read_and_normalize450K {normalize450K} | R Documentation |
Read 450K '.idat' files and compute raw or normalized beta-values.
read450K(idat_files) normalize450K(intensities,tissue='') dont_normalize450K(intensities)
idat_files |
a character vector containing the paths to the .idat files stripped from the '_Grn.idat' suffix with one entry for each sample (.idat files for green and red intensities have to be in the same folder). |
intensities |
List object containing raw signal intensities. Result of calling |
tissue |
If set to 'Blood', a set of prespecified reference values are used for normalization. This is recommended if you plan to use |
Function read450K
reads .idat files and returns a list object containing raw signal intensities. dont_normalize450K
returns an ExpressionSet containing beta-values without normalization. normalize450K
performs dye bias correction using the extension controls probes followed by normalization by local regression (Heiss and Brenner, 2015) and returns an ExpressionSet containing beta-values, too.
For read450K
a list containing the methylated, unmethylated and control signal intensities. For dont_normalize450K
and normalize450K
an ExpressionSet containing beta-values, rows corresponding to CpG sites (named) and columns to samples (in the same order as 'idat_files').
A benchmark comparing the performance of this method with other normalization approaches is provided in the vignette.
Jonathan A. Heiss
Heiss JA, Brenner H (2015). Between-array normalization for 450K data. Frontiers in Genetics, doi:10.3389/fgene.2015.00092
## Not run: library(minfiData) ## this package includes some .idat files library(data.table) path <- system.file("extdata",package="minfiData") samples = fread(file.path(path, 'SampleSheet.csv'),integer64='character') samples[,file:=file.path(path,Sentrix_ID,paste0(Sentrix_ID,'_',Sentrix_Position))] ## samples$file is a character vector containing the location of the ## .idat files, but without the suffixes "_Red.idat" or "_Grn.idat" raw = read450K(samples$file) none = dont_normalize450K(raw) ## no normalization norm = normalize450K(raw) ## End(Not run)