run_macs: Run Macs3

In GrahamHamilton/pipelineTools: Pipeline Tools for NGS Sequence Analysis Pipelines

Run Macs3

Description

Macs3 is a spatial clustering approach for the identification of ChIP-enriched regions which was developed for calling narrow and broad peaks, for transcription factor binding or histone modifications from ChIP-seq data.

Usage

run_macs(
  command = NULL,
  treatment = NULL,
  control = NULL,
  format = NULL,
  genome.size = NULL,
  qvalue = NULL,
  broad.peaks = NULL,
  broad.peaks.cutoff = NULL,
  out.dir = NULL,
  experiment.name = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  macs = NULL,
  version = FALSE
)

Arguments

command	Tool arguments, choose form callpeak,bdgpeakcall,bdgbroadcall, bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak,callvar,hmmratac
treatment	ChIP-seq treatment files list.
control	Control files list.
format	Format of the input files, choose from AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE
genome.size	Effective genome size.
qvalue	Minimum FDR (q-value) cutoff for peak detection.
broad.peaks	Boolean, if set to TRUE, MACS will try to call broad peaks
broad.peaks.cutoff	Minimum FDR (q-value) cutoff for broad region.
out.dir	Name of output directory
experiment.name	Experiment name, which will be used to generate output file names.
parallel	Run in parallel, default set to FALSE
cores	Number of cores/threads to use for parallel processing, default set to 4
execute	Whether to execute the commands or not, default set to TRUE
macs	Path to the Macs3 program, required
version	Returns the version number

Value

A list with the Macs3 commands

Examples

## Not run: 
macs_path <- "/home/gmh5n/.localpython/bin/macs3"

macs_version <- run_macs(macs = macs_path,
                         version = TRUE)

macs_version

macs_command <- "callpeak"
treatment <- c("1_sorted.bam","2_sorted.bam")
experiment.name <- gsub("_sorted.bam","",treatment)
control <- c("1-input_sorted.bam","2-input_sorted.bam")
size <- 1.9e9
macs_dir <- "macs"
macs_commands <- run_macs(command = command,
                          treatment = treatment,
                          control = control,
                          format = "BAM",
                          genome.size = size,
                          broad.peaks = TRUE,
                          broad.peaks.cutoff = 0.05,
                          out.dir = macs_dir,
                          parallel = TRUE,
                          cores = 2,
                          execute = FALSE,
                          experiment.name = experiment.name,
                          macs = macs_path)
macs_commands

## End(Not run)

GrahamHamilton/pipelineTools documentation built on Dec. 8, 2024, 3:53 p.m.