readPepo: readPepo - (unfinished) read any kind of Illumina DNA...

In schalkwyk/wateRmelon: Illumina 450 and EPIC methylation array normalization and metrics

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

Description

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

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

Value

A ‘MethyLumiSet’ object.

schalkwyk/wateRmelon documentation built on April 15, 2024, 12:06 p.m.