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Leading edge genes

Source: R/AllGenerics.R, R/leadingEdge-methods.R
leadingEdge.Rd

Leading edge genes

Usage

leadingEdge(object, ...)

# S4 method for 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
)
#> [1] "ADIPOR2" "NDUFAB1"