Build a cr_experiment object — cr_build

Assembles a validated cr_experiment from its components. A cr_experiment is the central S3 object in cellreportR and holds per-cell measurements, experimental design, channel metadata, plate information, a QC log and arbitrary user metadata.

Usage

cr_build_experiment(
  cells,
  design,
  channels = NULL,
  plate_info = list(),
  metadata = list()
)

Arguments

cells: A data frame / tibble of per-cell measurements. Must contain a cell_id column and a spatial unit column (either well or slide).
design: A data frame / tibble that maps each spatial unit to treatment information. Must contain the spatial unit column and a treatment column. Recommended columns: dose, dose_unit, replicate, group, timepoint.
channels: Optional tibble describing fluorescence channels. Columns: channel (required), role, antibody, fluorophore. If NULL, channels are auto-detected from numeric columns in cells that are not recognised as morphology fields.
plate_info: Optional list with plate metadata (e.g. format = "96", microscope, date, operator).
metadata: Optional list with arbitrary user metadata.

Value

A cr_experiment object (an S3 list).

Examples

exp <- cr_example_experiment(seed = 1, n_cells_per_well = 20)
print(exp)
#> ── cr_experiment ───────────────────────────────────────────────────────────────
#> • Cells: 1961 across 96 wells
#> • Channels: "DAPI", "marker_1", "marker_2", and "marker_3"
#> • Design: 6 treatment groups
#> • QC steps applied: 0
#> ℹ Metadata fields: project and sop