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