Package: BPRMeth 1.31.0

Chantriolnt-Andreas Kapourani

BPRMeth: Model higher-order methylation profiles

The BPRMeth package is a probabilistic method to quantify explicit features of methylation profiles, in a way that would make it easier to formally use such profiles in downstream modelling efforts, such as predicting gene expression levels or clustering genomic regions or cells according to their methylation profiles.

Authors:Chantriolnt-Andreas Kapourani [aut, cre]

BPRMeth_1.31.0.tar.gz
BPRMeth_1.31.0.zip(r-4.5)BPRMeth_1.31.0.zip(r-4.4)BPRMeth_1.31.0.zip(r-4.3)
BPRMeth_1.31.0.tgz(r-4.4-arm64)BPRMeth_1.31.0.tgz(r-4.4-x86_64)BPRMeth_1.31.0.tgz(r-4.3-arm64)BPRMeth_1.31.0.tgz(r-4.3-x86_64)
BPRMeth_1.31.0.tar.gz(r-4.5-noble)BPRMeth_1.31.0.tar.gz(r-4.4-noble)
BPRMeth_1.31.0.tgz(r-4.4-emscripten)BPRMeth_1.31.0.tgz(r-4.3-emscripten)
BPRMeth.pdf |BPRMeth.html✨
BPRMeth/json (API)
NEWS

# Install 'BPRMeth' in R:
install.packages('BPRMeth', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:BPRMeth-1.31.0(bioc 3.20)BPRMeth-1.30.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

47 exports 1.16 score 87 dependencies 1 dependents 2 mentions

Last updated 2 months agofrom:b599e4fbb0

Exports:betareg_gradientbetareg_log_likelihoodboxplot_cluster_exprbpr_cluster_wrapbpr_gradientbpr_log_likelihoodbpr_optimbpr_predict_wrapcluster_profiles_mlecluster_profiles_vbcreate_anno_regioncreate_fourier_objectcreate_polynomial_objectcreate_rbf_objectcreate_region_objectdesign_matrixeval_functioneval_probit_functionimpute_bulk_metinfer_profiles_gibbsinfer_profiles_mleinfer_profiles_vbinner_predict_model_exprinner_train_model_exprlr_log_likelihoodold_boxplot_cluster_gexold_plot_cluster_profold_plot_fitted_profilespartition_bulk_datasetplot_cluster_profilesplot_infer_profilesplot_predicted_exprpool_bs_seq_reppredict_exprpreprocess_bs_seqpreprocess_final_HTS_dataprocess_haib_caltech_wrapread_annoread_bs_encode_haibread_chrom_sizeread_exprread_metread_rna_encode_caltechsum_weighted_betareg_gradsum_weighted_betareg_liksum_weighted_bpr_gradsum_weighted_bpr_lik

Dependencies:askpassassertthatbase64encBiocGenericsBiocManagerBiocStylebookdownbslibcachemclassclicodetoolscolorspacecowplotcurldata.tabledigestdoParallele1071earthevaluatefansifarverfastmapfontawesomeforeachFormulafsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhtmltoolshttrIRangesisobanditeratorsjquerylibjsonlitekernlabknitrlabelinglatticelifecyclemagrittrMASSMatrixmatrixcalcmemoisemgcvmimemunsellmvtnormnlmeopensslpillarpkgconfigplotmoplotrixproxyR6randomForestrappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownS4VectorssassscalessystibbletinytextruncnormUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioc

Modelling methylation profiles

Andreas C. Kapourani, Guido Sanguinetti

Rendered fromBPRMeth_vignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2020-06-10
Started: 2018-01-09

Readme and manuals

Help Manual

Help pageTopics
Synthetic Bernoulli databernoulli_data
Synthetic Beta databeta_data
Synthetic Binomial databinomial_data
Boxplot of clustered expression levelsboxplot_cluster_expr
(DEPRECATED) Cluster methylation profilesbpr_cluster_wrap
Compute observation model log-likelihoodbetareg_gradient betareg_log_likelihood bpr_gradient bpr_log_likelihood lr_log_likelihood model_likelihood model_log_likelihood obs_log_likelihood obs_model_likelihood sum_weighted_betareg_grad sum_weighted_betareg_lik sum_weighted_bpr_grad sum_weighted_bpr_lik
(DEPRECATED) Optimize BPR negative log likelihood functionbpr_optim bpr_optim.list bpr_optim.matrix bpr_optimise bpr_optimize
(DEPRECATED) Predict gene expression from methylation profilesbpr_predict_wrap
'BPRMeth': Extracting higher order methylation features.datatable.aware BPRMeth
Cluster methylation profiles using EMcluster_mle cluster_profiles_mle cluster_profile_mle
Cluster methylation profiles using VBcluster_profiles_vb cluster_profile_vb cluster_vb
Create annotation regionscreate_anno_region
Create basis objectsbasis create_basis create_basis_function create_fourier_object create_polynomial_object create_rbf_object
Create genomic region datacreate_region create_region_obj create_region_object genomic_region met_region region_object
Generic function for creating design matricesdesignmatrix design_matrix design_matrix.default design_matrix.fourier design_matrix.polynomial design_matrix.rbf des_mat des_matrix
Processed ENCODE expression dataencode_expr
Processed ENCODE methylation dataencode_met
Evaluate basis functionseval_function eval_function.fourier eval_function.polynomial eval_function.rbf eval_functions eval_probit_function
Synthetic Gaussian datagaussian_data
Synthetic expression datagex_data
Impute/predict bulk methylation statesimpute_bulk_met
Infer methylation profiles using Gibbs samplinginference_gibbs infer_profiles_gibbs infer_profile_gibbs
Infer methylation profiles using MLEinference_mle infer_profiles_mle infer_profile_mle
Infer methylation profiles using VBinference_vb infer_profiles_vb infer_profile_vb
(INNER) Predict expressioninner_predict_model_expr
(INNER) Train expression model from methylation profilesinner_train_model_expr
Synthetic bulk methylation datameth_data
(DEPRECATED) Boxplot of clustered expression levelsold_boxplot_cluster_gex
(DEPRECATED) Plot of clustered methylation profilesold_plot_cluster_prof
(DEPRECATED) Plot the fit of methylation profiles across a regionold_plot_fitted_profiles
Partition bulk methylation dataset to training and test setpartition_bulk_dataset
Plot clustered methylation profiles across a regionplot_cluster_profiles
Plot inferred methylation profiles across a regionplot_infer_profiles
Scatter plot of predicted vs measured gene expression levelsplot_predicted_expr
(DEPRECATED) Read and pool replicates from BS-Seq datapool_bs_seq_rep
Predict gene expression from methylation profilespredict_expr
(DEPRECATED) Pre-process BS-Seq data in any given formatpreprocess_bs_seq
(DEPRECATED) Pre-process final HTS data for downstream analysispreprocess_final_HTS_data
(DEPRECATED) Wrapper for processing ENCODE HAIB and Caltech HTSprocess_haib_caltech_wrap
Read annotation fileread_anno
(DEPRECATED) Read ENCODE HAIB bed formatted BS-Seq fileread_bs_encode_haib
Read genome chromosome sizes fileread_chrom_size
Read expression data fileread_expr
Read methylation fileread_met
(DEPRECATED) Read ENCODE Caltech bed formatted RNA-Seq fileread_rna_encode_caltech