## ----setup, include=FALSE-----------------------------------------------------
suppressPackageStartupMessages({
    library(CMEnt)
})
knitr::opts_chunk$set(
    echo = TRUE,
    warning = FALSE,
    message = FALSE
)

## ----install, eval=FALSE------------------------------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE)) {
#     install.packages("BiocManager")
# }
# BiocManager::install("CMEnt")

## ----beta_example-------------------------------------------------------------
loadExampleInputDataChr5And11("beta")

## ----seeds_example------------------------------------------------------------
loadExampleInputDataChr5And11("dmps")
seeds <- dmps

## ----pheno_example------------------------------------------------------------
loadExampleInputDataChr5And11("pheno")

## ----basic_usage, eval=FALSE--------------------------------------------------
# dmrs <- buildDMRs(
#     beta = beta,
#     seeds = seeds,
#     pheno = pheno,
#     ignored_sample_groups = c("excluded_group1", "excluded_group2")
# )

## ----bsseq_usage, eval=FALSE--------------------------------------------------
# dmrs <- buildDMRs(
#     beta = beta,
#     seeds = seeds,
#     pheno = pheno,
#     entanglement = "weak"
# )

## ----njobs_option-------------------------------------------------------------
options("CMEnt.njobs" = 4)

## ----verbose_option-----------------------------------------------------------
options("CMEnt.verbose" = 2)

## ----beta_in_memory_option----------------------------------------------------
options("CMEnt.beta_in_mem_threshold_mb" = 200)

## ----annotation_cache_option--------------------------------------------------
options("CMEnt.use_annotation_cache" = TRUE)

## ----annotation_cache_dir_option----------------------------------------------
options("CMEnt.annotation_cache_dir" = "/path/to/cache")

## ----jaspar_cache_dir_option--------------------------------------------------
options("CMEnt.jaspar_cache_dir" = "/path/to/cache")

## ----jaspar_version_option----------------------------------------------------
options("CMEnt.jaspar_version" = 2024)

## ----min_motif_similarity_option----------------------------------------------
options("CMEnt.min_motif_similarity" = 0.75)

## ----jaspar_tax_group_option--------------------------------------------------
options("CMEnt.jaspar_tax_group" = "vertebrates")

## ----jaspar_corr_threshold_option---------------------------------------------
options("CMEnt.jaspar_corr_threshold" = 0.85)

## ----make_debug_dir_option----------------------------------------------------
options("CMEnt.make_debug_dir" = TRUE)

## ----scoring_nfold_option-----------------------------------------------------
options("CMEnt.scoring_nfold" = 3)

## ----scoring_example, eval=FALSE----------------------------------------------
# dmrs <- buildDMRs(
#     beta = beta,
#     seeds = seeds,
#     pheno = pheno,
#     sample_group_col = "Sample_Group",
#     array = "EPIC",
#     genome = "hg38",
#     ext_site_delta_beta = 0.2,
#     min_seeds = 3,
#     min_sites = 5,
#     max_lookup_dist = 5000,
#     max_pval = 0.01,
#     njobs = 4
# )

## ----custom_bed_example, eval=FALSE-------------------------------------------
# dmrs <- buildDMRs(
#     beta = beta,
#     seeds = seeds,
#     pheno = pheno,
#     sample_group_col = "Sample_Group",
#     array = "EPIC",
#     genome = "hg38",
#     min_seeds = 2,
#     min_sites = 3,
#     max_lookup_dist = 20000,
#     max_pval = 0.05,
#     njobs = 8
# )

## ----custom_locations_example, eval=FALSE-------------------------------------
# dmrs <- buildDMRs(
#     beta = beta,
#     seeds = seeds,
#     pheno = pheno,
#     sample_group_col = "Sample_Group",
#     array = "EPIC",
#     genome = "hg38",
#     testing_mode = "empirical",
#     empirical_strategy = "montecarlo",
#     ntries = 5000,
#     mid_p = TRUE,
#     njobs = 4
# )

## ----sessionInfo--------------------------------------------------------------
sessionInfo()