methyl_master_hm450: methyl_master_hm450

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

methyl_master_hm450

Description

MethylMaster version of HM450 analysis

Usage

methyl_master_hm450(
  hm450.input.dir = NULL,
  hm450.output.dir = NULL,
  hm450.sample.sheet.path = NULL,
  hm450.comparison = c("tumor", "normal"),
  hm450.split.by = NULL,
  hm450.reference = "internal",
  hm450.workflow = "B",
  hm450.file.sep = "/",
  hm450.sesame.data.cache = "EPIC",
  hm450.sesame.data.normal = "EPIC.5.normal",
  hm450.genome.version = "hg38",
  hm450.save.seg = FALSE,
  ...
)

Arguments

hm450.input.dir	The input .idat directory
hm450.output.dir	The output directory for the HM450 routine
hm450.comparison	The two-element MethylMaster comparison vector to splut up the HM450 analysis by
hm450.reference	The reference to use for the HM450 routine
hm450.workflow	The specific HM450 workflow to use: "A", "B", or "C"
hm450.file.sep	The system-specific file separator to use
hm450.sesame.data.cache	The sesame data control data cache: if using a sesame dataset as the reference
hm450.sesame.data.normal	The sesame data normal data set: if using a sesame dataset as the reference
hm450.genome.version	The sesame ref version (e.g. hg38) if using a sesame dataset as the reference
hm450.save.seg	Whether to save the HM450 routine segmentatin results
...	Additional parameters to pass to methyl_master_hm450
hm450.sample.sheet	The MethylMaster sample sheet path

Value

HM450 routine segmentation CNV results stored in a list

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