normalize {cytominer}

Normalize observation variables.

Description

normalize normalizes observation variables based on the specified normalization method.

Usage

normalize(
  population,
  variables,
  strata,
  sample,
  operation = "standardize",
  ...
)

Arguments

population

tbl with grouping (metadata) and observation variables.

variables

character vector specifying observation variables.

strata

character vector specifying grouping variables for grouping prior to normalization.

sample

tbl containing sample that is used by normalization methods to estimate parameters. sample has same structure as population. Typically, sample corresponds to controls in the experiment.

operation

optional character string specifying method for normalization. This must be one of the strings "standardize" (default), "robustize".

...

arguments passed to normalization operation

Value

normalized data of the same class as population.

Examples

suppressMessages(suppressWarnings(library(magrittr)))
population <- tibble::tibble(
  Metadata_group = c(
    "control", "control", "control", "control",
    "experiment", "experiment", "experiment", "experiment"
  ),
  Metadata_batch = c("a", "a", "b", "b", "a", "a", "b", "b"),
  AreaShape_Area = c(10, 12, 15, 16, 8, 8, 7, 7)
)
variables <- c("AreaShape_Area")
strata <- c("Metadata_batch")
sample <- population %>% dplyr::filter(Metadata_group == "control")
cytominer::normalize(population, variables, strata, sample, operation = "standardize")