| getGeneSetsForPlot {esetVis} | R Documentation |
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.
getGeneSetsForPlot(entrezIdentifiers, species = "Human",
geneSetSource = c("GOBP", "GOMF", "GOCC", "KEGG"),
useDescription = TRUE, trace = TRUE)
entrezIdentifiers |
string with Entrez Gene identifiers of the genes of interest |
species |
species to use, given to the |
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 |
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
Laure Cougnaud
the function used internally: getGeneSets
# 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