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| .datatable.aware | 'BPRMeth': Extracting higher order methylation features |
| basis | Create basis objects |
| bernoulli_data | Synthetic Bernoulli data |
| betareg_gradient | Compute observation model log-likelihood |
| betareg_log_likelihood | Compute observation model log-likelihood |
| beta_data | Synthetic Beta data |
| binomial_data | Synthetic Binomial data |
| boxplot_cluster_expr | Boxplot of clustered expression levels |
| BPRMeth | 'BPRMeth': Extracting higher order methylation features |
| bpr_cluster_wrap | (DEPRECATED) Cluster methylation profiles |
| bpr_gradient | Compute observation model log-likelihood |
| bpr_log_likelihood | Compute observation model log-likelihood |
| bpr_optim | (DEPRECATED) Optimize BPR negative log likelihood function |
| bpr_optim.list | (DEPRECATED) Optimize BPR negative log likelihood function |
| bpr_optim.matrix | (DEPRECATED) Optimize BPR negative log likelihood function |
| bpr_optimise | (DEPRECATED) Optimize BPR negative log likelihood function |
| bpr_optimize | (DEPRECATED) Optimize BPR negative log likelihood function |
| bpr_predict_wrap | (DEPRECATED) Predict gene expression from methylation profiles |
| cluster_mle | Cluster methylation profiles using EM |
| cluster_profiles_mle | Cluster methylation profiles using EM |
| cluster_profiles_vb | Cluster methylation profiles using VB |
| cluster_profile_mle | Cluster methylation profiles using EM |
| cluster_profile_vb | Cluster methylation profiles using VB |
| cluster_vb | Cluster methylation profiles using VB |
| create_anno_region | Create annotation regions |
| create_basis | Create basis objects |
| create_basis_function | Create basis objects |
| create_fourier_object | Create basis objects |
| create_polynomial_object | Create basis objects |
| create_rbf_object | Create basis objects |
| create_region | Create genomic region data |
| create_region_obj | Create genomic region data |
| create_region_object | Create genomic region data |
| designmatrix | Generic function for creating design matrices |
| design_matrix | Generic function for creating design matrices |
| design_matrix.default | Generic function for creating design matrices |
| design_matrix.fourier | Generic function for creating design matrices |
| design_matrix.polynomial | Generic function for creating design matrices |
| design_matrix.rbf | Generic function for creating design matrices |
| des_mat | Generic function for creating design matrices |
| des_matrix | Generic function for creating design matrices |
| encode_expr | Processed ENCODE expression data |
| encode_met | Processed ENCODE methylation data |
| eval_function | Evaluate basis functions |
| eval_function.fourier | Evaluate basis functions |
| eval_function.polynomial | Evaluate basis functions |
| eval_function.rbf | Evaluate basis functions |
| eval_functions | Evaluate basis functions |
| eval_probit_function | Evaluate basis functions |
| gaussian_data | Synthetic Gaussian data |
| genomic_region | Create genomic region data |
| gex_data | Synthetic expression data |
| impute_bulk_met | Impute/predict bulk methylation states |
| inference_gibbs | Infer methylation profiles using Gibbs sampling |
| inference_mle | Infer methylation profiles using MLE |
| inference_vb | Infer methylation profiles using VB |
| infer_profiles_gibbs | Infer methylation profiles using Gibbs sampling |
| infer_profiles_mle | Infer methylation profiles using MLE |
| infer_profiles_vb | Infer methylation profiles using VB |
| infer_profile_gibbs | Infer methylation profiles using Gibbs sampling |
| infer_profile_mle | Infer methylation profiles using MLE |
| infer_profile_vb | Infer methylation profiles using VB |
| inner_predict_model_expr | (INNER) Predict expression |
| inner_train_model_expr | (INNER) Train expression model from methylation profiles |
| lr_log_likelihood | Compute observation model log-likelihood |
| meth_data | Synthetic bulk methylation data |
| met_region | Create genomic region data |
| model_likelihood | Compute observation model log-likelihood |
| model_log_likelihood | Compute observation model log-likelihood |
| obs_log_likelihood | Compute observation model log-likelihood |
| obs_model_likelihood | Compute observation model log-likelihood |
| old_boxplot_cluster_gex | (DEPRECATED) Boxplot of clustered expression levels |
| old_plot_cluster_prof | (DEPRECATED) Plot of clustered methylation profiles |
| old_plot_fitted_profiles | (DEPRECATED) Plot the fit of methylation profiles across a region |
| partition_bulk_dataset | Partition bulk methylation dataset to training and test set |
| plot_cluster_profiles | Plot clustered methylation profiles across a region |
| plot_infer_profiles | Plot inferred methylation profiles across a region |
| plot_predicted_expr | Scatter plot of predicted vs measured gene expression levels |
| pool_bs_seq_rep | (DEPRECATED) Read and pool replicates from BS-Seq data |
| predict_expr | Predict gene expression from methylation profiles |
| preprocess_bs_seq | (DEPRECATED) Pre-process BS-Seq data in any given format |
| preprocess_final_HTS_data | (DEPRECATED) Pre-process final HTS data for downstream analysis |
| process_haib_caltech_wrap | (DEPRECATED) Wrapper for processing ENCODE HAIB and Caltech HTS |
| read_anno | Read annotation file |
| read_bs_encode_haib | (DEPRECATED) Read ENCODE HAIB bed formatted BS-Seq file |
| read_chrom_size | Read genome chromosome sizes file |
| read_expr | Read expression data file |
| read_met | Read methylation file |
| read_rna_encode_caltech | (DEPRECATED) Read ENCODE Caltech bed formatted RNA-Seq file |
| region_object | Create genomic region data |
| sum_weighted_betareg_grad | Compute observation model log-likelihood |
| sum_weighted_betareg_lik | Compute observation model log-likelihood |
| sum_weighted_bpr_grad | Compute observation model log-likelihood |
| sum_weighted_bpr_lik | Compute observation model log-likelihood |