getMethyLumiSet: Read idat files and create a 'MethyLumiSet' object
In skewr: Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/snUtils.R

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

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

`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.

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.

A MethyLumiSet object

One would probably not normally want to use the preprocess option at this stage. It is more likely that a MethyLumiSet of the raw data will be desired. Then the preprocess method may be used to normalize the raw data or use background subtraction only on the raw data. See the vignette for example workflow.

Ryan Putney ryanputney@gmail.com

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

getBarcodes, preprocess

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