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Get names of all features in an assay/experiment/modality

features_in_assay.Rd

Returns the names of all features in a modality. This utility function can be used in several applications:

  • In Shiny apps, return available features for passage to a selection menu

  • Before using fetch_data(), generate a list of features in the object for searching, or test if a feature is present before requesting data

Usage

features_in_assay(object, assay)

# S3 method for class 'Seurat'
features_in_assay(object, assay)

# S3 method for class 'SingleCellExperiment'
features_in_assay(object, assay)

# S3 method for class 'AnnDataR6'
features_in_assay(object, assay)

Arguments

object

A single cell object. Currently, Seurat, SingleCellExpleriment, and anndata objects are supported.

assay

the name of an assay/modality for which to view features.

Methods (by class)

  • features_in_assay(Seurat): Seurat objects

  • features_in_assay(SingleCellExperiment): SingleCellExperiment objects

  • features_in_assay(AnnDataR6): Anndata objects

Examples

features_in_assay(AML_Seurat, assay = "RNA") |> str()
#>  chr [1:462] "ACTG1" "ADGRG1" "AHSP" "AIF1" "ANK1" "ANKRD28" "ANLN" ...

# Check if a feature is present in an assay
"MEIS1" %in% features_in_assay(AML_Seurat, assay = "RNA")
#> [1] TRUE