readRegionSetAnnotation: Given a folder containing region collections in subfolders,...

In sheffien/LOLA: Locus overlap analysis for enrichment of genomic ranges

Description

Given a folder containing region collections in subfolders, this function will either read the annotation file if one exists, or create a generic annotation file.

Usage

readRegionSetAnnotation(
  dbLocation,
  collections = NULL,
  refreshCaches = FALSE,
  refreshSizes = TRUE,
  useCache = TRUE
)

Arguments

dbLocation	folder where your regionDB is stored.
collections	Restrict the database loading to this list of collections Leave NULL to load the entire database (Default).
refreshCaches	should I recreate the caches? Default: FALSE
refreshSizes	should I refresh the size files? Default:TRUE
useCache	Use simpleCache to store results and load them?

Value

Region set annotation (data.table)

Examples

dbPath = system.file("extdata", "hg19", package="LOLA")
regionAnno = readRegionSetAnnotation(dbLocation=dbPath)

sheffien/LOLA documentation built on Sept. 3, 2020, 8:29 p.m.