read_and_normalize450K {normalize450K} | R Documentation

## Normalization of 450K data by LOESS method

### Description

Read 450K '.idat' files and compute raw or normalized beta-values.

### Usage

    read450K(idat_files)
    normalize450K(intensities,tissue='')
    dont_normalize450K(intensities)

### Arguments

`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 `read450K`.
`tissue` | If set to 'Blood', a set of prespecified reference values are used for normalization. This is recommended if you plan to use `estimateLC`.

### Details

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.

### Value

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').

### Note

A benchmark comparing the performance of this method with other normalization approaches is provided in the vignette.

### Author(s)

Jonathan A. Heiss

### References

Heiss JA, Brenner H (2015). Between-array normalization for 450K data. Frontiers in Genetics, doi:10.3389/fgene.2015.00092

### Examples

    ## 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)

[Package normalize450K version 1.22.0 Index]