PCpheno (version 1.28.0)

gtResult-class: A class for representing the result of a graphTheory test.

Description

A class for representing the result of a graphTheory test.

Slots

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

Extends

Class "testResult", directly.

Methods

plot

Graphical representation of the test result

See Also

testResult,deResult,plot

Examples

## 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)