ccEnrichCollection-class: Class "ccEnrichCollection"

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

Class "ccEnrichCollection"

Description

Holds multiple classes of ccEnrichResult in one object to allow ccCompare to work on only the one object and generate all of the results of a comparison.

Objects from the Class

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

Slots

.Data:

Object of class "list"

names:

Object of class "character" The names (generally GO ontologies or KEGG, but can be changed) of each set of results

Extends

Class "namedList", directly. Class "list", by class "namedList", distance 2. Class "vector", by class "namedList", distance 3. Class "AssayData", by class "namedList", distance 3.

Methods

pvalueCutoff<-

signature(r = "ccEnrichCollection"): Changes the pvalueCutoff to be used to decide significant annotations for all of the contained ccEnrichResult objects

pvalueType<-

signature(object = "ccEnrichCollection"): Changes whether to use p-values or fdr values to determine those annotations that are significant in all of the contained ccEnrichResult objects

minCount<-

signature(object = "ccEnrichCollection"): how many features have to be annotated to a term to be reported as significant

graphType

signature(object = "ccEnrichCollection"): Gets the type of graph that should be output for this collection

Author(s)

Robert M Flight

See Also

ccEnrich hyperGTestCC ccCompare ccEnrichResult

Examples

data(ccData)
enrichLists

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