R/AllGenerics.R

In meshr: Tools for conducting enrichment analysis of MeSH

##
## Generic functions
##

## This is already defiend in Category/R/AllGenerics.R but seems like required.
## Probably because this is not listed in exportMethods() of Category/NAMESPACE?
setGeneric("universeGeneIds<-",
           function(r, value) standardGeneric("universeGeneIds<-"))
setGeneric("universeGeneIds", function(r) standardGeneric("universeGeneIds"))

setGeneric("pAdjust", function(r) standardGeneric("pAdjust"))
setGeneric("pAdjust<-", function(r, value) standardGeneric("pAdjust<-"))

setGeneric("pvalueCutoff<-", function(r, value) standardGeneric("pvalueCutoff<-"))

setGeneric("meshIds", function(r) standardGeneric("meshIds"))

setGeneric("meshTerms", function(r) standardGeneric("meshTerms"))

setGeneric("meshCategory", function(r) standardGeneric("meshCategory"))

setGeneric("meshAnnotation", function(r) standardGeneric("meshAnnotation"))

setGeneric("category", function(r) r@category)
setGeneric("category<-",
    function(r, value) standardGeneric("category<-")
)

setGeneric("database", function(r) r@database)
setGeneric("database<-",
    function(r, value) standardGeneric("database<-")
)

setGeneric("meshDatabase", function(r) standardGeneric("meshDatabase"))

setGeneric("meshHyperGTest",
           function(p) standardGeneric("meshHyperGTest"),
           valueClass="MeSHHyperGResult")

setGeneric("save.pdf",function(r){standardGeneric("save.pdf")})