Fetches information for a gene set — geneSet • multiGSEA

Gene sets inside a GeneSetDb() are indexed by their collection,name compound key. There is no special class to represent an individual gene set. Instead, gene sets are returned as a data.frame, the rows of which enumerate the features that belong to them.

When x is a MultiGSEAResult(), this function will append the differential expression statistics for the individual features generated across the contrast that defined x.

geneSet(x, i, j, ...)

# S4 method for GeneSetDb
geneSet(
  x,
  i,
  j,
  active.only = is.conformed(x),
  with.feature.map = FALSE,
  ...,
  collection = NULL,
  name = NULL,
  as.dt = FALSE
)

# S4 method for MultiGSEAResult
geneSet(
  x,
  i,
  j,
  active.only = TRUE,
  with.feature.map = FALSE,
  ...,
  collection = NULL,
  name = NULL,
  as.dt = FALSE
)

Arguments

x	Object to retrieve the gene set from, either a `GeneSetDb` or a `MultiGSEAResult`.
i	The collection,name compound key identifier of the gene set
j	The collection,name compound key identifier of the gene set
...	passed down to inner functinos
active.only	only look for gene sets that are "active"? Defaults to `TRUE` if `x` is conformed to a target expression object, else `FALSE`. `conform()` for further details.
with.feature.map	If `TRUE`, then details of the feature mapping from the original feature_id space to the target feature space are included (default: `FALSE`).
as.dt	If `FALSE` (default), the data.frame like thing that this funciton returns will be set to a data.frame. Set this to `TRUE` to keep this object as a `data.table`

Value

a data.(frame|table) of gene set information. If x is a MultiGSEAResult object, then differential expression statistics are added as columns to this result.