Model higher-order methylation profiles

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Documentation for package ‘BPRMeth’ version 1.4.0

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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