predictd: predictd

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

predictd

Description

Predict d or fragment size from alignment results. In case of PE data, report the average insertion/fragment size from all pairs. Will NOT filter duplicates

Usage

predictd(
  ifile,
  gsize = "hs",
  format = "AUTO",
  plot = normalizePath(tempdir(), "predictd_mode.pdf"),
  tsize = NULL,
  bw = 300,
  d_min = 20,
  mfold = c(5, 50),
  buffer_size = 1e+05,
  verbose = 2L,
  log = TRUE
)

Arguments

ifile	ChIP-seq alignment file. If multiple files are given as '-t A B C', then they will all be read and combined. REQUIRED.
gsize	Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2,913,022,398), 'mm' for mouse (2,652,783,500), 'ce' for C. elegans (100,286,401) and 'dm' for fruitfly (142,573,017), Default:hs. The effective genome size numbers for the above four species are collected from Deeptools https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html Please refer to deeptools to define the best genome size you plan to use.
format	Format of tag file, \"AUTO\", \"BED\" or \"ELAND\" or \"ELANDMULTI\" or \"ELANDEXPORT\" or \"SAM\" or \"BAM\" or \"BOWTIE\" or \"BAMPE\" or \"BEDPE\". The default AUTO option will let MACS decide which format the file is. However, if you want to decide the average insertion size/fragment size from PE data such as BEDPE or BAMPE, please specify the format as BAMPE or BEDPE since MACS3 won't automatically recognize three two formats with -f AUTO. Please be aware that in PE mode, -g, -s, –bw, –d-min, -m, and –rfile have NO effect. DEFAULT: \"AUTO\"
plot	PDF path of peak model and correlation plots.
tsize	Tag size. This will override the auto detected tag size. DEFAULT: Not set
bw	Band width for picking regions to compute fragment size. This value is only used while building the shifting model. DEFAULT: 300
d_min	Minimum fragment size in basepair. Any predicted fragment size less than this will be excluded. DEFAULT: 20
mfold	Select the regions within MFOLD range of high-confidence enrichment ratio against background to build model. Fold-enrichment in regions must be lower than upper limit, and higher than the lower limit. Use as "-m 10 30". DEFAULT:5 50
buffer_size	Buffer size for incrementally increasing internal array size to store reads alignment information. DEFAULT: 100000.
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
log	Whether to capture log.

Value

predicted fragment sizes.

Examples

eh <- ExperimentHub::ExperimentHub()
CHIP <- eh[["EH4558"]]
predictd(CHIP, d_min = 10, gsize=5.2e+7, plot = NULL)

macs3-project/MACSr documentation built on Sept. 24, 2024, 11:09 p.m.