readPepo: readPepo - read (any kind of) Illumina DNA methylation array...
In schalkwyk/wateRmelon: Illumina DNA methylation array normalization and metrics

readPepo

R Documentation

readPepo - read (any kind of) Illumina DNA methylation array idat files into a methylumi object

Description

Pepo is a botanical term for any melon-like fruit. Given the appropriate manifest file, this function should be able to read any of the Illumina Infinium DNAm arrays including 450k, EPIC, EPIC2, MSA and Mouse.

Usage

readPepo(
  idatdir = ".",
  filelist = NULL,
  barcodelist = NULL,
  manifest = NULL,
  parallel = F,
  n = F,
  pdat = NULL,
  oob = F,
  two = TRUE
)

Arguments

`idatdir`	the directory with the idatfiles. Currently only handle one directory.
`filelist`	optional list of idat files to process.
`barcodelist`	optional list of barcodes to process.
`manifest`	name of a IlluminaMethylationManifest object or a csv format manifest. If missing, will run idet() on one of the idat files.
`parallel`	try to use multiple cores.
`n`	keep beadcounts.
`pdat`	optional data.frame describing the samples.
`two`	are there two different assay types (true of human methylation arrays except 27k)
`keep`	out-of-band (OOB) or opposite-channel signals