importMSigDB.xml: Imports pathways data from an MSigDB XML file.

In franapoli/gep2pep: Creation and Analysis of Pathway Expression Profiles (PEPs)

Description

Creates a GeneSetCollection object using the XML distribution of the MSigDB (see references). The returned object can be passed to createRepository.

Usage

importMSigDB.xml(fname, organism = "Homo Sapiens")

Arguments

fname	Path to an XML file downloaded from MSigDB.
organism	Select only gene sets for a given organism. Default is "Homo Sapiens".

Details

This function now just calls getBroadSets(fname) from the GSEABase package. However, it is left for backward compatibility and as an entry point to package functionalities.

Value

A CategorizedCollection object

References

http://software.broadinstitute.org/gsea/downloads.jsp

Examples

## Not run: 

## To run this example, first obtain the MSigDB database in XML
## format (see
## http://software.broadinstitute.org/gsea/downloads.jsp). It is
## assumed that the database is locally available as the file
## "msigdb_v6.0.xml".

db <- importMSigDB.xml("msigdb_v6.0.xml")

## The database is now in an acceptable format to create a local
## repository using createRepository

## End(Not run)

## A small excerpt from the MSigDB is included in gep2pep. The
## following creates (and then deletes) a gep2pep repository.

db_sample <- loadSamplePWS()

repo_path <- file.path(tempdir(), "gep2pepTemp")
rp <- createRepository(repo_path, db_sample)

## removing temporary repository
unlink(repo_path, TRUE)

franapoli/gep2pep documentation built on May 30, 2019, 4:34 p.m.