R: Functions to create and manage lists of GO terms associated...
GOTermsList
R Documentation
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.
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
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.
Value
A list whose components -one per Entrez term- are character vectors with the most
specific GO identifiers associated with this term
Author(s)
Alex Sanchez
See Also
getAncestorsLst
Examples
#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"))