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Global feature set commands

Source: R/globals.R
global-FeatureSetCommands.Rd

Set the commands to define the global collection of feature sets. This is deprecated in favor of registerFeatureSetCommands.

Usage

setFeatureSetCommands(value)

Arguments

value

A list of two character vectors named "collections" and "sets". Both vectors should be of the same length and have the same names. Vectors should contain R commands to create collections and retrieve sets; see ?FeatureSetTable and the output of createGeneSetCommands for details.

Value

setFeatureSetCommands will set the current global feature set commands and return NULL invisibly.

See also

createGeneSetCommands, for one method of generating value.

Author

Aaron Lun

Examples

old <- getFeatureSetCommands()

new.cmds <- createGeneSetCommands(organism="org.Mm.eg.db",
    identifier="SYMBOL")
setFeatureSetCommands(new.cmds)

getFeatureSetCommands()
#> $collections
#>                                                                                                                                                                                                                                                                        GO 
#>                                                            ".all_terms <- AnnotationDbi::keys(org.Mm.eg.db::org.Mm.eg.db, keytype='GOALL');\ntab <- AnnotationDbi::select(GO.db::GO.db, keys=.all_terms, columns='TERM');\nrownames(tab) <- tab$GOID;\ntab$GOID <- NULL;" 
#>                                                                                                                                                                                                                                                                      KEGG 
#> ".all_terms <- AnnotationDbi::keys(org.Mm.eg.db::org.Mm.eg.db, keytype='PATH');\ntab <- KEGGREST::keggList('pathway');\ntab <- data.frame(ID=names(tab), Description=tab);\nrownames(tab) <- sub('map', '', tab$ID);\ntab <- tab[intersect(rownames(tab), .all_terms),];" 
#> 
#> $sets
#>                                                                                                                                                                                                                                     GO 
#> ".genes_in_set <- tryCatch(AnnotationDbi::select(org.Mm.eg.db::org.Mm.eg.db, keys=.set_id, keytype='GOALL',\n   column=\"SYMBOL\")[,\"SYMBOL\"], error=function(e) character(0));\nselected <- intersect(rownames(se), .genes_in_set)" 
#>                                                                                                                                                                                                                                   KEGG 
#>  ".genes_in_set <- tryCatch(AnnotationDbi::select(org.Mm.eg.db::org.Mm.eg.db, keys=.set_id, keytype='PATH',\n   column=\"SYMBOL\")[,\"SYMBOL\"], error=function(e) character(0));\nselected <- intersect(rownames(se), .genes_in_set)" 
#> 

setFeatureSetCommands(old)