The R package funtooNorm provides a function for normalization of Illumina Infinium Human Methylation 450
BeadChip (Illumina 450K) data when there are samples from multiple tissues or cell types.
Download the current build here and install it with
$ R CMD INSTALL funtooNorm_N.NN.N.tar.gzOr, if you want to build from source, you can also install from GitHub using the devtools package in R:
library(devtools)
install_github('GreenwoodLab/funtooNorm', local=TRUE, build_vignettes = TRUE)If you have difficulties with the function install_github you can download and install from source using the commands R CMD build and install:
$ git clone https://github.com/GreenwoodLab/funtooNorm.git
$ R CMD build ./funtooNorm
$ R CMD INSTALL funtooNorm_N.NN.N.tar.gz
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install_github('greenwoodLab/funtooNorm')There are two functions in the package, funtoonorm and agreement.
The output of funtoonorm is two matrices: both a normalized methylation data set of beta values and also raw, non-normalized beta values. As an input, the user needs to provide signal A and signal B matrices of data extracted from Illumina IDAT files, as well as control probes signals. The function also requires a list of cell types or tissues. Besides its main purpose of normalization, funtoonorm can be run in a validation mode and its graphical output is used to choose optimal parameters for normalization.
The function agreement accesses the performance of normalization measuring intra-replicate differences before and after normalization. It takes the output of funtoonorm as an input.
For more details, see the vignette provided with the package or download the pdf file from here.