BenchHubStudy Class

This class manages a collection of benchmark trios and mapping functions. It allows adding new trios, mapping functions, and running mappings on data.

Public fields

name

A character string to name the study.

trios

A list to store benchmark trios.

mappingFunctions

A list to store mapping functions with metadata.

description

A character string describing the study.

version

Integer specifying the version of the study.

Methods

Public methods

• BenchHubStudy$new()

• BenchHubStudy$addTrio()

• BenchHubStudy$addMappingFunction()

• BenchHubStudy$runMapping()

• BenchHubStudy$getMappingFunctionDocumentation()

• BenchHubStudy$listMappingFunctions()

• BenchHubStudy$generateVignetteTemplate()

• BenchHubStudy$evaluate()

• BenchHubStudy$writeBenchHubStudy()

• BenchHubStudy$print()

• BenchHubStudy$clone()

---

Method new()

Usage

BenchHubStudy$new(
  name = NULL,
  trios = list(),
  fetchFromCtd = FALSE,
  version = NULL
)

Arguments

name

A character string to name the study. If fetchFromCtd is TRUE, this name will be used to fetch the study from Curated Trio Datasets.

trios

A list of Trio objects to initialize the study.

fetchFromCtd

Logical indicating whether to fetch study details from Curated Trio Datasets.

version

Optional integer specifying which version of the study to fetch (when fetchFromCtd is TRUE).

---

Method addTrio()

Add a new trio to the study

Usage

BenchHubStudy$addTrio(trioObject)

Arguments

trioObject

A Trio object to be added.

---

Method addMappingFunction()

Add a mapping function with metadata

Usage

BenchHubStudy$addMappingFunction(
  name,
  func,
  inputDescription,
  outputDescription,
  exampleUsage = NULL
)

Arguments

name

A character string to name the mapping function.

func

A function that takes data as input and returns transformed data.

inputDescription

A character string describing the input data.

outputDescription

A character string describing the output data.

exampleUsage

An optional character string showing example usage of the function.

---

Method runMapping()

Apply a mapping function to data

Usage

BenchHubStudy$runMapping(mappingName, data)

Arguments

mappingName

A character string naming the mapping function to apply.

data

The data to which the mapping function will be applied.

Returns

The transformed data after applying the mapping function.

---

Method getMappingFunctionDocumentation()

Documentation getter for mapping function

Usage

BenchHubStudy$getMappingFunctionDocumentation(mappingName)

Arguments

mappingName

A character string naming the mapping function.

Returns

A list containing the input description, output description, and example usage.

---

Method listMappingFunctions()

available options

Usage

BenchHubStudy$listMappingFunctions()

Returns

A character vector of mapping function names.

---

Method generateVignetteTemplate()

Generate R Markdown vignette template

Usage

BenchHubStudy$generateVignetteTemplate(
  outputPath = "benchmark_study_template.Rmd"
)

Arguments

outputPath

A character string specifying the path to save the vignette template.

---

Method evaluate()

Evaluate a trio with input data

Usage

BenchHubStudy$evaluate(trioName, input)

Arguments

trioName

A character string naming the trio to evaluate.

input

The input data to evaluate the trio against.

Returns

The evaluation result from the trio.

---

Method writeBenchHubStudy()

Write the BenchHubStudy metadata to Curated Trio Datasets sheet.

Usage

BenchHubStudy$writeBenchHubStudy()

---

Method print()

Print method to display key information about the BenchHubStudy object.

Usage

BenchHubStudy$print()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

BenchHubStudy$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.