Enriched gene sets — enrichedGeneSets • AcidGSEA

Enriched pathways from gene set collections.

Usage

enrichedGeneSets(object, ...)

# S4 method for FgseaList
enrichedGeneSets(object, collection, direction = c("both", "up", "down"))

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.
direction: character(1). Include "both", "up", or "down" directions.
...: Additional arguments.

Value

list. Named list containing significant gene sets per contrast.

Note

Updated 2022-04-27.

See also

DESeqAnalysis::deg().

Examples

data(fgsea)

## FgseaList ====
object <- fgsea
alphaThreshold(object) <- 0.7
collection <- collectionNames(object)[[1L]]
enrichedGeneSets(
    object = object,
    collection = collection,
    direction = "up"
)
#> $condition_B_vs_A
#> character(0)
#> 
#> $treatment_D_vs_C
#> character(0)
#>