getGeneSetsForPlot: get gene sets for plot of eSet object.

In esetVis: Visualizations of expressionSet Bioconductor object

Description

get and format gene sets to be used as geneSets for the functions: esetSpectralMap, esetLda, or esetPlotWrapper Use the getGeneSets function to get the gene sets, combine all databases, and format the gene sets name if required.

Usage

getGeneSetsForPlot(entrezIdentifiers, species = "Human",
  geneSetSource = c("GOBP", "GOMF", "GOCC", "KEGG"),
  useDescription = TRUE, trace = TRUE)

Arguments

entrezIdentifiers	string with Entrez Gene identifiers of the genes of interest
species	species to use, given to the getGeneSets function
geneSetSource	gene set source, either 'GOBP', 'GOMF', 'GOCC' or 'KEGG'. Multiple choices are available
useDescription	logical, if TRUE (by default) use the description to label the gene sets, otherwise use the original gene set identifiers Function 'substr' is used.
trace	logical, if TRUE (by default) a few extra information are printed during the process

Value

list with gene sets, each element is a gene set and contains the ENTREZ IDs of the genes contained in this set. If useDescription is:

• FALSE: pathways are labelled with identifiers (Gene Ontology IDs for GOBP, GOMF and GOCC, KEGG IDs for KEGG)

• TRUE: pathways are labelled with gene sets descriptions

Author(s)

Laure Cougnaud

See Also

the function used internally: getGeneSets

Examples

# example dataset
library(ALL)
data(ALL)

# get gene annotation from probe IDs
library("hgu95av2.db")
probeIDs <- featureNames(ALL)
geneInfo <- select(hgu95av2.db, probeIDs,"ENTREZID", "PROBEID")

# get pathway annotation for the genes contained in the ALL dataset (can take a few minutes)
geneSets <- getGeneSetsForPlot(entrezIdentifiers = geneInfo$ENTREZID, species = "Human", 
	geneSetSource = 'GOBP',
	useDescription = FALSE, trace = TRUE)
head(geneSets) # returns a pathway list of genes

# gene sets labelled with gene sets description
geneSets <- getGeneSetsForPlot(entrezIdentifiers = geneInfo$ENTREZID, species = "Human", 
	geneSetSource = 'GOBP', useDescription = TRUE, trace = TRUE)
head(geneSets) # returns a pathway list of genes

# see also vignette for an example of the use of this function as input for the esetSpectralMap, esetLda or esetPlotWrapper functions

esetVis documentation built on Nov. 8, 2020, 4:51 p.m.