Package: GraphAT 1.85.0

Thomas LaFramboise

GraphAT: Graph Theoretic Association Tests

Functions and data used in Balasubramanian, et al. (2004)

Authors:R. Balasubramanian, T. LaFramboise, D. Scholtens

# Install 'GraphAT' in R:

install.packages('GraphAT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

causton - Yeast mRNA Expression Data
ccCM - Cell-Cycle Cluster Matrix
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
giaever - Yeast Gene-Knockout Fitness Data
mRNAclusters - Yeast mRNA Expression Data Cluster Memberships
nNamescc - Cell-Cycle Cluster Matrix
Phenoclusters - Yeast Gene-Knockout Fitness Data Cluster Memberships

On BioConductor:GraphAT-1.85.0(bioc 3.24)GraphAT-1.84.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

Last updated from:01e733a68e. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	139
linux-devel-x86_64	NOTE	143
source / vignettes	OK	176
linux-release-x86_64	NOTE	190
macos-release-arm64	NOTE	118
macos-oldrel-arm64	NOTE	88
windows-devel	NOTE	96
windows-release	NOTE	94
windows-oldrel	NOTE	96
wasm-release	OK	92

Help page	Topics
Yeast mRNA Expression Data	causton
Cell-Cycle Cluster Matrix	ccCM nNamescc
Function to compute adjacency matrix of cluster graph given a vector of cluster memberships	clust2Mat
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	depthmatBP depthmatCC depthmatMF
Function to obtain P values from the Edge permutation and Node permutation tests respectively	getpvalue
Yeast Gene-Knockout Fitness Data	giaever
Make an adjacency matrix for a cluster graph	makeClustM
Change graph representations	mat2UndirG
Yeast mRNA Expression Data Cluster Memberships	mRNAclusters
Function to compute estimated probability of detecting preferential connection of intracluster nodes	permPower
Randomly permute edges or node labels in a graph	permEdgesM2M permNodesM2M
Yeast Gene-Knockout Fitness Data Cluster Memberships	Phenoclusters