getCollections: Returns the names of the pathway collections in a repository.

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

Description

Given a gep2pep repository, returns the names of the stored collections by looking at appropriate repository item names.

Usage

getCollections(rp)

Arguments

rp	A repository created by createRepository.

Details

Each collection in a database has a "category" and a "subcategory" assigned, which are used to build the collection identifier as "category_subcategory". This function obtains the identifiers by looking at data stored in the repository rp (entries that are tagged with "sets").

Value

Vector of collection names (see details).

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

getCollections(rp)
## [1] "c3_TFT" "c3_MIR" "c4_CGN"

unlink(repo_path, TRUE)

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