epicopy.mm: epicopy.mm

In mmariani123/MethylMasteR: What the Package Does (One Line, Title Case)

epicopy.mm

Description

MethylMaster version of the main Epicopy::epicopy() function from Epicopy

Usage

epicopy.mm(
  target_dir,
  output_dir = NULL,
  single.file = TRUE,
  single.file.path = NULL,
  epic.manifest.path = getwd(),
  comparison = NULL,
  reference_group = "internal",
  project_name = NULL,
  Normals = NULL,
  sampNames = NULL,
  QN = FALSE,
  Ref = "mode",
  mode.bw = 0.1,
  mode.method = "naive",
  normal.cnv = NULL,
  mean.center = TRUE,
  filterProbes = FALSE,
  retainedProbes = NULL,
  ncores = 1L,
  seg.undo.splits = "sdundo",
  seg.undo.SD = 2,
  filterbycount = TRUE,
  min_probes = 50,
  verbose = TRUE,
  keep_fnobj = FALSE,
  fn_output = NULL,
  ...
)

Arguments

target_dir	The input directory
output_dir	The output directory
single.file	Specify a single file (logical)
single.file.path	The single file path
epic.manifest.path	The path to the epic.manifest file
comparison	The MehtylMaster comparison vector
reference_group	The reference group to specify
project_name	The project name
Normals	The specified Normals see documentaion
sampNames	Customize the sample names here
QN	The QN parameter to use
Ref	The Ref parameter to use
mode.bw	The mode.bw parameter to use
mode.method	The mode.method parameter to use
normal.cnv	The normal.cnv parameter to use
mean.center	Whether to use mean centering (default=TRUE)
filterProbes	The filterProbes parameter
retainedProbes	The retained Probes parameter
ncores	The number of cores to use, note that multiple cores may not work on every system
seg.undo.splits	The seg.undo.splits parameter
seg.undo.SD	The seg.undo.SD parameter
filterbycount	The filterbycount parameter
min_probes	The min_probes parameter
verbose	The verbose parameter
keep_fnobj	The keep_fnobj parameter
fn_output	The fn_output parameter
...	Additional parameters to pass to epicopy.mm()

Value

Return a cna list containing CNV frame(s)

mmariani123/MethylMasteR documentation built on June 22, 2022, 3:06 p.m.