GSCollectionIndex-methods: The GSCollectionIndex class

In malhamdoosh/EGSEA: Ensemble of Gene Set Enrichment Analyses

The GSCollectionIndex class

Description

The GSCollectionIndex class stores an indexed gene set collection.

The operator $ extracts a slot from an object of class GSCollectionIndex.

summary displays a brief summary of a gene set collection

show displays the details of a gene set collection

getSetByName retrieves the details of a given gene set indicated by name

getSetByID retrieves the details of a given gene set indicated by ID

Usage

## S4 method for signature 'GSCollectionIndex'
x$name

## S4 method for signature 'GSCollectionIndex'
summary(object)

## S4 method for signature 'GSCollectionIndex'
show(object)

getSetByName(object, set.name)

getSetByID(object, id)

Arguments

x	GSCollectionIndex, the indexed gene set collection generated from buildIdx, buildMSigDBIdx, buildKEGGIdx, buildGeneSetDBIdx, and buildCustomIdx.
name	character, the slot name
object	GSCollectionIndex, the indexed gene set collection generated from buildIdx, buildMSigDBIdx, buildKEGGIdx, buildGeneSetDBIdx, and buildCustomIdx.
set.name	character, a vector of gene set names as they appear in topSets.
id	character, a vector of gene set IDs as they appears in the plotSummary.

Details

The GSCollectionIndex is used by buildIdx, buildCustomIdx, buildKEGGIdx, buildMSigDBIdx and buildGeneSetDBIdx.

Value

$ returns the selected slot data.

summary does not return data.

show does not return data.

getSetByName returns a list of annotation records

getSetByID returns a list of the annotation records.

Slots

original

list, the original gene sets

idx

list, the gene set indexes

anno

data.frame, the annotations of the gene sets

featureIDs

character, vector of the original Entrez IDs that are used in the indexing procedure

species

character, the species name

name

character, the name of the gene set collection

label

character, a label to distnguish this collection

version

character, the database version from which the collection was extracted

date

character, the update/download date of the database from other collections

Examples

# Example of GSCollectionIndex
library(EGSEAdata)
data(il13.data)
v = il13.data$voom
gs.annots = buildIdx(entrezIDs=rownames(v$E), species="human", 
			msigdb.gsets="none", 
         kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
print(gs.annots[[1]]$name)

# Example of summary
library(EGSEAdata)
data(il13.data)
v = il13.data$voom
gs.annots = buildIdx(entrezIDs=rownames(v$E), species="human", 
			msigdb.gsets="none", 
         kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
summary(gs.annots[[1]])

# Example of show
library(EGSEAdata)
data(il13.data)
v = il13.data$voom
gs.annots = buildIdx(entrezIDs=rownames(v$E), species="human", 
			msigdb.gsets="none", 
         kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
show(gs.annots[[1]])

# Example of getSetByName
library(EGSEAdata)
data(il13.data)
v = il13.data$voom
gs.annots = buildIdx(entrezIDs=rownames(v$E), species="human", 
			msigdb.gsets="none", 
         kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
getSetByName(gs.annots[[1]], "Asthma")

# Example of getSetByID
library(EGSEAdata)
data(il13.data)
v = il13.data$voom
gs.annots = buildIdx(entrezIDs=rownames(v$E), species="human", 
			msigdb.gsets="none", 
         kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
getSetByID(gs.annots[[1]], "hsa04060")

malhamdoosh/EGSEA documentation built on Jan. 28, 2024, 1:17 p.m.