DOSE

Disease Ontology Semantic and Enrichment analysis Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring DO semantic similarities, and hypergeometric test for enrichment analysis.

Datasets

EXTID2NAME

GSEA_internal

clusterSim

Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.

compute information content

doSim

Enrichment analysis based on the DisGeNET (http://www.disgenet.org/)

enrichDGN

DO Enrichment Analysis

enrichNCG

Class "enrichResult" This class represents the result of enrichment analysis.

enrich.internal

convert Gene ID to DO Terms

geneID generic

geneInCategory generic

geneSim

DisGeNET Gene Set Enrichment Analysis

DO Gene Set Enrichment Analysis

NCG Gene Set Enrichment Analysis

Class "gseaResult" This class represents the result of GSEA analysis

gsfilter

mclusterSim

parse_ratio

rebuiding annotation data

Objects exported from other packages

setReadable

show method

simplot

summary method

theme_dose