methyl_master_sesame: ##methyl_master_sesame

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

##methyl_master_sesame

Description

MethylMasteR run SeSAMe function

Usage

methyl_master_sesame(
  sesame.idat.files.dir = NULL,
  sesame.output.dir = NULL,
  sesame.ref = NULL,
  sesame.sample.sheet.path = NULL,
  sesame.comparison = NULL,
  sesame.file.sep = NULL,
  sesame.data.cache = "EPIC",
  sesame.data.normal = "EPIC.5.normal",
  sesame.genome.version = "hg38",
  sesame.reference = "internal",
  sesame.split.by = NULL,
  sesame.save.seg = FALSE,
  ...
)

Arguments

sesame.idat.files.dir	The input directory for the sesame routine
sesame.output.dir	The ouptut directory for the sesame routine
sesame.sample.sheet.path	The path to the MethylMaster sample sheet
sesame.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
sesame.file.sep	the file separator to use
sesame.data.cache	the sesame data cache to use
sesame.data.normal	the sesame normal data set to use, e.g. Epic.5.Normal
sesame.genome.version	the sesame reference version (default is hg38)
sesame.reference	the sesame reference to use
sesame.split.by	which column, if any, to split the analyses by
sesame.save.seg	save the segmentation results as .RData object
...	additional parameters to passs to methyl_master_sesame

Value

A seg object for downstream analysis

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