GENccEnrichResult-class: Class '"GENccEnrichResult"'

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

Class "GENccEnrichResult"

Description

Holds generic ccEnrich type results

Objects from the Class

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

Slots

.Data:

Object of class "list" The actual list containing the ccEnrichResults

categoryName:

Object of class "character"

ontology:

Object of class "character"

geneAnnMapping:

Object of class "namedList"

graphType:

Object of class "character"

names:

Object of class "character"

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

[

signature(x = "GENccEnrichResult", i = "ANY", j = "ANY"): Subsets the object to just those lists that are desired

categoryName

signature(object = "GENccEnrichResult"):

ccCompareGeneric

signature(gccResult = "GENccEnrichResult", ccOptions = "ccOptions"): ...

geneAnnMapping

signature(object = "GENccEnrichResult"): ...

graphType

signature(object = "GENccEnrichResult"): ...

graphType<-

signature(object = "GENccEnrichResult"): ...

ontology

signature(object = "GENccEnrichResult"): ...

Author(s)

Robert M Flight

See Also

ccCompareGeneric ccSigList

Examples

data(ccData)
locA <- grep("A",gseaRes$Tissues)
locL <- grep("L",gseaRes$Tissues)
locM <- grep("M",gseaRes$Tissues)

A <- new("ccSigList",sigID=gseaRes$KEGGID[locA],categoryName="KEGG",annotation="org.Mm.eg")
L <- new("ccSigList",sigID=gseaRes$KEGGID[locL],categoryName="KEGG",annotation="org.Mm.eg")
M <- new("ccSigList",sigID=gseaRes$KEGGID[locM],categoryName="KEGG",annotation="org.Mm.eg")
ccEnrichCol <- list(A=A,L=L,M=M)
ccEnrichCol <- new("GENccEnrichResult", ccEnrichCol, categoryName="KEGG")

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