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 3.14.0 Index]