leadingEdge: Leading edge genes

In steinbaugh/pfgsea: Acid Genomics GSEA

Leading edge genes

Description

Leading edge genes

Usage

leadingEdge(object, ...)

## S4 method for signature 'FgseaList'
leadingEdge(object, contrast, collection, set)

Arguments

object	Object.
contrast	character(1). Contrast name.
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. Elements of gene set that correspond to leading edge.

Note

Updated 2022-04-27.

Examples

data(fgsea)

## FgseaList ====
object <- fgsea
contrast <- contrastNames(object)[[1L]]
collection <- collectionNames(object)[[1L]]
set <- geneSetNames(object = object, collection = collection)[[1L]]
leadingEdge(
    object = object,
    contrast = contrast,
    collection = collection,
    set = set
)

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