GOTermsList: Functions to create and manage lists of GO terms associated with a vector of 'Entrez' identifiers

Description

These functions prepare data to be processed by the 'basicProfile' function. To create a profile a set of GOterms belonging to one or more ontologies is needed The terms belonging to each gene must be given separately so that they can be counted. This function queries the environment 'GOENTREZID2GO' with the vector of Entrez terms and formats the output into a list whose components -one per Entrez term- contain the most specific GO identifiers associated with this term.

Usage

GOTermsList(LLids, onto = "any", evid = "any", na.rm = TRUE, orgPkg )
getAncestorsLst(GOtermslist, onto, unique.ancestor=TRUE, na.rm=TRUE, combine=TRUE)
getGOLevel(onto, level)

Arguments

LLids

Character vector of Entrez (formerly Locuslink identifiers)

onto

ontology to be queried using the genes list

evid

type of evidence supporting the selected GO Terms

na.rm

flag indicating if those ids returning NA must be removed from the output

orgPkg

Organism annotation package ('org.Xx.eg.db') required to obtain the GO terms associated with the Entrez identifiers

GOtermslist

List produced by a call to function GOTermsList

unique.ancestor

Flag to remove repeated ancestor identifiers

combine

Flag to combine ancestors

level

GO level at which the profile is built

Value

A list whose components -one per Entrez term- are character vectors with the most specific GO identifiers associated with this term

Details

During the call to this function there may appear two types of NAs.

By one side if a name is not mapped in LocusLink this yields an NA that must be eliminated because nothing can be found through LL about this name

By another side if a gene is identified in LL but yields NA it seems to mean that it is not mapped in the GO

This may be eliminated but it may be worth the pity to keep track of them and to put these terms in an 'Seemingly unnanotated' category. In the case that its number was very high it migt suggest reviewing the list or reconsidering the results.

Examples

Run this code

#data(CD4Ids)
#simpleLLids<- as.character(c(2189,5575,5569,11)) #1 is not a Locuslink identifier
#simpleGOlist<- GOTermsList (simpleLLids, orgPkg="org.Hs.eg.db")
#print(simpleGOlist.CC<-GOTermsList (simpleLLids,"CC", orgPkg="org.Hs.eg.db"))
#print(simpleGOlist.IEA<-GOTermsList (simpleLLids,evid="IEA",na.rm=TRUE, orgPkg="org.Hs.eg.db"))