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neurogenomics / ConsensusPeak

GNU General Public License v3.0
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NULL License: GPL (\>= 3)
R build status

Authors: Thomas Roberts

2024-02-04

Introduction

ConsensusPeak is an R Package for calling consensus peaks from multiple biological replicates. We implement several methods for thresholding, including IDR conservative, IDR optimal, MSPC and ChIP-R.

Installation

if(!require("remotes")) install.packages("remotes")
remotes::install_github("neurogenomics/ConsensusPeak")

Usage

Load example data:

rep_treat_1 <- system.file("extdata",
                           "r1_creb_chr22.bam",
                           package = "ConsensusPeak")
rep_treat_2 <- system.file("extdata",
                           "r2_creb_chr22.bam",
                           package = "ConsensusPeak")

Run MACS3 peak calling and IDR thresholding with a single command:

result <- idr_analysis(treat_files = c(rep_treat_1, rep_treat_2),
                       control_files = NULL,
                       type = "conservative",
                       is_paired = FALSE, # Is the data paired-end?
                       idr_stringent = TRUE # Threshold at 0.01 or 0.05
                       out_dir = ".", # Directory to write the output files
                       nomodel = TRUE # MACS3 setting
                       )