aggregate: Aggregate data based on given grouping.

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

Aggregate data based on given grouping.

Description

aggregate aggregates data based on the specified aggregation method.

Usage

aggregate(
  sqlite_file,
  output_file,
  compartments = c("cells", "cytoplasm", "nuclei"),
  operation = "mean",
  strata = c("Metadata_Plate", "Metadata_Well"),
  image_table = "image",
  image_variables = NULL,
  variables = "all",
  univariate = TRUE
)

Arguments

sqlite_file	SQLite database storing morphological profiles.
output_file	Output file for storing aggregated profiles.
compartments	Optional character vector specifying cellular compartments. default: c("cells", "cytoplasm", "nuclei").
operation	Optional character string specifying method for aggregation, e.g. "mean", "median", "mean+sd". See aggregate. default: "mean".
strata	Character vector specifying grouping variables for aggregation. default: c("Metadata_Plate", "Metadata_Well").
image_table	Optional character string image table name. default: "image".
image_variables	Optional character vector specifying observation variables in image table. default: NULL.
variables	Optional character vector specifying observation variables. default: "all".
univariate	Optional boolean specifying whether aggregation function is univariate (vs multivariate). default: "TRUE".

cytomining/cytotools documentation built on Sept. 18, 2024, 11:58 p.m.