HyperGParamsCC-class: Class "HyperGParamsCC"

In rmflight/categoryCompare: Meta-analysis of high-throughput experiments using feature annotations

Class "HyperGParamsCC"

Description

This class extends the HyperGParams class in Category by providing options for multiple testing and the storing of extra data in addition to the gene list of interest (not currently used, but might be in the future).

Objects from the Class

Objects can be created by calls of the form new("HyperGParamsCC", ...). In general the user will not create these directly, but they are created and used by to carry out the enrichment calculations.

Slots

fdr:

Object of class "numeric" The number of FDR runs to perform

data:

Object of class "data.frame" Extra data stored in the object

geneIds:

Object of class "ANY" The genes of interest

universeGeneIds:

Object of class "ANY" The gene universe or background used (all the genes on the chip)

annotation:

Object of class "character" The annotation package used to get information about the geneIds

datPkg:

Object of class "DatPkg" Generated automatically from the annotation slot

categorySubsetIds:

Object of class "ANY" A specific set of category IDs that one wants to restrict the testing to

categoryName:

Object of class "character" What type of category to use, currently either "GO" or "KEGG"

pvalueCutoff:

Object of class "numeric" What should be the p-value to decide significance

testDirection:

Object of class "character" "over" or "under" represented annotation terms

Extends

Class "GOHyperGParams", directly.

Methods

No methods defined with class "HyperGParamsCC" in the signature.

Author(s)

Robert M Flight

See Also

HyperGResultCC ccEnrich Category-package

Examples

showClass("HyperGParamsCC")

rmflight/categoryCompare documentation built on April 25, 2024, 11:20 a.m.