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Find All Markers

Source: R/cluster.R
find_all_markers.Rd

Find all markers at a range of resolutions

Usage

find_all_markers(object, group_by = NULL, experiment = "gene", ...)

Arguments

object

An object.

group_by

A metadata variable to group by.

experiment

Assay to use, Default "gene".

...

extra args passed to stash_marker_features

Value

a SingleCellExperiment object containing marker genes

Examples

data("small_example_dataset")
find_all_markers(small_example_dataset, "gene_snn_res.1")
#> stashing markers for gene_snn_res.1
#> class: SingleCellExperiment 
#> dim: 1000 200 
#> metadata(1): markers
#> assays(2): counts logcounts
#> rownames(1000): Gene_0001 Gene_0002 ... Gene_0999 Gene_1000
#> rowData names(0):
#> colnames(200): Cell_001 Cell_002 ... Cell_199 Cell_200
#> colData names(9): Mutation_Status Cell_Cycle ... gene_snn_res.0.8
#>   gene_snn_res.1
#> reducedDimNames(3): PCA TSNE UMAP
#> mainExpName: gene
#> altExpNames(1): Spikes