normalize450K (version 1.0.0)

read_and_normalize450K: 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.

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').

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.

References

Heiss, Jonathan A., and Hermann Brenner. Between-array normalization for 450K data. Frontiers in genetics 6 (2015). 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)