Aggregate cells

Combine cells into groups based on shared variables and aggregate feature counts.

# S4 method for class 'SingleCellExperiment'
aggregate_cells(
  .data,
  .sample = NULL,
  slot = "data",
  assays = NULL,
  aggregation_function = Matrix::rowSums,
  ...
)

Arguments

.data

A tidySingleCellExperiment object

.sample

A vector of variables by which cells are aggregated

slot

The slot to which the function is applied

assays

The assay to which the function is applied

aggregation_function

The method of cell-feature value aggregation

...

Used for future extendibility

Value

A tibble object

References

Hutchison, W.J., Keyes, T.J., The tidyomics Consortium. et al. The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 21, 1166–1170 (2024). https://doi.org/10.1038/s41592-024-02299-2

Examples

data(pbmc_small)
pbmc_small_pseudo_bulk <- pbmc_small |>
  aggregate_cells(c(groups, ident), assays="counts")