refinepeak: refinepeak

In macs3-project/MACSr: MACS: Model-based Analysis for ChIP-Seq

refinepeak

Description

(Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of waston/crick tags. Inspired by SPP.

Usage

refinepeak(
  bedfile,
  ifile,
  format = c("AUTO", "BAM", "SAM", "BED", "ELAND", "ELANDMULTI", "ELANDEXPORT", "BOWTIE"),
  cutoff = 5,
  windowsize = 200L,
  buffer_size = 100000L,
  verbose = 2L,
  outdir = "./",
  outputfile = character(),
  log = TRUE
)

Arguments

bedfile	Candidate peak file in BED format. REQUIRED.
ifile	ChIP-seq alignment file. If multiple files are given as '-t A B C', then they will all be read and combined. Note that pair-end data is not supposed to work with this command. REQUIRED.
format	Format of tag file, \"AUTO\", \"BED\" or \"ELAND\" or \"ELANDMULTI\" or \"ELANDEXPORT\" or \"SAM\" or \"BAM\" or \"BOWTIE\". The default AUTO option will let '%(prog)s' decide which format the file is. Please check the definition in README file if you choose ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. DEFAULT: \"AUTO\""
cutoff	Cutoff DEFAULT: 5
windowsize	Scan window size on both side of the summit (default: 100bp)
buffer_size	Buffer size for incrementally increasing internal array size to store reads alignment information. In most cases, you don't have to change this parameter. However, if there are large number of chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size in order to decrease memory usage (but it will take longer time to read alignment files). Minimum memory requested for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8 Bytes. DEFAULT: 100000
verbose	Set verbose level. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. If you want to know where are the duplicate reads, use 3. DEFAULT:2
outdir	The output directory.
outputfile	Output bedGraph file name. If not specified, will write to standard output. REQUIRED.
log	Whether to capture logs.

Value

macsList object.

Examples

eh <- ExperimentHub::ExperimentHub()
CHIP <- eh[["EH4558"]]
CTRL <- eh[["EH4563"]]
res <- callpeak(CHIP, CTRL, gsize = 5.2e7, cutoff_analysis = TRUE,
                outdir = tempdir(), name = "callpeak_narrow0")
refinepeak(grep("narrowPeak", res$outputs, value = TRUE), CHIP,
           outdir = tempdir(), outputfile = "refine")

macs3-project/MACSr documentation built on Nov. 24, 2023, 12:47 p.m.