topGOresult-class {topGO} | R Documentation |
Class instance created by
getSigGroups-methods
or by runTest
Objects can be created by calls of the form new("topGOresult",
description, score, testName, algorithm, geneData)
.
description
:character string containing a short description on how the object was build.
score
:named numerical vector containing the p-values or the scores of the tested GO terms.
testName
:character string containing the name of the test statistic used.
algorithm
:character string containing the name of the algorithm used.
geneData
:list containing summary statistics on the genes/gene universe/annotations.
score
:method to access the score
slot.
testName
:method to access the testName
slot.
algorithm
:method to access the algorithm
slot.
geneData
:method to access the geneData
slot.
show
:method to print the object.
combineResults
:method to aggregate two or more
topGOresult objects. method = c("gmean", "mean", "median",
"min", "max")
provides the way the object scores (which most of
the time are p-values) are combined.
.
Adrian Alexa
groupStats-class
,
getSigGroups-methods
data(results.tGO) s <- score(resultFisher) go <- sort(names(s)) go.sub<- sample(go, 100) go.mixed <- c(sample(go, 50), sample(ls(GOCCTerm), 20)) go.others <- sample(ls(GOCCTerm), 100) str(go) str(go.sub) str(go.mixed) str(go.others) str(score(resultFisher, whichGO = go)) str(score(resultFisher, whichGO = go.sub)) str(score(resultFisher, whichGO = go.mixed)) str(score(resultFisher, whichGO = go.others)) avgResult <- combineResults(resultFisher, resultKS) avgResult combineResults(resultFisher, resultKS, method = "min")