ccEnrichResult-class: Class "ccEnrichResult"

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

Description

Acts as a container object for multiple HyperGResultCC objects.

Objects from the Class

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

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

fdr

signature(object = "ccEnrichResult"): get the number of runs using random feature lists were performed

pvalueCutoff

signature(r = "ccEnrichResult"): what is the pvalueCutoff to determine significant annotations

pvalueCutoff<-

signature(r = "ccEnrichResult"): change the pvalueCutoff for an annotation to be considered significant

pvalueType<-

signature(object = "ccEnrichResult"): change whether p-values used are from "FDR" or raw p-values

minCount

signature(object = "ccEnrichResult"): how many features need to belong to an annotation to be reported

minCount<-

signature(object = "ccEnrichResult"): adjust the minCount

graphType

signature(object = "ccEnrichResult"): what type of graph should be generated (generally set by the class of object)

graphType<-

signature(object = "ccEnrichResult"): change the type of graph to generate by ccCompare

Author(s)

Robert M Flight

Examples

data(ccData)
enrichRes <- enrichLists[[1]]
fdr(enrichRes)
pvalueType(enrichRes)
enrichRes
pvalueType(enrichRes) <- 'pval'
enrichRes

pvalueCutoff(enrichRes)
pvalueCutoff(enrichRes) <- 0.01
enrichRes

categoryCompare documentation built on Nov. 8, 2020, 5:59 p.m.