Toy example for using NetGSA on a two-class test with directed acyclic graphs

Description

This dataset contains an example for using Network-based Gene Set Analysis on a two-sample test with directed acyclic graphs.

Usage

data("netgsaexDAG")

Format

A list with components

A

A list ot two weighted adjacency matrices.

x

The p x n data matrix.

y

The vector of class indicators of length n.

B

The npath by p indicator matrix for pathways.

References

Shojaie, A., & Michailidis, G. (2010). Network enrichment analysis in complex experiments. Statistical applications in genetics and molecular biology, 9(1), Article 22. http://www.ncbi.nlm.nih.gov/pubmed/20597848.

Shojaie, A., & Michailidis, G. (2009). Analysis of gene sets based on the underlying regulatory network. Journal of Computational Biology, 16(3), 407-426. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131840/

Examples

data(netgsaexDAG)
A = netgsaexDAG$A
B = netgsaexDAG$B
x = netgsaexDAG$x
y = netgsaexDAG$y
fitDAG = NetGSA(A, x, y, B, lklMethod="REML", directed=TRUE)

Results