GenStatMsp {FEM} | R Documentation

## Generation of differential DNA methylation statistics for SingleProbe Mode

### Description

Given an Illumina 450k or EPIC (850k) data matrix and a phenotype vector, similiar to the function of GenStatM, it will generate statistics of differential DNA methylation using limma, at the gene-level, for all pairwise comparisons of phenotype levels. However, instead of the average beta values for the probes in each region, it will select the most significant differentially methylated CpGs among TSS200 and 1st Exon regions, if not present then select the the most significant differentially methylated CpGs among TSS1500

### Usage

    GenStatMsp(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.
`probeID` | A list of vectors, with each entry a vector of probeIDs that present the most differentially methylated cpg associated with each gene, i.e. probeID[[i]] will contain the vector for the i'th contrast.

### 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]