normalize: Normalize profiles based on given control subset

In cytomining/cytotools: Command-Line Tools to Get Things Done Using Cytominer

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: ""

cytomining/cytotools documentation built on Nov. 19, 2020, 10:23 p.m.