normalize: Normalize observation variables.

In cytominer: Methods for Image-Based Cell Profiling

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")

Example output

Attaching package: 'cytominer'

The following object is masked from 'package:stats':

    aggregate

The following object is masked from 'package:base':

    transform

# A tibble: 8 x 3
  Metadata_group Metadata_batch AreaShape_Area
  <chr>          <chr>                   <dbl>
1 control        a                      -0.707
2 control        a                       0.707
3 experiment     a                      -2.12 
4 experiment     a                      -2.12 
5 control        b                      -0.707
6 control        b                       0.707
7 experiment     b                     -12.0  
8 experiment     b                     -12.0  

cytominer documentation built on July 8, 2020, 5:08 p.m.