macs2.Rd
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") )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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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 |
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.
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") }