# Graph Theoretic Association Tests

## Documentation for package `GraphAT' version 1.4.0

## Help Pages

causton | Yeast mRNA Expression Data
ccCM | Cell-Cycle Cluster Matrix
clust2Mat | Function to compute adjacency matrix of cluster graph given a vector of cluster memberships
depthmatBP | Matrices of depth of association for pairs of YEAST genes with respect to each of the BP,CC and MF ontologies of the GO database
depthmatCC | Matrices of depth of association for pairs of YEAST genes with respect to each of the BP,CC and MF ontologies of the GO database
depthmatMF | Matrices of depth of association for pairs of YEAST genes with respect to each of the BP,CC and MF ontologies of the GO database
getpvalue | Function to obtain P values from the Edge permutation and Node permutation tests respectively
giaever | Yeast Gene-Knockout Fitness Data
makeClustM | Make an adjacency matrix for a cluster graph
mat2UndirG | Change graph representations
mRNAclusters | Yeast mRNA Expression Data Cluster Memberships
nNamescc | Cell-Cycle Cluster Matrix
permEdgesM2M | Randomly permute edges or node labels in a graph
permNodesM2M | Randomly permute edges or node labels in a graph
permPower | Function to compute estimated probability of detecting preferential connection of intracluster nodes
Phenoclusters | Yeast Gene-Knockout Fitness Data Cluster Memberships