Given a bunch of region set files, read in all those flat (bed) files and create a GRangesList object holding all the region sets. This function is used by readRegionGRL to process annotation objects.

Given a bunch of region set files, read in all those flat (bed) files and create a GRangesList object holding all the region sets. This function is used by readRegionGRL to process annotation objects.

readCollection(filesToRead, limit = NULL)

Arguments

filesToRead

a vector containing bed files
limit

for testing purposes, limit the number of files read. NULL for no limit (default).

Value

A GRangesList with the GRanges in the filesToRead.

Examples

files = list.files(system.file("extdata", "hg19/ucsc_example/regions",
 package="LOLA"), pattern="*.bed")
regionAnno = readCollection(files)
#> Reading 5 files...
#> 1: cpgIslandExt.bed
#> Skipping (file not found):cpgIslandExt.bed
#> 2: laminB1Lads.bed
#> Skipping (file not found):laminB1Lads.bed
#> 3: numtSAssembled.bed
#> Skipping (file not found):numtSAssembled.bed
#> 4: vistaEnhancers_colNames.bed
#> Skipping (file not found):vistaEnhancers_colNames.bed
#> 5: vistaEnhancers.bed
#> Skipping (file not found):vistaEnhancers.bed