normalize: Normalize profiles based on given control subset
In cytomining/cytotools: Command-Line Tools to Get Things Done Using Cytominer

View source: R/normalize.R

normalize

R Documentation

Normalize profiles based on given control subset

Description

normalize normalizes data based on the specified normalization method.

Usage

normalize(
  input_file = NULL,
  output_file = NULL,
  subset = NULL,
  sample_single_cell = FALSE,
  input_sqlite_file = NULL,
  compartments = c("cells", "cytoplasm", "nuclei"),
  operation = "robustize",
  strata = c("Metadata_Plate"),
  batch_id = NULL,
  plate_id = NULL,
  workspace_dir = ".",
  image_object_join_columns = c("TableNumber", "ImageNumber"),
  well_unique_id_columns = c("Metadata_Plate", "Metadata_Well"),
  well_unique_id_columns_db_prefix = ""
)

Arguments

`input_file`	Input file with profiles to be normalized. If `NULL`, reads from `workspace_dir/backend/batch_id/plate_id/plate_id_augmented.csv`. default: `NULL`.
`output_file`	Output file for storing normalized profiles. If `NULL`, writes to `workspace_dir/backend/batch_id/plate_id/plate_id_normalized.csv`. default: `NULL`.
`subset`	Query to define the control poulation used for normalization. Default value selects all wells. default: `("Metadata_Plate != 'dummy'")`.
`sample_single_cell`	Subset comprises single cell samples if `TRUE`. default: `FALSE`.
`input_sqlite_file`	Input file with single cell profiles. If `NULL` and `sample_single_cell` is `TRUE` then reads from `workspace_dir/backend/batch_id/plate_id/plate_id.sqlite`. default: `NULL`.
`compartments`	Optional character vector specifying cellular compartments. default: `c("cells", "cytoplasm", "nuclei")`.
`operation`	Method used for normalization. See normalize. default: `"robustize"`.
`strata`	Character vector specifying grouping variables for normalization. default: `c("Metadata_Plate")`.
`batch_id`	Batch ID. Used for generating input_file and output_file if either is not specified. default: `NULL`.
`plate_id`	Plate ID. Used for generating input_file and output_file if either is not specified. default: `NULL`.
`workspace_dir`	Root directory containing backend and metadata subdirectories. Can be relative or absolute. default: `"."`.
`image_object_join_columns`	Columns by which to join image table and object tables. default: `c("TableNumber", "ImageNumber")`.
`well_unique_id_columns`	Columns by which to uniquely identify a well. default: `c("Metadata_Plate", "Metadata_Well")`.
`well_unique_id_columns_db_prefix`	Prefix for `well_unique_id_columns` in the SQLite db. default: `""`