refinepeak

Take raw reads alignment, refine peak summits. Inspired by SPP.

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(),
  oprefix = 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. Regions with SPP wtd score lower than cutoff will not be considerred. 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

Output file name. Mutually exclusive with –o-prefix.

outputfile

Output bedGraph file name. If not specified, will write to standard output. REQUIRED.

oprefix

Output file prefix. Mutually exclusive with -o/–ofile.

log

Whether to capture logs.

Value

macsList object.

Examples

eh <- ExperimentHub::ExperimentHub()
CHIP <- eh[["EH4558"]]
#> see ?MACSdata and browseVignettes('MACSdata') for documentation
#> loading from cache
CTRL <- eh[["EH4563"]]
#> see ?MACSdata and browseVignettes('MACSdata') for documentation
#> loading from cache
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")
#> 
#> macsList class
#> $outputs:
#>  /tmp/RtmpkYWDbh/refine 
#> $arguments: bedfile, ifile, outdir, outputfile 
#> $log:
#>