# Model higher-order methylation profiles

## Documentation for package ‘BPRMeth’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

BPRMeth-package | 'BPRMeth': Extracting higher order methylation features
.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