getPaths: Get set of cellular pathways

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

Description

Get Path_Detail object, housing gene sets for cellular pathways.

Usage

getPaths(path_file = NULL,
  referenceFileName = "./reference_data/paths/pathMetaData.txt",
  symtab = NULL, verbose = T)

Arguments

path_file	String giving path to file from which pathways should be loaded. Alternatively, a Study object can be provided here and pathways will automatically be retreived from it.
referenceFileName	Optional. String giving path to file where pathway meta data (date loaded, path repository name, etc..) can be found.
symtab	A gene identifier lookup table. If not provided, one will be automatically obtained (may take longer)
verbose	Logical flag indicating if interactive user prompts and additional information should be displayed.

Details

Pathways are stored in the local working directory in the folder ./reference_data/paths/. Pathways must be imported into this package so that meta-data and import records can be maintained. Path meta data is stored in the file ./reference_data/paths/pathMetaData.txt . Any time a path repository is imported, a record of its import is added to the path meta data file. When loading a path repository for use in a study, this program checks the path meta data file, for available path repositories and for path repository file locations.

Value

Path_Detail object.

Examples

## Not run: 
#select and/or load pathways interactively
path_detail = getPaths()

## End(Not run)

#Get pathways from a study object:
study=getTestStudyObject()
path_detail=getPaths(study)

#select pathways from their file name:
path_detail = getPaths(path_file="./reference_data/paths/Reactome.2014.04.06.12.52.27.txt", 
										verbose=FALSE)

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