osat_score: Compute OSAT score for sample assignment.

In designit: Blocking and Randomization for Experimental Design

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) \Sexpr[results=rd]{tools:::Rd_expr_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")
)

designit documentation built on May 29, 2024, 12:04 p.m.