BPRMeth: Model higher-order methylation profiles

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.

AuthorChantriolnt-Andreas Kapourani [aut, cre]
Date of publicationNone
MaintainerChantriolnt-Andreas Kapourani <kapouranis.andreas@gmail.com>
LicenseGPL-3
Version1.0.0

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

Functions

basis Man page
boxplot_cluster_gex Man page
bpr_cluster_wrap Man page
BPRMeth Man page
BPRMeth-package Man page
bpr_optim Man page
bpr_optimise Man page
bpr_optimize Man page
bpr_optim.list Man page
bpr_optim.matrix Man page
bpr_predict_wrap Man page
create_basis Man page
create_methyl_region Man page
create_polynomial_object Man page
create_prom_region Man page
create_rbf_object Man page
.datatable.aware Man page
eval_function Man page
eval_function.polynomial Man page
eval_function.rbf Man page
eval_functions Man page
eval_probit_function Man page
gex_data Man page
meth_data Man page
plot_cluster_prof Man page
plot_fitted_profiles Man page
plot_scatter_gex Man page
pool_bs_seq_rep Man page
predict_model_gex Man page
preprocess_bs_seq Man page
preprocess_final_HTS_data Man page
process_haib_caltech_wrap Man page
read_bs_bismark_cov Man page
read_bs_encode_haib Man page
read_chrom_size Man page
read_encode_cgi Man page
read_rna_encode_caltech Man page
train_model_gex Man page

Files

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

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