PCpheno (version 1.28.0)

CoHyperGResult-class: Class "CoHyperGResult"

Description

This class represents the results of a test for over-representation of genes in a selected gene set based among protein complexes upon the Hypergeometric distribution.

Objects from the Class

Objects is created by calls to the funtion hyperGTest.

Slots

pvalues:

"numeric" vector: the ordered p-values for each category term tested.

oddsRatios:

Object of class "numeric" Odds ratio for each category term tested

expectedCounts:

Object of class "numeric" The expected number of genes for each gene term tested

geneCounts:

"integer" vector: for each category term tested, the number of genes from the gene set that are annotated at the term.

universeCounts:

"integer" vector: for each category term tested, the number of genes from the gene universe that are annotated at the term.

catToGeneId:

Object of class "list". The names of the list are category IDs. Each element is a vector of gene IDs annotated at the given category ID and in the specified gene universe.

Extends

Class "HyperGResultBase", directly.

Methods

geneCounts

signature(r = "CoHyperGResult"): return an "numeric" vector: for each category term tested, the number of genes from the gene set that are annotated at the term.

pvalues

signature(r = "HyperGResult"): return a "numeric" vector: the ordered p-values for each category term tested.

oddsRatios

signature(r = "HyperGResult"): return a "numeric" vector: the odds ratio for each category term tested.

expectedCounts

signature(r = "HyperGResult"): return a "numeric" vector: the expected number of genes for each GO term tested.

universeCounts

signature(r = "HyperGResult"): return an "numeric" vector: for each category term tested, the number of genes from the gene universe that are annotated at the term.

geneIdUniverse

signature(r = "CoHyperGResult"): return a list named by the protein Complexes. Each element of the list is a vector of gene identifiers (from the gene universe) annotated at the corresponding protein complex.

summary

signature(r = "CoHyperGResult"): Returns a data.frame summarizing the test result. Optional arguments pvalue and categorySize allow specification of minimum p-value and cateogyrSize, respectively. Optional argument htmlLinks is a logical value indicating whether to add HTML links (useful in conjunction with xtables print method with type set to "html").

See Also

HyperGResultBase-class

Examples

data(DudleyPhenoM)
data(ScISIC)

## Select genes sensitive to paraquat
DudleyPhenoL <- apply(DudleyPhenoM,2,function(x) names(which(x==1)))
paraquat <- DudleyPhenoL[["Paraq"]]

## Apply a hypergeometric test
params <- new("CoHyperGParams",
              geneIds=paraquat, 
              universeGeneIds=rownames(ScISIC),
              annotation="org.Sc.sgd.db",
              categoryName="ScISIC",
              pvalueCutoff=0.01,
              testDirection="over")

paraquat.complex <- hyperGTest(params)

## access the p-values
pvalues(paraquat.complex)[1:5]

## Display a summary of the results
summary(paraquat.complex)[,1:4]