Create gene set commands

Create the commands required to populate FeatureSetTables with commonly used gene sets.

Usage

createGeneSetCommands(
  collections = c("GO", "KEGG"),
  organism = "org.Hs.eg.db",
  identifier = "ENTREZID"
)

Arguments

collections: Character vectors specifying the gene set collections of interest.
organism: String containing the org.*.eg.db package to use to extract mappings of gene sets to gene IDs.
identifier: String specifying the identifier to use to extract IDs for the organism package.

Value

A list of two character vectors describing how to create collections and retrieve gene sets. This follows the expectations for commands in registerFeatureSetCommands.

Details

GO terms are extracted using the "GOALL" mode, which extracts both direct and indirect children of each term. A description for each GO term is extracted using the GO.db package.

Mappings of genes to KEGG pathway are extracted from the organism package using the "PATH" term. Unfortunately, this is not up to date due to the licensing around KEGG terms. Descriptions for each pathway are extracted from http://rest.kegg.jp/list/pathway.

The output of this function can be used as the commands argument of registerFeatureSetCommands. It is also used by default in the FeatureSetTable constructor when no collections are registered.

Author

Aaron Lun

Examples

out <- createGeneSetCommands()
cat(out$collections['GO'], "\n")
#> .all_terms <- AnnotationDbi::keys(org.Hs.eg.db::org.Hs.eg.db, keytype='GOALL');
#> tab <- AnnotationDbi::select(GO.db::GO.db, keys=.all_terms, columns='TERM');
#> rownames(tab) <- tab$GOID;
#> tab$GOID <- NULL; 
cat(out$sets['GO'], "\n")
#> .genes_in_set <- tryCatch(AnnotationDbi::select(org.Hs.eg.db::org.Hs.eg.db, keys=.set_id, keytype='GOALL',
#>    column="ENTREZID")[,"ENTREZID"], error=function(e) character(0));
#> selected <- intersect(rownames(se), .genes_in_set)