GenStatM


The DNA methylation beta valued data matrix with rownames annotated to
Illumina 450k probe IDs


dnaM.m

pheno.v


Given an Illumina 450k 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.


 ~kwd1 

 ~kwd2 

The FEM package performs a systems-level integrative analysis of DNA methylation and gene expression data. It seeks modules of functionally related genes which exhibit differential promoter DNA methylation and differential expression, where an inverse association between promoter DNA methylation and gene expression is assumed. For full details, see Jiao et al Bioinformatics 2014.

Andrew E Teschendorff

Identification of Functional Epigenetic Modules

GenStatM function

The DNA methylation beta valued data matrix with rownames annotated to
Illumina 450k probe IDs

Given an Illumina 450k 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.

Generation of differential DNA methylation statistics

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.

The contrasts matrix, with columns labeling the contrasts.

cont

The beta-valued DNAm data matrix at the gene-level,
  following the procedure as described in Jiao et al Bioinformatics 2014.

GenStatM: Generation of differential DNA methylation statistics

Description

Usage

Arguments

Value

Details

References

See Also

Examples