preselect: Create a list of variables using various variable selection...

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

Description

preselect

Usage

preselect(
  input,
  operations,
  replicates = NULL,
  batch_id = NULL,
  subset = NULL,
  cores = NULL,
  output_dir = NULL,
  workspace_dir = "."
)

Arguments

input	Test data on which to perform variable selection operations. Must be CSV, rds, or feather.
operations	List of operations to perform, as strings. Supported operations: "correlation_threshold", "variance_threshold", "replicate_correlation". See cytominer::select.
replicates	Number of replicates to select per plate map. Required for the operation "replicate_correlation". See cytominer::preselect. default: NULL.
batch_id	Batch ID. Used for generating output_dir if the latter is not specified. default: NULL.
subset	Query to create the training data by subsetting. Regex must select CSVs only. Default selects everything. default: NULL.
cores	Optional integer specifying number of CPU cores used for parallel computing using doParallel. default: NULL.
output_dir	Output directory for preselected feature names. By default, writes to workspace_dir/parameters/batch_id/variable_selection/. default: NULL.
workspace_dir	Root directory containing backend and metadata subdirectories. Can be relative or absolute. default: ".".

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