predictd

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

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"]]
#> see ?MACSdata and browseVignettes('MACSdata') for documentation
#> loading from cache
predictd(CHIP, d_min = 10, gsize=5.2e+7, plot = NULL)
#> 
#> [1] 229