singleCellExperiment object containing expression values and experimental information. Must have been appropriately prepared.

character, indicating slot of the assays of the object that should be used to define expression. Valid options are counts as default. tpm, fpkm and logcounts, or anything else in the object added manually by the user.

file (one cell per line) to be used to derive a vector of cell (sample) names used to identify cell controls (for example, blank wells or bulk controls).

Each element is treated as a number of top genes to compute the percentage of library size occupied by the most highly expressed genes in each cell.

A numeric scalar to be passed to 'nexprs', specifying the lower detection limit for expression.

A logical scalar indicating whether existing spike-in sets in 'object' should be automatically added to 'feature_controls'