macs2: A function to handle a MACS2 containier

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

A function to handle a MACS2 containier

Description

This function executes a MACS2 docker that produces as output peaks call

Usage

macs2(
  group = c("sudo", "docker"),
  control.bam,
  chipseq.bam,
  experiment.name,
  histone.marks = FALSE,
  broad.cutoff = 0.1,
  qvalue = 0.05,
  organism = c("hs", "mm")
)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
control.bam	a character string indicating the path to the control bam file. IMPORTANT control.bam and chipseq.bam are in the same folder
chipseq.bam	a character string indicating the path to the chipseq bam file. IMPORTANT control.bam and chipseq.bam are in the same folder
experiment.name	a character string indicating the prefix for MCS2 output
histone.marks	boolean if TRUE activate the broad option to call histone marks
broad.cutoff	if histone.mark is TRUE broad.cutoff can be set, default 0.1
qvalue	The qvalue (minimum FDR) cutoff to call significant regions. Default is 0.05. For broad marks, you can try 0.05 as cutoff.
organism	required to select the correct genome size avaialble options hs, mm

Value

NAME_peaks.xls, which is a tabular file which contains information about called peaks. You can open it in excel and sort/filter using excel functions. Information include: chromosome name, start position of peak, end position of peak, length of peak region, absolute peak summit position, pileup height at peak summit, -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then this value should be 10), fold enrichment for this peak summit against random Poisson distribution with local lambda, -log10(qvalue) at peak summit. NAME_peaks.narrowPeak is BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue. You can load it to UCSC genome browser. Definition of some specific columns are: 5th: integer score for display calculated as int(-10*log10qvalue). Please note that currently this value might be out of the [0-1000] range defined in UCSC Encode narrowPeak format, 7th: fold-change, 8th: -log10pvalue, 9th: -log10qvalue, 10th: relative summit position to peak start. NAME_peaks.broadPeak is in BED6+3 format which is similar to narrowPeak file.

Author(s)

raffaele.calogero [at] unito [dot] it, University of Torino

Examples

## Not run: 
    #running MACS for conventional peaks
    macs2(group="docker", control.bam=paste(getwd(),"igg_dedup_reads.bam", sep="/"), 
            chipseq.bam=paste(getwd(),"prdm51_dedup_reads.bam", sep="/"), 
            experiment.name="prdm51_igg", histone.marks=FALSE, qvalue=0.05, 
            organism="mm")
            
    #running MACS for histone marks
    macs2(group="docker", control.bam=paste(getwd(),"igg_dedup_reads.bam", sep="/"), 
            chipseq.bam=paste(getwd(),"prdm51_dedup_reads.bam", sep="/"), 
            experiment.name="prdm51_igg", histone.marks=TRUE, broad.cutoff=0.1, 
            organism="mm")     

## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.