readidat {ENmix}R Documentation

Parsing IDAT files from Illumina methylation arrays.

Description

Read in IDAT files and create a rgDataSet with probe annotation

Usage

readidat(path = NULL,manifestfile=NULL,recursive = FALSE, verbose = FALSE)

Arguments

path

Directory where idat files are located

manifestfile

The file name of array manifestfile, which can be downloaded from Illumina website. Bioconductor manifest package will be used if not provided

recursive

if TRUE, idat files in the subdirectories will also be read in

verbose

if TRUE, detailed running info will be printed on screen

Value

An object of class rgDataSet

Author(s)

Zongli Xu

Examples

## Not run: 
require(minfidata)
path <- file.path(find.package("minfiData"),"extdata")
#based on rgDataset
rgSet <- readidat(path = path,recursive = TRUE)

## End(Not run)

[Package ENmix version 1.21.6 Index]