aggregate_cells: Aggregate cells

In stemangiola/tidySCE: Brings SingleCellExperiment to the Tidyverse

Aggregate cells

Description

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

Usage

## S4 method for signature '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

Examples

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

stemangiola/tidySCE documentation built on Sept. 22, 2024, 10:05 p.m.