Subset a GeneSetDb to only include geneSets with specified features.

subsetByFeatures(x, features, value = c("feature_id", "x.id", "x.idx"), ...)

Arguments

x	`GeneSetDb`
featureIds	Character vector of featureIds

Value

A subset of x which contains only the geneSets that contain features found in featureIds

Examples

gdb <- exampleGeneSetDb()
features <- c("55839", "8522", "29087")
(gdb.sub <- subsetByFeatures(gdb, features))
#> ===============================================================================
#> GeneSetDb with 5 defined genesets across 3 collections (0 gene sets are active)
#>   Conformed: no
#> -------------------------------------------------------------------------------
#>    collection                                   name active   N  n
#> 1:         c2    MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN  FALSE 172 NA
#> 2:         c2 SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP  FALSE 151 NA
#> 3:         c6                         MEL18_DN.V1_DN  FALSE 148 NA
#> 4:         c7       GSE14000_UNSTIM_VS_16H_LPS_DC_UP  FALSE 200 NA
#> 5:         c7                 GSE14308_TH2_VS_TH1_UP  FALSE 199 NA
#> -------------------------------------------------------------------------------
#> GeneSetDb with 5 defined genesets across 3 collections (0 gene sets are active)
#>   Conformed: no
#> ===============================================================================