RegRegSEA: Regulatory Region Set Enrichment Analysis

RegRegSEA is an R package for performing regulatory region set enrichment analysis on differentially methylated regions (DMRs) using transcription factor binding site databases.

Installation

# Install from GitHub (once uploaded)
# devtools::install_github("example/RegRegSEA")

# Or install locally
devtools::install_local("path/to/RegRegSEA")

Features

• Regulatory Region Enrichment: Analyze DMRs for enrichment in transcription factor binding sites
• LOLA Database Integration: Works with LOLA core and extended databases
• Visualization Tools: Create running enrichment score plots
• Parallel Processing: Support for multi-core processing
• Flexible Input: Accepts GenomicRanges objects with methylation data (dmrseq output format)

Quick Start

library(RegRegSEA)
library(dplyr)

# Prepare LOLA database
lola_db <- prepareLolaDatabase(
  lola_core_path = "path/to/cached/version/of/lola/core",
  lola_ext_path = "path/to/cached/version/of/lola/ext"
)

# Run RegRegSEA analysis
analysis <- runRegRegSEA(
  gr = granges_object_with_candidate_dmrs,
  lola_db = lola_db,
  nPermSimple = 10000,
  nproc = 4
)

# Filter significant results
enriched_region_sets <- analysis$results %>%
  filter(padj < 0.05)

# Plot running enrichment score of a region set
plot <- plotRunningES(
  ranking = analysis$ranking,
  region_sets = analysis$region_sets,
  region_set_name = "exampleLOLAcollectionName"
)

Input Data Format

DMRs should be provided as a list of GenomicRanges objects with metadata columns:

• pval: P-values for differential methylation
• beta: Beta differences (effect sizes)

Citation

If you use RegRegSEA in your research, please cite:

[Citation information to be added]

License

MIT License - see LICENSE file for details.