Aggregate cells

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

Usage

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

Arguments

.data

A tidyseurat 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, letter.idents), assays="RNA")
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `data = map(...)`.
#> Caused by warning:
#> ! `when()` was deprecated in purrr 1.0.0.
#> ℹ Please use `if` instead.
#> ℹ The deprecated feature was likely used in the tidyseurat package.
#>   Please report the issue at
#>   <https://github.com/stemangiola/tidyseurat/issues>.
#> Joining with `by = join_by(letter.idents, groups)`