expandedLevel: Function to create expanded levels which can contain GO Terms...

In alexsanchezpla/goProfiles: goProfiles: an R package for the statistical analysis of functional profiles

Description

This function, combined with function expandTerm, allows to create mixed levels which can contain terms belonging to different GO levels. Specifically one can take one (or several, but one by one) term at a given GO level and expand it into its children terms using function expandTerm and then combine them into a new level using this function.

Usage

expandedLevel(LevelTerms, Term2Expand, onto)
expandTerm(GOTerm, onto)

Arguments

LevelTerms	Other terms which have not been expanded, and will be combined with the expanded ones
Term2Expand	The GO term which will be substituted by its children terms
GOTerm	The GO term which will be substituted by its children terms
onto	The ontology ('MF','BP','CC'

Value

The value returned is the vector combining the original terms with the children of the term that had to be expanded.

Author(s)

Alex Sanchez

Examples

got<-toTable(GOTERM)[,2:3]
desc<-function(s) got[got[,1]==s,2]
MFLevel2<-getGOLevel("MF",2)
bindingLevel2<-MFLevel2 [2]
bindingLevel3 <- expandTerm(bindingLevel2,"MF")
print(descbindingLevel3<-as.matrix(sapply(bindingLevel3,desc )))
mixedLevel<-c(MFLevel2[-2],bindingLevel3)
print(mixedLevel<-as.matrix(sapply(mixedLevel,desc )))

alexsanchezpla/goProfiles documentation built on May 28, 2019, 4:54 p.m.