getMethyLumiSet {skewr} | R Documentation |
MethyLumiSet
object
This a wrapper function for methylumIDAT
that does not require a vector of barcodes to be provided.
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 |
bg.corr |
logical; if |
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.
if(require('minfiData')) { path <- system.file("extdata/5723646052", package="minfiData") barcodes <- getBarcodes(path = path) methylumiset.raw <- getMethyLumiSet(path = path, barcodes = barcodes[1]) }