DoIntExp:
Integrates statistics of differential expression for a specified
contrast with a network adjacency matrix.
Description
Integrates statistics of differential expression for a specified
contrast with a network adjacency matrix. Output of this function is
required input for DoExpMod.
Usage
DoIntExp(statR.o,adj.m,c)
Arguments
statR.o
The output of GenStatR, 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 statR.o$cont is the one of interest.
Value
A list with following entries:
statR
matrix of gene expression 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
for subsequent inference)
avexp
average expression 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.