randomGODB

Description

The Gene Ontology (GO) Consortium <https://geneontology.org/> organizes genes into hierarchical categories based on biological process (BP), molecular function (MF) and cellular component (CC, i.e., subcellular localization). Tools such as 'GoMiner' (see Zeeberg, B.R., Feng, W., Wang, G. et al. (2003) <doi:10.1186/gb-2003-4-4-r28>) can leverage GO to perform ontological analysis of microarray and proteomics studies, typically generating a list of significant functional categories. The significance is traditionally determined by randomizing the input gene list to computing the false discovery rate (FDR) of the enrichment p-value for each category. We explore here the novel alternative of randomizing the GO database rather than the gene list.

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Running examples in ‘randomGODB-Ex.R’ failed
The error most likely occurred in:

> ### Name: addName2List
> ### Title: addName2List
> ### Aliases: addName2List
> 
> ### ** Examples
> 
> BP_ANCESTOR<-addName2List(as.list(GO.db::GOBPANCESTOR))
Error in loadNamespace(x) : there is no package called ‘GO.db’
Calls: addName2List ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted

Package suggested but not available for checking: ‘GO.db’

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Package suggested but not available for checking: ‘GO.db’

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