Man pages for BPRMeth
Model higher-order methylation profiles

bernoulli_dataSynthetic Bernoulli data
beta_dataSynthetic Beta data
binomial_dataSynthetic Binomial data
boxplot_cluster_exprBoxplot of clustered expression levels
bpr_cluster_wrap(DEPRECATED) Cluster methylation profiles
BPRMeth'BPRMeth': Extracting higher order methylation features
bpr_optimize(DEPRECATED) Optimize BPR negative log likelihood function
bpr_predict_wrap(DEPRECATED) Predict gene expression from methylation...
cluster_profiles_mleCluster methylation profiles using EM
cluster_profiles_vbCluster methylation profiles using VB
create_anno_regionCreate annotation regions
create_basisCreate basis objects
create_region_objectCreate genomic region data
design_matrixGeneric function for creating design matrices
encode_exprProcessed ENCODE expression data
encode_metProcessed ENCODE methylation data
eval_functionsEvaluate basis functions
gaussian_dataSynthetic Gaussian data
gex_dataSynthetic expression data
infer_profiles_gibbsInfer methylation profiles using Gibbs sampling
infer_profiles_mleInfer methylation profiles using MLE
infer_profiles_vbInfer methylation profiles using VB
inner_predict_model_expr(INNER) Predict expression
inner_train_model_expr(INNER) Train expression model from methylation profiles
meth_dataSynthetic bulk methylation data
model_log_likelihoodCompute observation model log-likelihood
old_boxplot_cluster_gex(DEPRECATED) Boxplot of clustered expression levels
old_plot_cluster_prof(DEPRECATED) Plot of clustered methylation profiles
old_plot_fitted_profiles(DEPRECATED) Plot the fit of methylation profiles across a...
plot_cluster_profilesPlot clustered methylation profiles across a region
plot_infer_profilesPlot inferred methylation profiles across a region
plot_predicted_exprScatter plot of predicted vs measured gene expression levels
pool_bs_seq_rep(DEPRECATED) Read and pool replicates from BS-Seq data
predict_exprPredict gene expression from methylation profiles
preprocess_bs_seq(DEPRECATED) Pre-process BS-Seq data in any given format
preprocess_final_HTS_data(DEPRECATED) Pre-process final HTS data for downstream...
process_haib_caltech_wrap(DEPRECATED) Wrapper for processing ENCODE HAIB and Caltech...
read_annoRead annotation file
read_bs_encode_haib(DEPRECATED) Read ENCODE HAIB bed formatted BS-Seq file
read_chrom_sizeRead genome chromosome sizes file
read_exprRead expression data file
read_metRead methylation file
read_rna_encode_caltech(DEPRECATED) Read ENCODE Caltech bed formatted RNA-Seq file
BPRMeth documentation built on May 2, 2018, 2:53 a.m.