DoIntExp: Integrates statistics of differential expression for a...
In FEM: Identification of Functional Epigenetic Modules

Description Usage Arguments Value Author(s) References

Integrates statistics of differential expression for a specified contrast with a network adjacency matrix. Output of this function is required input for DoExpMod.

1	DoIntExp(statR.o,adj.m,c)

`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.

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

"Yinming Jiao"<20907099@zju.edu.cn>, "Andrew E Teschendorff"<andrew@picb.ac.cn>

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.