enrichedGeneSets: Enriched gene sets

enrichedGeneSetsR Documentation

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.