GOHyperGResult-class {GOstats}R Documentation

Class "GOHyperGResult"

Description

This class represents the results of a test for overrepresentation of GO categories among genes in a selected gene set based upon the Hypergeometric distribution.

Objects from the Class

Objects can be created by calls of the form new("GOHyperGResult", ...).

Slots

goDag:
Object of class "graph" representing the DAG of GO terms tested.
pvalue.order:
Object of class "integer". The sort order of the computed p-values.
annotation:
Object of class "character". The name of the annotation data package used in the analysis.
geneIds:
Object of class "ANY". The intersection of the gene identifiers given as input and the computed gene universe.
testName:
Object of class "character". Identifies the testing method used to produce this result instance.
pvalueCutoff:
Object of class "numeric". The cutoff for significance used for some testing methods. Also used for pretty display in the show method.

Extends

Class "HyperGResultBase", directly.

Methods

geneCounts
signature(r = "GOHyperGResult"): return an "integer" vector: for each category term tested, the number of genes from the gene set that are annotated at the term.
goDag
signature(r = "GOHyperGResult"): return the graph instance representing the DAG of the GO terms that were tested.
pvalues
signature(r = "GOHyperGResult"): return a "numeric" vector: the ordered p-values for each category term tested.
oddsRatios
signature(r = "GOHyperGResult"): return a "numeric" vector: the odds ratio for each category term tested.
expectedCounts
signature(r = "GOHyperGResult"): return a "numeric" vector: the expected number of genes for each GO term tested.
universeCounts
signature(r = "GOHyperGResult"): return an "integer" vector: for each category term tested, the number of genes from the gene universe that are annotated at the term.
universeMappedCount
signature(r = "GOHyperGResult"): return an "integer" vector of length one giving the size of the gene universe set.
geneIdUniverse
signature(r = "GOHyperGResult"): return a list named by the tested GO terms. Each element of the list is a vector of gene identifiers (from the gene universe) annotated at the corresponding GO term.
condGeneIdUniverse
signature(r = "GOHyperGResult"): return a list named by the tested GO terms. Each element of the list is a vector of the remaining gene identifiers (from the gene universe) annotated at the corresponding GO term after the identifiers from significant children were removed. This is only available when the calculation performed used the conditional Hypergeometric algorithm.
summary
signature(r = "GOHyperGResult"): Returns a data.frame summarizing the test result. Optional arguments pvalue and categorySize allow specification of maximum p-value and minimum 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").
htmlReport
signature(r = "GOHyperGResult"): Write an HTML version of the table produced by the summary method. The path of a file to write the report to can be specified using the file argument. The default is file="" which will cause the report to be printed to the screen. If you wish to create a single report comprising multiple results you can set append=TRUE. The default is FALSE (overwrite preexisting report file). You can specify a string to use as an identifier for each table by providing a value for the label argument. Additional named arguments will be passed to the summary method.
description
signature(object = "GOHyperGResult"): Return a string giving a one-line description of the result.
isConditional
signature(r = "GOHyperGResult"): Return a TRUE if the result was created using a conditional algorithm and FALSE otherwise.

Author(s)

Seth Falcon

See Also

GeneCategoryHyperGeoTestResult


[Package GOstats version 2.0.4 Index]