getStudyObject: getStudyObject

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

Description

Function to initilize a new study object.

Usage

getStudyObject(study.name = "", settings = list(), resf = list(),
  GeneIdentifierLookup = data.frame(), path_detail = Path_Detail$new(),
  arms = list(), geneIdentifierType = "HUGO",
  rootFolder = "./output/")

Arguments

study.name	The name of the study (this will be used as a folder name if study is saved, so this should be valid as a file name.)
settings	A settings list object.
resf	a results list object.
GeneIdentifierLookup	Depricated. A table of approved gene identifiers.
path_detail	A Path_Detail object.
arms	The list of arm objects.
geneIdentifierType	String, a one word name of the type of gene identifiers used (ex : HUGO, Uniprot)
rootFolder	character string. The file path where the study should be saved.

Examples

study = getStudyObject() #this will give a study object with no pathways loaded (pathways must first be loaded for analyses to take place)
study2 = getStudyObject(study.name="testStudy", path_detail=getDefaultPaths())

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