createRepository {gep2pep} | R Documentation |
Given a database of collections, stores them in a local repository
to be used by gep2pep
functions.
createRepository(path, sets, name = NULL, description = NULL)
path |
Path to a non-existing directory where the repository will be created. |
sets |
An object of class |
name |
Name of the repository. Defaults to |
description |
Description of the repository. If NULL (default), a generic description will be given. |
sets
can be created by
importMSigDB.xml
or using GSEABase
GeneSetCollection
class and then converting it to
CategorizedCollection. See examples.
An object of class repo
that can be passed to
gep2pep
functions.
buildPEPs
db <- loadSamplePWS() db <- as.CategorizedCollection(db) 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)