Integrates statistics of differential expression for a specified contrast with a network adjacency matrix.

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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

1
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

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.