macsCallpeak: Perform peak-calling with MACS2
In dvera/gyro: gyro: Genomic utility wrappers in R

macs is a wrapper for macs2 callpeak.

macsCallpeak(treatmentFiles, controlFiles = NULL, genomeSize = "hs",
  inputFormat = "AUTO", noLambda = TRUE, sampleNames = NULL,
  callSummits = TRUE, qvalue = 0.01, verbosity = 3,
  threads = getOption("threads", 1L))

`treatmentFiles`	A character vector of paths to treatment read files. treatmentFiles are treated as separate samples and are not used in combination when running macs2.
`controlFiles`	A (optional) character vector of paths to control read files that correspond to treatmentFiles.
`genomeSize`	A macs2-compatible string (hs,mm,ce,dm) or integer (in bp) specifying the genome size.
`inputFormat`	String specifying the format of tag file, can be "ELAND", "BED", "ELANDMULTI", "ELANDEXPORT", "ELANDMULTIPET", "SAM", "BAM", "BOWTIE" or "BAMPE". Default is "AUTO" which will allow MACS to decide the format automatically.
`noLambda`	A boolean indicating if local input read densities should be skipped when computing lambda.
`callSummits`	Boolean. If TRUE, MACS will reanalyze the shape of the signal profile to deconvolve subpeaks within each peak called from general procedure. The output subpeaks of a big peak region will have the same peak boundaries, and different scores and peak summit positions.
`qvalue`	The qvalue (minimum FDR) cutoff to call significant regions. Q-values are calculated from p-values using Benjamini-Hochberg procedure.
`verbosity`	Integer. If you don't want to see any message during the running of MACS, set it to 0. But the CRITICAL messages will never be hidden. If you want to see rich information like how many peaks are called for every chromosome, you can set it to 3 or larger than 3.'
`threads`	A positive integer specifying how many samples to process simultaneously.
`sampleName`	Character vector of name strings corresponding to treatmentFiles. MACS will use this string NAME to create output files like 'NAME_peaks.xls', 'NAME_negative_peaks.xls', 'NAME_peaks.bed' , 'NAME_summits.bed', 'NAME_model.r' and so on. If NULL will reuse names of treatmentFiles.