methyl_master_custom: ##methyl_master_custom

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

##methyl_master_custom

Description

MethylMasteR run custom function

Usage

methyl_master_custom(
  custom.idat.files.dir = getwd(),
  custom.output.dir = getwd(),
  custom.ref = NULL,
  custom.sample.sheet.path = NULL,
  custom.comparison = NULL,
  custom.file.sep = NULL,
  custom.data.cache = "EPIC",
  custom.data.normal = "EPIC.5.normal",
  custom.ref.version = "hg38",
  custom.reference = "internal",
  custom.save.seg = FALSE,
  ...
)

Arguments

custom.idat.files.dir	The input directory for the custom routine
custom.output.dir	The ouptut directory for the custom routine
custom.sample.sheet.path	The path to the MethylMaster sample sheet
custom.comparison	the 2-element vector of Sample_Group levels to be compared. First element is taken as the treatment and second as the control if "reference" is set to "internal" the second element is ignored
custom.file.sep	the file separator to use
custom.data.cache	the custom data cache to use
custom.data.normal	the custom normal data set to use, e.g. Epic.5.Normal
custom.ref.version	the custom reference version (default is hg38)
custom.reference	the custom reference to use
custom.save.seg	save the segmentation results as .RData object
...	additional parameters to passs to methyl_master_custom

Value

A seg object for downstream analysis

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