loadDataArm: loadDataArm

In biodev/packageDir: Tool for in silico functional analysis design and exploration of relation between genomic function and aberration.

Description

Connects data input arm to program, providing essential information and the main execution function.

Usage

loadDataArm(mainFunction, arms, title, description,
  scriptFile = "no script file provided, loading data arm main function from local environment")

Arguments

mainFunction	The main execution function for the arm. If the script provided, the function does not need to be loaded into memory when the call is made to loadDataArm – the script file will be run then the function will be called upon to be placed into the mainFunction slot of a DataArm object.
arms	The list containing all DataArm objects for the study.
title	character string. The one word description of the data arm. (ex: functional_drug_screen_summary) This will be used internally to refer to any results associated with the data arm, and externally to name folders when saving data.
description	The description of the data input arm to be used as a main menu option. (ex: "Process drug screen data")
scriptFile	A file providing the script where the functions implementing the data import arm can be found. Note: This allows that a script can be provied which contains the definition of the function provided for the mainFunction argument. Thus, this script will be executed before the mainFunction is called or referened.

Value

The arms list with the additional arm added.

Examples

study = getStudyObject(study.name="testDataSets", 
											 geneIdentifierType="HUGO")
arms = slot(object=study, name="arms")
arms = loadDataArm(description="Load drug screen data",
title="functional_drug_screen_summary", 
mainFunction=packageDir:::RunDrugScreen, 
arms=arms)

biodev/packageDir documentation built on Nov. 4, 2019, 7:19 a.m.