gtResult-class {PCpheno} | R Documentation |
A class for representing the result of a graphTheory
test.
Pvalue
:Object of class "numeric"
Observed
:Return a "numeric"
vector: the observed number of interactions between genes inducing a specific phenotype and each
cellular organizational units
Expected
:Return a matrix: the expected number of interactions between genes inducing a specific phenotype and each cellular organizational units
Class "testResult"
, directly.
plot
Graphical representation of the test result
N. LeMeur
## apply a densityEstimate test data(DudleyPhenoM) data(ScISIC) DudleyPhenoL <- apply(DudleyPhenoM,2,function(x) names(which(x==1))) NaCl <- DudleyPhenoL[["NaCl"]] perm <- 20 NaClGraph <- graphTheory(genename=NaCl, interactome=ScISIC, perm=perm) ## access results slotNames(NaClGraph) NaClGraph@Pvalue[1:5] ## use of the plot method plot(NaClGraph)