BPRMeth: Model higher-order methylation profiles
Version 1.2.0

BPRMeth package uses the Binomial Probit Regression likelihood to model methylation profiles and extract higher order features. These features quantitate precisely notions of shape of a methylation profile. Using these higher order features across promoter-proximal regions, we construct a powerful predictor of gene expression. Also, these features are used to cluster proximal-promoter regions using the EM algorithm.

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AuthorChantriolnt-Andreas Kapourani [aut, cre]
Bioconductor views Bayesian Clustering Coverage DNAMethylation Epigenetics FeatureExtraction GeneExpression GeneRegulation Genetics KEGG RNASeq Regression Sequencing
Date of publicationNone
MaintainerChantriolnt-Andreas Kapourani <kapouranis.andreas@gmail.com>
LicenseGPL-3
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BPRMeth")

Man pages

boxplot_cluster_gex: Boxplot of clustered expression levels
bpr_cluster_wrap: Cluster methylation profiles
BPRMeth: 'BPRMeth': Extracting higher order methylation features
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.
eval_functions: 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...
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

Functions

.datatable.aware Man page
BPRMeth Man page
BPRMeth-package Man page
basis Man page
boxplot_cluster_gex Man page Source code
bpr_EM Source code
bpr_cluster_wrap Man page Source code
bpr_gradient Source code
bpr_likelihood Source code
bpr_optim Man page Source code
bpr_optim.default Source code
bpr_optim.list Man page Source code
bpr_optim.matrix Man page Source code
bpr_optimise Man page
bpr_optimize Man page
bpr_predict_wrap Man page Source code
calculate_errors Source code
center_loc Source code
create_basis Man page
create_methyl_region Man page Source code
create_polynomial_object Man page Source code
create_prom_region Man page Source code
create_rbf_object Man page Source code
design_matrix Source code
design_matrix.default Source code
design_matrix.polynomial Source code
design_matrix.rbf Source code
discard_bs_noise_reads Source code
discard_chr Source code
do_EM_checks Source code
do_checks Source code
eval_function Man page Source code
eval_function.default Source code
eval_function.polynomial Man page Source code
eval_function.rbf Man page Source code
eval_functions Man page
eval_probit_function Man page Source code
extract_fpkm Source code
extract_gene_name Source code
gex_data Man page
log_sum_exp Source code
meth_data Man page
minmax_scaling Source code
partition_data Source code
plot_cluster_prof Man page Source code
plot_fitted_profiles Man page Source code
plot_scatter_gex Man page Source code
polynomial_basis Source code
pool_bs_seq_rep Man page Source code
predict_model_gex Man page Source code
preprocess_bs_seq Man page Source code
preprocess_final_HTS_data Man page Source code
process_haib_caltech_wrap Man page Source code
rbf_basis Source code
read_bs_bismark_cov Man page Source code
read_bs_encode_haib Man page Source code
read_chrom_size Man page Source code
read_encode_cgi Man page Source code
read_rna_encode_caltech Man page Source code
sum_weighted_bpr_grad Source code
sum_weighted_bpr_lik Source code
train_model_gex Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/BPRMeth_package.R
R/basis_functions.R
R/bpr.R
R/bpr_cluster_wrap.R
R/bpr_optimize.R
R/bpr_predict_wrap.R
R/create_methyl_region.R
R/create_prom_region.R
R/data.R
R/design_matrix.R
R/evaluate_functions.R
R/plotting_functions.R
R/pool_bs_seq_rep.R
R/preprocess_bs_seq.R
R/preprocess_final_HTS_data.R
R/process_haib_caltech_wrap.R
R/read_bs_bismark_cov.R
R/read_bs_encode_haib.R
R/read_chrom_size.R
R/read_encode_cgi.R
R/read_rna_encode_caltech.R
R/regression_model_gex.R
R/utils.R
README.md
build
build/vignette.rds
data
data/gex_data.rda
data/meth_data.rda
inst
inst/NEWS.Rd
inst/doc
inst/doc/BPRMeth_vignette.R
inst/doc/BPRMeth_vignette.Rnw
inst/doc/BPRMeth_vignette.pdf
inst/extdata
inst/extdata/hg19.chr.sizes
inst/extdata/rnaseq.bed
inst/extdata/rrbs.bed
man
man/BPRMeth.Rd
man/boxplot_cluster_gex.Rd
man/bpr_cluster_wrap.Rd
man/bpr_optimize.Rd
man/bpr_predict_wrap.Rd
man/create_basis.Rd
man/create_methyl_region.Rd
man/create_prom_region.Rd
man/eval_functions.Rd
man/gex_data.Rd
man/meth_data.Rd
man/plot_cluster_prof.Rd
man/plot_fitted_profiles.Rd
man/plot_scatter_gex.Rd
man/pool_bs_seq_rep.Rd
man/predict_model_gex.Rd
man/preprocess_bs_seq.Rd
man/preprocess_final_HTS_data.Rd
man/process_haib_caltech_wrap.Rd
man/read_bs_bismark_cov.Rd
man/read_bs_encode_haib.Rd
man/read_chrom_size.Rd
man/read_encode_cgi.Rd
man/read_rna_encode_caltech.Rd
man/train_model_gex.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test-basis.R
tests/testthat/test-bpr.R
tests/testthat/test-design_matrix.R
tests/testthat/test-eval_function.R
tests/testthat/test-utils.R
vignettes
vignettes/BPRMeth_vignette-concordance.tex
vignettes/BPRMeth_vignette.Rnw
vignettes/BPRMeth_vignette.bib
vignettes/figure
vignettes/figure/figureexample-1.pdf
vignettes/figure/figureexample2-1.pdf
vignettes/figure/figureexample3-1.pdf
vignettes/model-bpr.pdf
BPRMeth documentation built on May 20, 2017, 10 p.m.