BPRMeth: Model higher-order methylation profiles

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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.

Author
Chantriolnt-Andreas Kapourani [aut, cre]
Date of publication
None
Maintainer
Chantriolnt-Andreas Kapourani <kapouranis.andreas@gmail.com>
License
GPL-3
Version
1.0.0

View on Bioconductor

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

Files in this package

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