DoIntEpi450k:
Integrates statistics of differential DNA methylation for a specified
contrast with a network adjacency matrix.
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)
Arguments
statM.o
The output of GenStatM, 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.
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
Details
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