as.CategorizedCollection: Converts GeneSetCollection objects to CategorizedCollection...

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

Description

Converts GeneSetCollection objects to CategorizedCollection objects.

Usage

as.CategorizedCollection(GScollection, category = "uncategorized",
  subCategory = "uncategorized")

Arguments

GScollection	An object of class GeneSetCollection.
category	The name of the category that all the gene sets will be assigned to (see details).
subCategory	The name of the subcategory that all the gene sets will be assigned to (see details).

Details

This function sets the CollectionType for each set in the collection to CategorizedCollection. If GScollection contains BroadCollection gene sets, their fields category and subcategory will be used. Otherwise the category and subcategory fields will be used.

Value

A CategorizedCollection object

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".

The \code{importMSigDB.xml} function is just a shortcut to the
following:

db <- getBroadSets("msigdb_v6.1.xml")
db <- as.CategorizedCollection(db)

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

## End(Not run)

## A small sample of the MSigDB as imported by importMSigDB.xml is
## included in gep2pep. The following creates (and deletes) a
## gep2pep repository.

db_sample <- loadSamplePWS()

## The function \code{as.CategorizedCollection} can also be used to
## create arbitrary gene set collections specifying the categories
## and subcategories once for all the sets:

library(GSEABase)
mysets <- as.CategorizedCollection(
              GeneSetCollection(
                  list(GeneSet(c("g1", "g2"), setName="set1"),
                       GeneSet(c("g3", "g4"), setName="set2"))
                  ),
              category="mycategory",
              subCategory="mysubcategory"
              )
newCollection <- GeneSetCollection(c(db_sample, mysets))

## The created repository will include both the sample gene sets
## and the two sets just created:

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

## removing temporary repository
unlink(repo_path, TRUE)

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