readmanifest: Parsing Illumina methylation arrays manifest file.
In ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Description Usage Arguments Value Author(s) Examples

Parsing Illumina methylation arrays manifest file.

1	readmanifest(file)

file

Illumina methylation array manifest file, downloaded from Illuminal website

An object of dataframe caintaining probe annotation information

Zongli Xu

#for MethylationEPIC v1.0 B5
system("wget http://webdata.illumina.com.s3-website-us-east-1.amazonaws.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 ftp://webdata2:webdata2@ussd-ftp.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 ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/ProductFiles
/HumanMethylation450/HumanMethylation450_15017482_v1-2.csv")
mf="HumanMethylation450_15017482_v1-2.csv"
manifest=readmanifest(mf)