geneSet {sparrow} | R Documentation |
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 SparrowResult()
, 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 signature 'GeneSetDb' geneSet( x, i, j, active.only = is.conformed(x), with.feature.map = FALSE, ..., collection = NULL, name = NULL, as.dt = FALSE ) ## S4 method for signature 'SparrowResult' geneSet( x, i, j, active.only = TRUE, with.feature.map = FALSE, ..., collection = NULL, name = NULL, as.dt = FALSE )
x |
Object to retrieve the gene set from, either a |
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
|
with.feature.map |
If |
collection |
using |
name |
the same for the |
as.dt |
If |
a data.(frame|table)
of gene set information. If x
is a
SparrowResult
object, then differential expression statistics
are added as columns to this result.
gdb <- exampleGeneSetDb() geneSet(gdb, "c2", "KOMMAGANI_TP63_GAMMA_TARGETS") geneSet(gdb, collection = "c2", name = "KOMMAGANI_TP63_GAMMA_TARGETS") geneSet(gdb, name = "KOMMAGANI_TP63_GAMMA_TARGETS")