I used the packages topGO in R to analyze gene enrichment with the following code:
sampleGOdata <- new("topGOdata", description = "Simple session", ontology = "BP",
allGenes = geneList, geneSel = topDiffGenes, nodeSize = 10,
annot = annFUN.db, affyLib = affyLib)
resultFisher <- runTest(sampleGOdata, algorithm = "classic", statistic = "fisher")
allRes <- GenTable(sampleGOdata, classicFisher = resultFisher, orderBy = "fisher",
ranksOf = "classicFisher",topNodes = 10)
I want to see and change the RunTest
function and the GenTable
function to change the ResultTable
, but I don't know how to show the function. With the getAnywhere("GenTable")
I do not get the hard code I want.
getAnywhere("GenTable")
A single object matching ‘GenTable’ was found
It was found in the following places
package:topGO namespace:topGO
with value
function (object, ...) standardGeneric("GenTable") <environment: 0x16a30c10> attr(,"generic") [1] "GenTable" attr(,"generic")attr(,"package") [1] "topGO" attr(,"package") [1] "topGO" attr(,"group") list() attr(,"valueClass") character(0) attr(,"signature") [1] "object" attr(,"default") `NULL` attr(,"skeleton") function (object, ...) stop("invalid call in method dispatch to \"GenTable\" (no default method)", domain = NA)(object, ...) attr(,"class") [1] "standardGeneric" attr(,"class")attr(,"package") [1] "methods"
How can I do this?
Use getMethod()
and specify the signature. In your case, that could be eg :
getMethod("GenTable","topGOdata")
to show the GenTable method for topGOdata objects. In this case, there is only a method defined for topGOdata objects. In case there are methods with different signatures, showMethods()
will tell you which ones. In your case :
showMethods("GenTable")
# Function: GenTable (package topGO)
# object="topGOdata"
You can get the code for the signature you want by specifying it in the getMethod()
function.