enrichedGeneSets: Enriched gene sets

In steinbaugh/pfgsea: Acid Genomics GSEA

Enriched gene sets

Description

Enriched pathways from gene set collections.

Usage

enrichedGeneSets(object, ...)

## S4 method for signature '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"
)

steinbaugh/pfgsea documentation built on Oct. 17, 2023, 11:24 a.m.