createRepository: Creates a repository of pathway collections.

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

Description

Given a database of collections, stores them in a local repository to be used by gep2pep functions.

Usage

createRepository(path, sets, name = NULL, description = NULL)

Arguments

path	Path to a non-existing directory where the repository will be created.
sets	An object of class CategorizedCollection.
name	Name of the repository. Defaults to NULL (a generic name will be given).
description	Description of the repository. If NULL (default), a generic description will be given.

Details

sets can be created by importMSigDB.xml or using GSEABase GeneSetCollection class and then converting it to CategorizedCollection. See examples.

Value

An object of class repo that can be passed to gep2pep functions.

See Also

buildPEPs

Examples

db <- loadSamplePWS()
repo_path <- file.path(tempdir(), "gep2pepTemp")

rp <- createRepository(repo_path, db)
## Repo root created.
## Repo created.
## [15:45:06] Storing pathway data for collection: c3_TFT
## [15:45:06] Storing pathway data for collection: c3_MIR
## [15:45:06] Storing pathway data for collection: c4_CGN

rp
##         ID    Dims     Size
## c3_TFT_sets   10 18.16 kB
## c3_MIR_sets   10 17.25 kB
## c4_CGN_sets   10   6.9 kB

unlink(repo_path, TRUE)

gep2pep documentation built on Nov. 8, 2020, 5:59 p.m.