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CACTI: Leveraging Correlated Regulatory Elements for Powerful Chromatin QTL Detection

Overview

CACTI (ChromAtin quantitative loCi of mulTIple peaks) implements a powerful method for chromatin QTL mapping that leverages the correlation structure of nearby regulatory elements.

The package offers two main modules:

  1. CACTI (Peak-window method):
  • Groups pre-defined peaks into non-overlapping windows of fixed genomic size.
  • Residualizes peak intensities with respect to covariates.
  • Runs multi-peak association tests using a principal-component omnibus (PCO) test.
  • Aggregates results and computes window-level FDR.
  1. CACTI-S (Sample-based pipeline):
  • An end-to-end preprocessing workflow to go from raw BAM files to normalized phenotype matrices to QTL mapping.
  • Performs segmentation, read counting, QC/filtering, and normalization.
  • Runs cis-QTL mapping to generate input files for CACTI.

Installation 

install.packages("devtools")   # if not installed yet
devtools::install_github("liliw-w/cacti", build_vignettes = TRUE)

After installation:

Documentation

Vignettes

See the full documentation and vignettes for -

  • CACTI Peak-Window Pipeline

  • CACTI-S Pipeline

Vignettes can also be viewed within the installed package -

vignette("cacti_peak_window", package = "cacti")
vignette("cacti_s_prep", package = "cacti")

Main functions documentation 

?cacti_run_chr
?cacti_run_genome
?cacti_add_fdr
?cacti_s_prep

Citation

If you use the CACTI method, please cite:

Wang, L., & Liu, X. (2025). Improved chromatin QTL mapping with CACTI. bioRxiv, 2025-06.