readidat: Parsing IDAT files for Illumina methylation arrays .

In xuz1/ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Parsing IDAT files for Illumina methylation arrays .

Description

Read in IDAT files and create a rgDataSet with probe annotation

Usage

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

Arguments

path	Directory where idat files are located
manifestfile	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
force	if TRUE, arrays with different sizes will be merged together

Details

Some array types and corresponding manifestfiles can be guessed by the program based on the number of probes per array. However, we recommand to provide correct manifest file directly, which can be easily downloaded from Illumina website, see below for some examples.

Probe annotation info can be extracted using command rowData

Value

An object of class rgDataSet,

Author(s)

Zongli Xu

Examples

#Illumina methylation array manifestfile

#Infinium Mouse Methylation Manifest File (CSV)
system("wget https://support.illumina.com/content/dam/illumina-support/documents/
       downloads/productfiles/mouse-methylation/infinium-mouse-methylation-
       manifest-file-csv.zip")
system("unzip infinium-mouse-methylation-manifest-file-csv.zip")
mf="infinium-mouse-methylation-manifest-file.csv"



#for MethylationEPIC v1.0 B5
system("wget https://webdata.illumina.com/downloads/productfiles/
       methylationEPIC/infinium-methylationepic-v-1-0-b5-
       manifest-file-csv.zip")
system("unzip infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip")
mf="infinium-methylationepic-v-1-0-b5-manifest-file.csv"
manifest=readmanifest(mf)

#for MethylationEPIC v1.0 B4
system("wget https://webdata.illumina.com/downloads/productfiles/
       methylationEPIC/infinium-methylationepic-v-1-0-b4-
       manifest-file-csv.zip")
system("unzip infinium-methylationepic-v-1-0-b4-manifest-file-csv.zip")
mf="MethylationEPIC_v-1-0_B4.csv"
manifest=readmanifest(mf)

#for HumanMethylation450
system("wget https://webdata.illumina.com/downloads/productfiles/
       humanmethylation450/humanmethylation450_15017482_v1-2.csv")
mf="HumanMethylation450_15017482_v1-2.csv"

mf="HumanMethylation450_15017482_v1-2.csv"
if(require(minfiData)){
path <- file.path(find.package("minfiData"),"extdata")
rgSet <- readidat(path = path,manifestfile=mf,recursive = TRUE)

#without providing manifest file, corresponding R manifestfile package will be used
rgSet <- readidat(path = path,recursive = TRUE)
}

xuz1/ENmix documentation built on Nov. 24, 2024, 4:31 a.m.