Man pages for andreaskapou/BPRMeth-devel
Model higher-order methylation profiles
| betareg_cluster_wrap | Cluster methylation profiles |
| betareg_model | Compute the Beta regression model |
| betareg_optimize | Optimize Beta regression negative log likelihood function |
| blr | Fitting linear models using Basis Functions |
| blr_cluster | Cluster methylation profiles with Gaussian noise |
| boxplot_cluster_gex | Boxplot of clustered expression levels |
| bpr_bayes | Gibbs sampling approach for the BPR model |
| bpr_bayes_predict_wrap | Predict gene expression from methylation profiles using Gibbs... |
| bpr_cluster_wrap | Cluster methylation profiles |
| bpr_diff_classify_wrap | Predict differential gene expression from differential... |
| bpr_diff_eval_predict_wrap | Predict differential gene expression from differential... |
| bpr_diff_predict_wrap | Predict differential gene expression from differential... |
| bpr_diff_test_data_wrap | Predict differential gene expression from differential... |
| bpr_diff_test_wrap | Perform likelihood ratio test between methylation samples |
| bpr_EM_fast | Cluster methylation profiles fast method |
| BPRMeth | 'BPRMeth-devel': Extracting higher order methylation features |
| bpr_model | Compute the BPR functions |
| 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_prom_region | Create promoter regions from gene annotation data. |
| design_matrix | Generic function for creating design matrices |
| eval_functions | Evaluate basis functions |
| gex_data | Synthetic data for mpgex package |
| lm_data | Synthetic data for BPRMeth 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.blr | Make predictions using the Basis Linear Model |
| predict_classification_model | Predict gene expression model from methylation profiles |
| 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 |
| print.blr | Print the output of the Basis Linear Model |
| print.summary.blr | Print summary output of the Basis Linear Model |
| process_bismark_beatson_wrap | Wrapper method for processing ENCODE HAIB and Caltech HTS... |
| process_haib_caltech_wrap | Wrapper method for processing ENCODE HAIB and Caltech HTS... |
| read_bs_bismark_cov | Read Bismark Cov formatted BS-Seq file |
| read_bs_encode_haib | Read ENCODE HAIB bed formatted BS-Seq file |
| read_bs_sc | Read Bismark Cov single cell formatted BS-Seq file |
| read_chrom_size | Read genome chromosome sizes file. |
| read_encode_cgi | Read file containing CpG island locations |
| read_rna_beatson | Read Beatson bed formatted RNA-Seq file |
| read_rna_encode_caltech | Read ENCODE Caltech bed formatted RNA-Seq file |
| sc_bayes_bpr_fdmm | Gibbs sampling algorithm for sc-Bayesian BPR finite mixture... |
| sc_bayes_bpr_fdmm_old | Gibbs sampling algorithm for sc-Bayesian BPR finite mixture... |
| sc_bpr_cluster_wrap | Cluster single cells based on methylation profiles |
| summary.blr | Summary output of the Basis Linear Model |
| train_classification_model | Train gene expression model from methylation profiles |
| train_model_gex | Train gene expression model from methylation profiles |
