filterdup: filterdup

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

filterdup

Description

filterdup

Usage

filterdup(
  ifile,
  gsize = "hs",
  format = "AUTO",
  tsize = NULL,
  pvalue = 1e-05,
  keepduplicates = "auto",
  outputfile = character(),
  outdir = ".",
  verbose = 2L,
  buffer_size = 10000,
  dryrun = FALSE,
  log = TRUE
)

Arguments

ifile	Input file(s).
gsize	Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs.
format	Input file format.
tsize	Tag size. This will override the auto detected tag size.
pvalue	Pvalue cutoff for binomial distribution test. DEFAULT:1e-5.
keepduplicates	It controls the behavior towards duplicate tags at the exact same location – the same coordination and the same strand. The 'auto' option makes MACS calculate the maximum tags at the exact same location based on binomal distribution using 1e-5 as pvalue cutoff; and the 'all' option keeps every tags. If an integer is given, at most this number of tags will be kept at the same location. Note, if you've used samtools or picard to flag reads as 'PCR/Optical duplicate' in bit 1024, MACS2 will still read them although the reads may be decided by MACS2 as duplicate later. If you plan to rely on samtools/picard/any other tool to filter duplicates, please remove those duplicate reads and save a new alignment file then ask MACS2 to keep all by '–keep-dup all'. The default is to keep one tag at the same location. Default: 1".
outputfile	The output file.
outdir	The output directory.
verbose	Set verbose level of runtime message. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. DEFAULT: 2.
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.
dryrun	When set, filterdup will only output numbers instead of writing output files, including maximum allowable duplicates, total number of reads before filtering, total number of reads after filtering, and redundant rate. Default: not set.
log	Whether to capture logs.

Value

macsList object.

Examples

eh <- ExperimentHub::ExperimentHub()
CHIP <- eh[["EH4558"]]
res <- filterdup(ifile = CHIP, outputfile = "test.bed", outdir = tempdir())

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