Helper function to annotate and load a regionDB, a folder with subfolder collections of regions.

Helper function to annotate and load a regionDB, a folder with subfolder collections of regions.

loadRegionDB(dbLocation, useCache = TRUE, limit = NULL,
  collections = NULL)

Arguments

dbLocation	folder where your regionDB is stored, or list of such folders
useCache	uses simpleCache to cache and load the results
limit	You can limit the number of regions for testing. Default: NULL (no limit)
collections	Restrict the database loading to this list of collections

Value

regionDB list containing database location, region and collection annotations, and regions GRangesList

Examples

dbPath = system.file("extdata", "hg19", package="LOLA")
regionDB = loadRegionDB(dbLocation=dbPath)
#> Reading collection annotations: 
#> 	ucsc_example: found collection annotation:/sfs/lustre/scratch/ns5bc/code/LOLA/inst/extdata/hg19/ucsc_example/collection.txt
#> Reading region annotations...
#> ::Loading cache::	/sfs/lustre/scratch/ns5bc/code/LOLA/inst/extdata/hg19/ucsc_example//ucsc_example_files.RData
#> ucsc_example
#> ::Loading cache::	/sfs/lustre/scratch/ns5bc/code/LOLA/inst/extdata/hg19/ucsc_example/ucsc_example.RData