osat_score {designit}

Compute OSAT score for sample assignment.

Description

The OSAT score is intended to ensure even distribution of samples across batches and is closely related to the chi-square test contingency table (Yan et al. (2012) doi:10.1186/1471-2164-13-689).

Usage

osat_score(bc, batch_vars, feature_vars, expected_dt = NULL, quiet = FALSE)

Arguments

bc

BatchContainer with samples or data.table/data.frame where every row is a location in a container and a sample in this location.

batch_vars

character vector with batch variable names to take into account for the score computation.

feature_vars

character vector with sample variable names to take into account for score computation.

expected_dt

A data.table with expected number of samples sample variables and batch variables combination. This is not required, however it does not change during the optimization process. So it is a good idea to cache this value.

quiet

Do not warn about NAs in feature columns.

Value

a list with two attributes: ⁠$score⁠ (numeric score value), ⁠$expected_dt⁠ (expected counts data.table for reuse)

Examples

sample_assignment <- tibble::tribble(
  ~ID, ~SampleType, ~Sex, ~plate,
  1, "Case", "Female", 1,
  2, "Case", "Female", 1,
  3, "Case", "Male", 2,
  4, "Control", "Female", 2,
  5, "Control", "Female", 1,
  6, "Control", "Male", 2,
  NA, NA, NA, 1,
  NA, NA, NA, 2,
)

osat_score(sample_assignment,
  batch_vars = "plate",
  feature_vars = c("SampleType", "Sex")
)