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 1.6.0 Index]