Summarize an assay in a SingleCellExperiment

Creates a table of summary metrics from an input SingleCellExperiment

summarizeSCE(inSCE, useAssay = NULL, sampleVariableName = NULL)

Arguments

inSCE

Input SingleCellExperiment object.

useAssay

Indicate which assay to summarize. If NULL, then the first assay in inSCE will be used. Default NULL.

sampleVariableName

Variable name in colData denoting which sample each cell belongs to. If NULL, all cells will be assumed to come from the same sample. Default "sample".

Value

A data.frame object of summary metrics.

Examples

data("mouseBrainSubsetSCE")
summarizeSCE(mouseBrainSubsetSCE, sample = NULL)
#>   Sample Number of Cells Mean counts per cell Median counts per cell
#> 1 Sample              30                 5969                   4758
#>   Mean features detected per cell Median features detected per cell
#> 1                            1107                              1085