Man pages for BPRMeth
Model higher-order methylation profiles

boxplot_cluster_gexBoxplot of clustered expression levels
bpr_cluster_wrapCluster methylation profiles
BPRMeth'BPRMeth': Extracting higher order methylation features
bpr_optimizeOptimize BPR negative log likelihood function
bpr_predict_wrapPredict gene expression from methylation profiles
create_basisCreate basis objects
create_methyl_regionCreate methylation regions for each gene promoter.
create_prom_regionCreate promoter regions from gene annotation data.
eval_functionsEvaluate basis functions
gex_dataSynthetic data for mpgex package
meth_dataSynthetic data for BPRMeth package
plot_cluster_profPlot of clustered methylation profiles
plot_fitted_profilesPlot the fit of methylation profiles across a region
plot_scatter_gexScatter plot of predicted vs measured gene expression levels
pool_bs_seq_repRead and pool replicates from BS-Seq data
predict_model_gexPredict gene expression model from methylation profiles
preprocess_bs_seqPre-process BS-Seq data in any given format
preprocess_final_HTS_dataPre-process final HTS data for downstream analysis
process_haib_caltech_wrapWrapper method for processing ENCODE HAIB and Caltech HTS...
read_bs_bismark_covRead Bismark Cov formatted BS-Seq file
read_bs_encode_haibRead ENCODE HAIB bed formatted BS-Seq file
read_chrom_sizeRead genome chromosome sizes file.
read_encode_cgiRead file containing CpG island locations
read_rna_encode_caltechRead ENCODE Caltech bed formatted RNA-Seq file
train_model_gexTrain gene expression model from methylation profiles
BPRMeth documentation built on Nov. 17, 2017, 10:13 a.m.