depthmat {GraphAT}R Documentation

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

Description

This matrix of depths is used to obtain the predictome data in the paper. This is a symmetric matrix, where the i,j element corresponds to is the maximum depth of all annotations shared by genes i and j. Note that depth of a term in a specific Gene Ontology (BP, CC, MF) is defined as the shortest path between the term and the root node, where distance between nodes is measured by the number of edges traversed. Row labels of the matrix can be obtained by the row.names() function

Usage

data(depthmatBP)

Format

Each of three matrices, namely depthmatBP.rda, depthmatCC.rda, depthmatMF.rda is a symmetric matrix whose rows and columns correspond to specific YEAST genes (see row labels using row.names()). The i,j entry of each matrix refers to the maximum depth shared by genes i and j under each of the BP, CC and MF ontlogies respectively

Source

http://www.geneontology.org

References

Examples

 
data(depthmatBP)
print(row.names(depthmatBP)[1:10])

[Package GraphAT version 1.0.0 Index]