Package: BPRMeth 1.33.0

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_1.33.0.tar.gz
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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'))

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

bernoulli_data - Synthetic Bernoulli data
beta_data - Synthetic Beta data
binomial_data - Synthetic Binomial data
encode_expr - Processed ENCODE expression data
encode_met - Processed ENCODE methylation data
gaussian_data - Synthetic Gaussian data
gex_data - Synthetic expression data
meth_data - Synthetic bulk methylation data

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.

immunooncology dnamethylation geneexpression generegulation epigenetics genetics clustering featureextraction regression rnaseq bayesian kegg sequencing coverage singlecell

5.45 score 1 packages 94 scripts 230 downloads 47 exports 87 dependencies

Last updated 21 days agofrom:5371378b7a. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win-x86_64	NOTE	Oct 30 2024
R-4.5-linux-x86_64	NOTE	Oct 30 2024
R-4.4-win-x86_64	NOTE	Oct 30 2024
R-4.4-mac-x86_64	NOTE	Oct 30 2024
R-4.4-mac-aarch64	NOTE	Oct 30 2024
R-4.3-win-x86_64	NOTE	Oct 30 2024
R-4.3-mac-x86_64	NOTE	Oct 30 2024
R-4.3-mac-aarch64	NOTE	Oct 30 2024

Exports:betareg_gradient betareg_log_likelihood boxplot_cluster_expr bpr_cluster_wrap bpr_gradient bpr_log_likelihood bpr_optim bpr_predict_wrap cluster_profiles_mle cluster_profiles_vb create_anno_region create_fourier_object create_polynomial_object create_rbf_object create_region_object design_matrix eval_function eval_probit_function impute_bulk_met infer_profiles_gibbs infer_profiles_mle infer_profiles_vb inner_predict_model_expr inner_train_model_expr lr_log_likelihood old_boxplot_cluster_gex old_plot_cluster_prof old_plot_fitted_profiles partition_bulk_dataset plot_cluster_profiles plot_infer_profiles plot_predicted_expr pool_bs_seq_rep predict_expr preprocess_bs_seq preprocess_final_HTS_data process_haib_caltech_wrap read_anno read_bs_encode_haib read_chrom_size read_expr read_met read_rna_encode_caltech sum_weighted_betareg_grad sum_weighted_betareg_lik sum_weighted_bpr_grad sum_weighted_bpr_lik

Dependencies:askpass assertthat base64enc BiocGenerics BiocManager BiocStyle bookdown bslib cachem class cli codetools colorspace cowplot curl data.table digest doParallel e1071 earth evaluate fansi farver fastmap fontawesome foreach Formula fs GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable highr htmltools httr IRanges isoband iterators jquerylib jsonlite kernlab knitr labeling lattice lifecycle magrittr MASS Matrix matrixcalc memoise mgcv mime munsell mvtnorm nlme openssl pillar pkgconfig plotmo plotrix proxy R6 randomForest rappdirs RColorBrewer Rcpp RcppArmadillo rlang rmarkdown S4Vectors sass scales sys tibble tinytex truncnorm UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml zlibbioc

Modelling methylation profiles

Andreas C. Kapourani, Guido Sanguinetti

Rendered fromBPRMeth_vignette.Rmdusingknitr::rmarkdownon Oct 30 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Synthetic Bernoulli data	bernoulli_data
Synthetic Beta data	beta_data
Synthetic Binomial data	binomial_data
Boxplot of clustered expression levels	boxplot_cluster_expr
(DEPRECATED) Cluster methylation profiles	bpr_cluster_wrap
Compute observation model log-likelihood	betareg_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 function	bpr_optim bpr_optim.list bpr_optim.matrix bpr_optimise bpr_optimize
(DEPRECATED) Predict gene expression from methylation profiles	bpr_predict_wrap
'BPRMeth': Extracting higher order methylation features	.datatable.aware BPRMeth
Cluster methylation profiles using EM	cluster_mle cluster_profiles_mle cluster_profile_mle
Cluster methylation profiles using VB	cluster_profiles_vb cluster_profile_vb cluster_vb
Create annotation regions	create_anno_region
Create basis objects	basis create_basis create_basis_function create_fourier_object create_polynomial_object create_rbf_object
Create genomic region data	create_region create_region_obj create_region_object genomic_region met_region region_object
Generic function for creating design matrices	designmatrix design_matrix design_matrix.default design_matrix.fourier design_matrix.polynomial design_matrix.rbf des_mat des_matrix
Processed ENCODE expression data	encode_expr
Processed ENCODE methylation data	encode_met
Evaluate basis functions	eval_function eval_function.fourier eval_function.polynomial eval_function.rbf eval_functions eval_probit_function
Synthetic Gaussian data	gaussian_data
Synthetic expression data	gex_data
Impute/predict bulk methylation states	impute_bulk_met
Infer methylation profiles using Gibbs sampling	inference_gibbs infer_profiles_gibbs infer_profile_gibbs
Infer methylation profiles using MLE	inference_mle infer_profiles_mle infer_profile_mle
Infer methylation profiles using VB	inference_vb infer_profiles_vb infer_profile_vb
(INNER) Predict expression	inner_predict_model_expr
(INNER) Train expression model from methylation profiles	inner_train_model_expr
Synthetic bulk methylation data	meth_data
(DEPRECATED) Boxplot of clustered expression levels	old_boxplot_cluster_gex
(DEPRECATED) Plot of clustered methylation profiles	old_plot_cluster_prof
(DEPRECATED) Plot the fit of methylation profiles across a region	old_plot_fitted_profiles
Partition bulk methylation dataset to training and test set	partition_bulk_dataset
Plot clustered methylation profiles across a region	plot_cluster_profiles
Plot inferred methylation profiles across a region	plot_infer_profiles
Scatter plot of predicted vs measured gene expression levels	plot_predicted_expr
(DEPRECATED) Read and pool replicates from BS-Seq data	pool_bs_seq_rep
Predict gene expression from methylation profiles	predict_expr
(DEPRECATED) Pre-process BS-Seq data in any given format	preprocess_bs_seq
(DEPRECATED) Pre-process final HTS data for downstream analysis	preprocess_final_HTS_data
(DEPRECATED) Wrapper for processing ENCODE HAIB and Caltech HTS	process_haib_caltech_wrap
Read annotation file	read_anno
(DEPRECATED) Read ENCODE HAIB bed formatted BS-Seq file	read_bs_encode_haib
Read genome chromosome sizes file	read_chrom_size
Read expression data file	read_expr
Read methylation file	read_met
(DEPRECATED) Read ENCODE Caltech bed formatted RNA-Seq file	read_rna_encode_caltech