DoIntEpi450k: Integrates statistics of differential DNA methylation for a...

In FEM: Identification of Functional Epigenetic Modules

Description

Integrates statistics of differential DNA methylation for a specified contrast with a network adjacency matrix. Output of this function is required input for DoEpiMod.

Usage

DoIntEpi450k(statM.o,adj.m,c,"dmaMode")

Arguments

statM.o	The output of GenStatM, GenStatMsp, or analogous object generated by user.
adj.m	The adjacency matrix defining the network of gene relations, e.g. a PPI network, annotated to NCBI entrez gene IDs.
c	An integer specifying the desired contrast, i.e. column of the contrast matrix. User needs to check which column of statM.o$cont is the one of interest.
dmaMode	An parameter specifying the object mode for statM.o, "avbeta" for the average beta mode object generated by GenStatM, whereas "singleProbe" for the single probe mode object generated by the GenStatMsp, default for "avbeta"

Value

A list with following entries:

statM	matrix of DNA methylation moderated t-statistics and P-values for the genes in the integrated network
adj	adjacency matrix of the maximally connected integrated network (at present only the maximally connected subnetwork is used in the subsequent inference
avbeta	average DNA methylation data matrix mapped to unique Entrez IDs
probeID	vector of the probe IDs that most differentially methylated for each gene

Author(s)

"Yinming Jiao"<[e-mail]>, "Andrew E Teschendorff"<[e-mail]>

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

FEM documentation built on April 28, 2020, 8:56 p.m.