |
| .infer_profiles_mle_beta.default | Source code |
| .infer_profiles_mle_beta.list | Source code |
| .infer_profiles_mle_beta.matrix | Source code |
| .infer_profiles_mle_bpr | Source code |
| .infer_profiles_mle_bpr.default | Source code |
| .infer_profiles_mle_bpr.list | Source code |
| .infer_profiles_mle_bpr.matrix | Source code |
| .infer_profiles_mle_gaussian | Source code |
| .infer_profiles_mle_gaussian.default | Source code |
| .infer_profiles_mle_gaussian.list | Source code |
| .infer_profiles_mle_gaussian.matrix | Source code |
| .infer_profiles_vb_bpr | Source code |
| .infer_profiles_vb_bpr.default | Source code |
| .infer_profiles_vb_bpr.list | Source code |
| .infer_profiles_vb_bpr.matrix | Source code |
| .infer_profiles_vb_gaussian | Source code |
| .infer_profiles_vb_gaussian.default | Source code |
| .infer_profiles_vb_gaussian.list | Source code |
| .infer_profiles_vb_gaussian.matrix | Source code |
| .inv_minmax_scaling | Source code |
| .log_sum_exp | Source code |
| .minmax_scaling | Source code |
| .old_bpr_gradient | Source code |
| .old_bpr_likelihood | Source code |
| .old_sum_weighted_bpr_grad | Source code |
| .old_sum_weighted_bpr_lik | Source code |
| .onLoad | Source code |
| .parallel_cores | Source code |
| .partition_data | Source code |
| .polynomial_basis | Source code |
| .predictive_cluster_profile | Source code |
| .predictive_infer_profile | Source code |
| .rbf_basis | Source code |
| .read_bs_bismark_cov | Source code |
| .update_Ez | Source code |
| BPRMeth | Man page |
| basis | Man page |
| bernoulli_data | Man page |
| beta_data | Man page |
| betareg_gradient | Man page Source code |
| betareg_log_likelihood | Man page Source code |
| binomial_data | Man page |
| boxplot_cluster_expr | Man page Source code |
| bpr_cluster_wrap | Man page Source code |
| bpr_gradient | Man page Source code |
| bpr_log_likelihood | Man page Source code |
| bpr_optim | Man page Source code |
| bpr_optim.default | Source code |
| bpr_optim.list | Man page Source code |
| bpr_optim.matrix | Man page Source code |
| bpr_optimise | Man page |
| bpr_optimize | Man page |
| bpr_predict_wrap | Man page Source code |
| cluster_mle | Man page |
| cluster_profile_mle | Man page |
| cluster_profile_vb | Man page |
| cluster_profiles_mle | Man page Source code |
| cluster_profiles_vb | Man page Source code |
| cluster_vb | Man page |
| create_anno_region | Man page Source code |
| create_basis | Man page |
| create_basis_function | Man page |
| create_fourier_object | Man page Source code |
| create_polynomial_object | Man page Source code |
| create_rbf_object | Man page Source code |
| create_region | Man page |
| create_region_obj | Man page |
| create_region_object | Man page Source code |
| des_mat | Man page |
| des_matrix | Man page |
| design_matrix | Man page Source code |
| design_matrix.default | Man page Source code |
| design_matrix.fourier | Man page Source code |
| design_matrix.polynomial | Man page Source code |
| design_matrix.rbf | Man page Source code |
| designmatrix | Man page |
| encode_expr | Man page |
| encode_met | Man page |
| eval_function | Man page Source code |
| eval_function.default | Source code |
| eval_function.fourier | Man page Source code |
| eval_function.polynomial | Man page Source code |
| eval_function.rbf | Man page Source code |
| eval_functions | Man page |
| eval_probit_function | Man page Source code |
| gaussian_data | Man page |
| genomic_region | Man page |
| gex_data | Man page |
| impute_bulk_met | Man page Source code |
| infer_profile_gibbs | Man page |
| infer_profile_mle | Man page |
| infer_profile_vb | Man page |
| infer_profiles_gibbs | Man page Source code |
| infer_profiles_mle | Man page Source code |
| infer_profiles_vb | Man page Source code |
| inference_gibbs | Man page |
| inference_mle | Man page |
| inference_vb | Man page |
| inner_predict_model_expr | Man page Source code |
| inner_train_model_expr | Man page Source code |
| lr_log_likelihood | Man page Source code |
| met_region | Man page |
| meth_data | Man page |
| model_likelihood | Man page |
| model_log_likelihood | Man page |
| obs_log_likelihood | Man page |
| obs_model_likelihood | Man page |
| old_boxplot_cluster_gex | Man page Source code |
| old_plot_cluster_prof | Man page Source code |
| old_plot_fitted_profiles | Man page Source code |
| partition_bulk_dataset | Man page Source code |
| plot_cluster_profiles | Man page Source code |
| plot_infer_profiles | Man page Source code |
| plot_predicted_expr | Man page Source code |
| pool_bs_seq_rep | Man page Source code |
| predict_expr | Man page Source code |
| preprocess_bs_seq | Man page Source code |
| preprocess_final_HTS_data | Man page Source code |
| process_haib_caltech_wrap | Man page Source code |
| read_anno | Man page Source code |
| read_bs_encode_haib | Man page Source code |
| read_chrom_size | Man page Source code |
| read_expr | Man page Source code |
| read_met | Man page Source code |
| read_rna_encode_caltech | Man page Source code |
| region_object | Man page |
| sum_weighted_betareg_grad | Man page Source code |
| sum_weighted_betareg_lik | Man page Source code |
| sum_weighted_bpr_grad | Man page Source code |
| sum_weighted_bpr_lik | Man page Source code |
