Register a Custom Screening Method for Phenotype-Driven Analysis

Registers one or more user-defined screening functions into a shared registry (i.e., ScreenStrategy), enabling dynamic dispatch based on phenotype type (binary, survival, or continuous). Each method is stored with metadata including supported phenotypes and an optional parameter remapping function.

This function supports community-driven extension of analysis pipelines—ideal for integrating novel single cell phenotypic screening methods while maintaining compatibility with downstream validation and execution frameworks

Usage

RegisterScreenMethod(
  ...,
  supported_phenotypes = c("binary", "survival", "continuous"),
  parameter_mapper = NULL,
  registry = ScreenStrategy,
  verbose = getFuncOption("verbose") %||% TRUE
)

Arguments

...

Named arguments where each value is a function implementing a screening method. The name becomes the method identifier (e.g., Scissor = DoScissor registers DoScissor under the key "Scissor"). Unnamed arguments are auto-named using their expression (e.g., Scissor → name "Scissor").

supported_phenotypes

Character vector specifying which phenotype types the method supports. Must be a subset of c("binary", "survival", "continuous"). Default: all three.

parameter_mapper

A function that transforms the input parameter list before passing it to the executor. Useful for changing parameters from interface function. Receives a named list params and must return a modified list. Default: NULL.

registry

An environment used as a method registry (e.g., ScreenStrategy). New methods are stored as registry[["MethodName"]] = metadata list. Default: ScreenStrategy.

verbose

Logical. Whether to print a success message upon registration. Default: TRUE.

Value

Invisibly returns TRUE on successful registration.

Registry Entry Structure

Each registered method is stored as a list with four elements:

method_name

Character: the method key (e.g., "Scissor")

executor

Function: the actual screening implementation

phenotypes

Character vector: supported phenotype classes

mapper

Function: parameter transformation hook

Examples

if (FALSE) { # \dontrun{
# Example: Register a custom screen method for survival data
DoMyScreen <- function(...) {
  stop("Not implemented")
}

RegisterScreenMethod(
  # Key = function
  MyCox = DoMyScreen,
  # If `continuous` phenotype is not supported
  supported_phenotypes = c("survival", "binary"),
  parameter_mapper = function(params) {
    # If I perfer to use `quiet` instead of `verbose`
    params$quiet <- !params$verbose
    params
  }
)
} # }