Interrogate "active" status of a given geneset.

Source: R/GeneSetDb-methods.R

Returns the active status of genesets, which are specified by their collection,name compound keys. This function is vectorized and supports query of multiple gene sets at a time. If a requested collection,name gene set doesn't exist, this throws an error.

is.active(x, i, j)

Arguments

x

GeneSetDb()

i

collection of geneset(s)

j

name of geneset(s) (must be same length as i.

Value

logical indicating if geneset is active. throws an error if any requested geneset does not exist in x.

Examples

dge.stats <- exampleDgeResult()
y <- exampleExpressionSet(do.voom = FALSE)
gdb <- conform(exampleGeneSetDb(), y, min.gs.size = 10)
#> Warning: Deactivating 5 gene sets because conformation of GeneSetDb to the target creates gene sets smaller than 10 or greater than Inf
# size 9 geneset:
geneSet(gdb, "c2", "BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA")
#>   collection                                   name active N n feature_id
#> 1         c2 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA  FALSE 9 6      10134
#> 2         c2 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA  FALSE 9 6      29950
#> 3         c2 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA  FALSE 9 6       4297
#> 4         c2 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA  FALSE 9 6       5879
#> 5         c2 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA  FALSE 9 6       7423
#> 6         c2 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA  FALSE 9 6        896
is.active(gdb, "c2", "BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA")
#> [1] FALSE
# geneset with >100 genes
is.active(gdb, "c7", "GSE3982_MAC_VS_NEUTROPHIL_LPS_STIM_DN")
#> [1] TRUE