CoHyperGResult-class {PCpheno}R Documentation

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.
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.
annotation:
A string giving the name of the chip annotation data package used.
geneIds:
Object of class "ANY": the input vector of gene identifiers intersected with the universe of gene identifiers used in the computation. The class of this slot is specified as "ANY" because gene IDs may be integer or character vectors depending on the annotation package.
testName:
A string identifying the testing method used.
pvalueCutoff:
Numeric value used a a p-value cutoff. Used by the show method to count number of significant terms.

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").

Author(s)

S. Falcon and N. LeMeur

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]

[Package PCpheno version 1.4.1 Index]