Construct a batch key

A batch is rarely identified by a single column. Once an assay spans several plates, acquisition runs or experiment days, the analytical batch is the combination of those columns, and any analysis that standardizes against a control has to respect that combination. cr_batch_key() collapses any number of design or cell columns into one character key that can be grouped on, joined on and reported.

Usage

cr_batch_key(x, batch_vars, sep = " | ", na_label = "<NA>")

Arguments

x

A cr_experiment or a data frame. For a cr_experiment the design columns are joined onto the cells first; a column present in both tables is taken from cells.

batch_vars

Character vector of column names that jointly define a batch, for example c("compound", "run", "plate", "experiment", "interval").

sep

Separator placed between the parts of the key.

na_label

Label substituted for missing values.

Value

A character vector with one key per row of x (one key per cell when x is a cr_experiment).

Details

Missing values are replaced by na_label rather than propagated, so that two rows with an unrecorded plate are grouped together visibly instead of silently producing NA keys.

See also

cr_batch_reference(), cr_standardize_batch()

Other batch standardization functions: cr_batch_reference(), cr_correct_batch(), cr_standardize_batch()

Examples

exp <- cr_example_experiment(seed = 1, n_cells_per_well = 10)
exp$design$plate <- rep(c("P1", "P2"), length.out = nrow(exp$design))
key <- cr_batch_key(exp, c("plate", "timepoint"))
head(unique(key))
#> [1] "P1 | 24" "P2 | 24"

# Works on a plain data frame too
cr_batch_key(data.frame(a = c("x", "y"), b = 1:2), c("a", "b"))
#> [1] "x | 1" "y | 2"