skewr (version 1.4.2)

getMethyLumiSet: Read idat files and create a MethyLumiSet object

Description

This a wrapper function for methylumIDAT that does not require a vector of barcodes to be provided.

Usage

getMethyLumiSet(path = getwd(), barcodes = NULL,
                norm = c("none", "illumina", "SWAN", "dasen"),
                bg.corr = TRUE)

Arguments

path

The path to the directory containing the idat files.

barcodes

A vector of barcodes specifying which idat's to read.

norm

Should normalization be done on the resulting MethyLumiSet. The default is "none"

bg.corr

logical; if TRUE, an Illumina style background subtraction will be performed only if norm is set to 'illumina'. Otherwise, it is ignored. If background subtraction without any normalization is desired, the preprocess method must be used.

Value

• A MethyLumiSet object

Details

If only path is provided, all idat's found in the given folder will be pulled. If only barcodes is given, corresponding idat's will be pulled from the current working directory. Both path and barcodes may be passed for finer control. The default is to pull all idat's found in the current working directory.

References

Davis S, Du P, Bilke S, Triche T, Jr. and Bootwalla M (2014). methylumi: Handle Illumina methylation data. R package version 2.12.0.

See Also

getBarcodes, preprocess

Examples

if(require('minfiData')) {
  path <- system.file("extdata/5723646052", package="minfiData")
  barcodes <- getBarcodes(path = path)
  methylumiset.raw <- getMethyLumiSet(path = path, barcodes = barcodes[1])
}