Build an ingested data set

A cr_dataset is what comes out of ingest: the cells of every export, the per-file provenance that lets any row be traced back to the acquisition it came from, and optionally the design those files encode. It is the object to inspect before committing to an analysis, and it converts to a cr_experiment with cr_build_experiment().

Usage

cr_dataset(
  cells,
  design = NULL,
  unit_var = NULL,
  provenance = NULL,
  file_col = "source_path",
  metadata = list(),
  call = rlang::caller_env()
)

# S3 method for class 'cr_dataset'
print(x, ...)

# S3 method for class 'cr_dataset'
summary(object, ...)

Arguments

cells: A data frame of cells, typically from cr_read_exports().
design: Optional cr_design() object, or a data frame that is passed to cr_design().
unit_var: Name of the analysis unit column. Defaults to the design's unit column, or the first of well, slide, well_id or unit present in cells.
provenance: Optional per-file table. When NULL it is derived from cells: one row per file with its cell count and every column that is constant within the file.
file_col: Name of the file column used for provenance. Default "source_path".
metadata: Optional list of arbitrary user metadata.
call: The execution environment of the calling function. Used for error reporting; experts only.
x: A cr_dataset.
...: Ignored.
object: A cr_dataset.

Value

An object of class cr_dataset:

cells: Tibble of per-cell measurements.
provenance: Tibble with one row per source file, or NULL.
design: A cr_design, or NULL.
unit_var: Name of the analysis unit column, or NULL.
metadata: List of user metadata.

x, invisibly.

A tibble with one row per source file, or NULL when the data set carries no provenance.

Examples

cells <- tibble::tibble(
  source_path = rep(c("a.csv", "b.csv"), each = 3),
  source_file = rep(c("a.csv", "b.csv"), each = 3),
  well = rep(c("A01", "A02"), each = 3),
  treatment = rep(c("Vehicle", "CompoundA"), each = 3),
  target_signal = c(10, 12, 11, 30, 33, 29)
)
ds <- cr_dataset(cells)
ds
#> 
#> ── cr_dataset 
#> • cells: 6 x 5
#> • source files: 2
#> • unit column: well
#> • units: 2
#> • design: not set
ds$provenance
#> # A tibble: 2 × 5
#>   source_path source_file well  treatment n_cells
#>   <chr>       <chr>       <chr> <chr>       <int>
#> 1 a.csv       a.csv       A01   Vehicle         3
#> 2 b.csv       b.csv       A02   CompoundA       3

Usage

Arguments

Value

See also

Examples