Gene set

Gene set

Usage

geneSet(object, ...)

# S4 method for FgseaList
geneSet(object, collection, set)

Arguments

object

Object.

collection

character(1). Gene set collection name. Typically refers to h (hallmark), c1-c7 collections from MSigDb. Can obtain using collectionNames() on FgseaList object.

set

character(1). Gene set name, in a defined collection. For example, "HALLMARK_ADIPOGENESIS".

...

Additional arguments.

Value

character.

Note

Updated 2022-04-27.

Examples

data(fgsea)

## FgseaList ====
object <- fgsea
collection <- collectionNames(object)[[1L]]
set <- geneSetNames(object = object, collection = collection)[[1L]]
x <- geneSet(
    object = object,
    collection = collection,
    set = set
)
head(x)
#> [1] "FABP4"  "ADIPOQ" "PPARG"  "LIPE"   "DGAT1"  "LPL"