# Model higher-order methylation profiles

## Documentation for package ‘BPRMeth’ version 1.4.0

- 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
boxplot_cluster_gex | Boxplot of clustered expression levels
BPRMeth | 'BPRMeth': Extracting higher order methylation features
bpr_cluster_wrap | Cluster methylation profiles
bpr_optim | Optimize BPR negative log likelihood function
bpr_optim.list | Optimize BPR negative log likelihood function
bpr_optim.matrix | Optimize BPR negative log likelihood function
bpr_optimise | Optimize BPR negative log likelihood function
bpr_optimize | Optimize BPR negative log likelihood function
bpr_predict_wrap | Predict gene expression from methylation profiles
create_basis | Create basis objects
create_methyl_region | Create methylation regions for each gene promoter.
create_polynomial_object | Create basis objects
create_prom_region | Create promoter regions from gene annotation data.
create_rbf_object | Create basis objects
eval_function | 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
gex_data | Synthetic data for mpgex package
meth_data | Synthetic data for BPRMeth package
plot_cluster_prof | Plot of clustered methylation profiles
plot_fitted_profiles | Plot the fit of methylation profiles across a region
plot_scatter_gex | Scatter plot of predicted vs measured gene expression levels
pool_bs_seq_rep | Read and pool replicates from BS-Seq data
predict_model_gex | Predict gene expression model from methylation profiles
preprocess_bs_seq | Pre-process BS-Seq data in any given format
preprocess_final_HTS_data | Pre-process final HTS data for downstream analysis
process_haib_caltech_wrap | Wrapper method for processing ENCODE HAIB and Caltech HTS data
read_bs_bismark_cov | Read Bismark Cov formatted BS-Seq file
read_bs_encode_haib | Read ENCODE HAIB bed formatted BS-Seq file
read_chrom_size | Read genome chromosome sizes file.
read_encode_cgi | Read file containing CpG island locations
read_rna_encode_caltech | Read ENCODE Caltech bed formatted RNA-Seq file
train_model_gex | Train gene expression model from methylation profiles