Model higher-order methylation profiles

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Documentation for package ‘BPRMeth’ version 1.34.0

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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