A function to handle a MACS2 containier

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

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

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

Examples

if (FALSE) {
    #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")     
}