Given a database and a collection, this will create the region annotation data.table; either giving a generic table based on file names, or by reading in the annotation data.

Given a database and a collection, this will create the region annotation data.table; either giving a generic table based on file names, or by reading in the annotation data.

readCollectionFiles(dbLocation, collection, refreshSizes = FALSE)

Arguments

dbLocation

folder where your regionDB is stored.
collection

Collection folder to load
refreshSizes

should I recreate the sizes files documenting how many regions (lines) are in each region set?

Value

A data.table annotating the regions in the collections.

Examples

dbPath = system.file("extdata", "hg19", package="LOLA")
regionAnno = readCollectionFiles(dbLocation=dbPath, "ucsc_example")
#> /sfs/lustre/scratch/ns5bc/code/LOLA/inst/extdata/hg19/ucsc_example/regions
#> 	In 'ucsc_example', found index file:/sfs/lustre/scratch/ns5bc/code/LOLA/inst/extdata/hg19/ucsc_example/index.txt