# Two-sample tests on a graph

## Documentation for package ‘DEGraph’ version 1.4.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

AN.test | Performs the Adaptive Neyman test of Fan and Lin (1998)
annLoi2008 | Annotation data used in the DEGraph package vignette
BS.test | Performs the test of Bai and Saranadasa (1996)
classLoi2008 | Tamoxifen treatment resistance status data used in the DEGraph package vignette
exprLoi2008 | Gene expression data used in the DEGraph package vignette
getConnectedComponentList | Given a graph, returns a list of its connected components (which are also graph objects), ordered by decreasing number of nodes
getKEGGPathways | Builds a graph for each of the KEGG pathways
getSignedGraph | Given a graph, builds a signed version of the adjacency matrix taking into account the type of interaction (e.g., activation or inhibition)
graph.T2.test | Performs the Hotelling T2 test in Fourier space
grListKEGG | KEGG networks used in the DEGraph package vignette
hyper.test | Performs an hypergeometric test of enrichment of a set of hypotheses in significant elements
is.NCIgraph | Assess whether a graph is a NCI graph
laplacianFromA | Calculates the Laplacian associated to an adjacency matrix
plotValuedGraph | Plots a graph with nodes colored according to a quantitative variable
randomWAMGraph | Generates a random graph
testOneConnectedComponent | Applies a series of two-sample tests to a connected graph using various statistics
testOneGraph | Applies a serie of two-sample tests to each connected component of a graph using various statistics
twoSampleFromGraph | Given a basis (typically the eigenvectors of a graph Laplacian), builds two multivariate normal samples with mean shift located in the first elements of the basis
writeAdjacencyMatrix2KGML | Writes an adjacency matrix into an XML file