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 |