getGeneSets {MLP} | R Documentation |
The return value of the getGeneSets function has as primary use to serve as geneSet argument for the MLP function
getGeneSets(species = "Mouse", geneSetSource = NULL, entrezIdentifiers)
species |
character vector of length one indicating the species, one of 'Mouse', 'Human' or 'Rat'; defaults to 'Mouse'. |
geneSetSource |
source to be used to construct the list of pathway categories; for public data sources, the user can specify a string (one of 'GOBP', 'GOMF', 'GOCC', 'KEGG' or 'REACTOME') and BioC packages will be used to construct the list of pathway categories; for non-public data sources, the user can pass the pathway data as a dataframe with (at least) the following four columns: PATHWAYID, TAXID, PATHWAYNAME and GENEID. It is assumed all columns are of type character. |
entrezIdentifiers |
Entrez Gene identifiers used to subset the relevant gene set |
object of class geneSetMLP which is essentially a named
list of pathway categories.
Each list component is named with the pathway ID and
contains a vector of Entrez Gene identifiers
related to that particular pathway.
The object contains additionally the attributes:
'species' and 'geneSetSource': species
and geneSetSource
(as provided as input)
'descriptions': named character vector with pathway descriptions. The vector is named with the pathway ID.
if (require(GO.db) && require(org.Mm.eg.db)){ pathExamplePValues <- system.file("exampleFiles", "examplePValues.rda", package = "MLP") load(pathExamplePValues) geneSet <- getGeneSets(species = "Mouse", geneSetSource = "GOBP", entrezIdentifiers = names(examplePValues)[seq_len(2000)]) geneSet <- getGeneSets(species = "Mouse", geneSetSource = "KEGG", entrezIdentifiers = names(examplePValues)[seq_len(2000)]) }