preprocessGEOMethylation: Preprocess IDAT files from Illumina HumanMethylation450...

In mensxmachina/BioDataome: Functions used to preprocess datasets stored in BioDataome

Description

This function utilizes minfi Package to convert data into methylation measurements. Example: Assuming there is a directory named GSE78279 in the working directory where idat files are stored and "GSM2071074_8655685078_R03C02" and "GSM2071074_8655685078_R03C02" are the file names for the idat files, then x should be:

Usage

preprocessGEOMethylation(x)

Arguments

x	a character array with the paths to the idat files

Value

a matrix of dimensions: probes x samples with the normalized methylation values

Examples

## Not run: 
x<-c("GSM2071074_8655685078_R03C02","GSM2071075_8655685078_R04C02")
x<-file.path(getwd(),"GSE78279",x)
dataNorm<-preprocessGEOMethylation(x) 
## End(Not run)
meth<-data

mensxmachina/BioDataome documentation built on July 24, 2021, 1:05 p.m.