readmanifest: Parsing Illumina methylation arrays manifest file.

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

Parsing Illumina methylation arrays manifest file.

Description

Parsing Illumina methylation arrays manifest file.

Usage

readmanifest(file)

Arguments

file	Illumina methylation array manifest file, downloaded from Illuminal website

Value

An object of dataframe caintaining probe annotation information

Author(s)

Zongli Xu

Examples

#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"
manifest=readmanifest(mf)

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