simMatSmall: A Resnik Similarity Matrix.

In GOGANPA: GO-Functional-Network-based Gene-Set-Analysis

Description

A Resnik Similarity Matrix (normalized) for 2000 human genes sampled from 14173 annotated human genes.

Details

The similarity matrix was computed using the R package csbl.go (http://csbi.ltdk.helsinki.fi/csbl.go/), using a GO term specificity table computed using GO BP annotations for all human Entrez Genes available in the Bioconductor package org.Hs.eg.db, version 2.6.4 (not the default table provided csbl.go).

Note

This matrix is provided for test-running GOGANPA only. Although it is sampled from the similarity matrix used in Chang et. al. (2012), it cannot be used to reproduce the results presented in Chang et. al. (2012).

Author(s)

Billy Chang

References

Ovaska, K, Laakso M, and Hautaniemi, S. (2008) Fast Gene Ontology based clustering for microarray experiments. BioData Mining. 1:11.

Chang, B., Kustra, R. and Tian, WD (2012) Functional-Network-based Gene Set Analysis using Gene Ontology. Submitted.

Examples

#Not to Run
data("simMatSmall",package='GOGANPA')

GOGANPA documentation built on May 2, 2019, 6:04 a.m.