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

View source: R/methyl_master_champ_helper_functions.R

champ.load.mm

R Documentation

champ.load.mm

Description

MethylMaster modified champ.load() function

Usage

champ.load.mm(
  directory = getwd(),
  sample.sheet = NULL,
  compare.group = compare.group,
  control = FALSE,
  method = "ChAMP",
  methValue = "B",
  autoimpute = TRUE,
  filterDetP = TRUE,
  ProbeCutoff = 0,
  SampleCutoff = 0.1,
  detPcut = 0.01,
  filterBeads = TRUE,
  beadCutoff = 0.05,
  filterNoCG = TRUE,
  filterSNPs = TRUE,
  population = NULL,
  filterMultiHit = TRUE,
  filterXY = TRUE,
  force = FALSE,
  arraytype = "450K"
)

Arguments

`directory`	The input directory
`sample.sheet`	The MethylMaster sample sheet
`compare.group`	The MethylMaster comparison vector
`control`	Whether to specify control or not
`method`	Specify the method parameter
`methValue`	Specify the methValue parameter
`autoimpute`	Specify the autoimpute parameter
`filterDetP`	Specify the filterDetP parameter
`ProbeCutoff`	Specify the ProbeCutoff parameter
`SampleCutoff`	Specify the SampleCutoff parameter
`detPcut`	Specify the detPcut parameter
`filterBeads`	Specify the filterBeads parameter
`beadCutoff`	Specify the beadCutoff parameter
`filterNoCG`	Specify the NoCG parameter
`filterSNPs`	Specify the filterSNPs parameter
`population`	Specify the population parameter
`filterMultiHit`	Specify the filterMultiHit parameter
`filterXY`	Specify the filterXY parameter
`force`	Specify the force parameter
`arraytype`	Specify the arraytype parameter