GenStatM {FEM} | R Documentation

## Generation of differential DNA methylation statistics

### Description

Given an Illumina 450k or EPIC (850k) data matrix and a phenotype vector, it will generate statistics of differential DNA methylation using limma, at the gene-level, for all pairwise comparisons of phenotype levels.

### Usage

    GenStatM(dnaM.m,pheno.v,"chiptype")

### Arguments

`dnaM.m` | The DNA methylation beta valued data matrix with rownames annotated to Illumina 450k or EPIC(850k) probe IDs
`pheno.v` | The phenotype vector.
`chiptype` | A parameter specifying the the input data matrix, it should be either "450k" for Illumina 450k matrix or "EPIC" for Illumina EPIC matrix. default for "450k"

### Value

`top` | A list of matrices, from the limma output, ranking genes according to differential methylation between two phenotypes as specified in the contrasts matrix, i.e. top[[i]] will contain the ranking for the i'th contrast.
`cont` | The contrasts matrix, with columns labeling the contrasts.
`avbeta` | The beta-valued DNAm data matrix at the gene-level, following the procedure as described in Jiao et al Bioinformatics 2014.

### Author(s)

"Yinming Jiao"<20907099@zju.edu.cn>, "Andrew E Teschendorff"<andrew@picb.ac.cn>

### References

A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control. Jiao Y, Widschwendter M, Teschendorff AE. Bioinformatics. 2014;30(16):2360-2366

[Package FEM version 3.12.0 Index]