efdr_support_from_coldata

Per-cell-type perturbation-arm support, from a plain coldata table.

efdr_support_from_coldata(
  coldata,
  sample_group = "embryo_ID",
  cell_group = "cell_type",
  control_ids = c("ctrl-inj"),
  perturbation_col = "perturbation"
)

Arguments

• coldata
  data.frame
  A table with embryo, perturbation, and cell-type columns.

• sample_group, cell_group, control_ids, perturbation_col
  Column names / control labels.

Details

The single source of truth for every support quantity the empirical-FDR model needs, computed from a (embryo, perturbation, cell_type) table so it can be driven from either a cell_data_set's colData (efdr_perturbation_support()) or a lightweight coldata TSV (the mcclintock eFDR pipeline stage) without duplicating the definitions across repos:

• n_pert_pb — perturbation embryos with the cell type (the gate's replicate count).
• n_ctrl_pb — control embryos with the cell type.
• n_eff_pb — cell-weighted effective perturbation replicates; an embryo is a full replicate only once it carries enough cells, which drives the degrees-of-freedom correction.
• n_pert_cells / n_ctrl_cells — total cells per arm, feeding the theoretical SE floor.

Examples

support <- efdr_support_from_coldata(coldata_tbl,
  sample_group = "embryo",
  cell_group = "cell_type",
  control_ids = c("ctrl-inj"),
  perturbation_col = "gene_target"
)