Class that represents a geneSet

An S4 class to manage an individual geneSet record. Usually multiple geneSets will be included in a geneSetList or geneSetFile object, which can be generated using the buildGeneSet method.

Slots

geneSetName

name of the geneset

units

units (usually genes) in the geneSet

w

optional weights (defaults to 1 for each unit)

metadata

optional metadata for each geneset

Getters

In the following code snippets, x is a geneSet object.

• listUnits(x): Return a vector of all units included in the geneSet

• listWeights(x): Return a vector of all weights in the geneSet

See also

geneSetFile

geneSetList

buildGeneSet

Examples

genesetlist <- buildGeneSet(
  list("geneset1" = c("SOD1", "NEK1"),
       "geneset2" = c("ABCA4", "SOD1", "NEK1"),
       "geneset3" = c("FUS", "NEK1")
       ))
geneset <- genesetlist[[1]]

# list units and weights included in the geneSet
listUnits(geneset)
#> [1] "SOD1" "NEK1"
listWeights(geneset)
#> SOD1 NEK1 
#>  "1"  "1" 

# note that usually you'll work with geneSets in either a geneSetList or 
# a geneSetFile (see ?geneSetList and ?geneSetFile)