Like getRegionSet but returns a filename instead of a GRanges object. Given a local filename, returns a complete absolulte path so you can read that file in.

getRegionFile(dbLocation, filenames, collections = NULL)

Arguments

dbLocation

folder of regionDB

filenames

Filename(s) of a particular region set to grab.

collections

(optional) subset of collections to list

Value

A filename the specified file in the regionDB.

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
data("sample_universe", package="LOLA") data("sample_input", package="LOLA") getRegionSet(regionDB, collections="ucsc_example", filenames="vistaEnhancers.bed")
#> GRangesList object of length 1: #> [[1]] #> GRanges object with 1339 ranges and 0 metadata columns: #> seqnames ranges strand #> <Rle> <IRanges> <Rle> #> 1 chr1 [ 3190582, 3191428] * #> 2 chr1 [ 8130440, 8131887] * #> 3 chr1 [10593124, 10594209] * #> 4 chr1 [10732071, 10733118] * #> 5 chr1 [10757665, 10758631] * #> ... ... ... ... #> 1335 chrX [139380917, 139382199] * #> 1336 chrX [139593503, 139594774] * #> 1337 chrX [139674500, 139675403] * #> 1338 chrX [147829017, 147830159] * #> 1339 chrX [150407693, 150409052] * #> #> ------- #> seqinfo: 69 sequences from an unspecified genome; no seqlengths
getRegionSet(dbPath, collections="ucsc_example", filenames="vistaEnhancers.bed")
#> Reading collection annotations: ucsc_example
#> 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
#> Reading 1 files...
#> 1: /sfs/lustre/scratch/ns5bc/code/LOLA/inst/extdata/hg19/ucsc_example/regions/vistaEnhancers.bed
#> GRangesList object of length 1: #> [[1]] #> GRanges object with 1339 ranges and 0 metadata columns: #> seqnames ranges strand #> <Rle> <IRanges> <Rle> #> 1 chr1 [ 3190582, 3191428] * #> 2 chr1 [ 8130440, 8131887] * #> 3 chr1 [10593124, 10594209] * #> 4 chr1 [10732071, 10733118] * #> 5 chr1 [10757665, 10758631] * #> ... ... ... ... #> 1335 chrX [139380917, 139382199] * #> 1336 chrX [139593503, 139594774] * #> 1337 chrX [139674500, 139675403] * #> 1338 chrX [147829017, 147830159] * #> 1339 chrX [150407693, 150409052] * #> #> ------- #> seqinfo: 23 sequences from an unspecified genome; no seqlengths
getRegionFile(dbPath, collections="ucsc_example", filenames="vistaEnhancers.bed")
#> Reading collection annotations: ucsc_example
#> 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
#> [1] "/sfs/lustre/scratch/ns5bc/code/LOLA/inst/extdata/hg19/ucsc_example/regions/vistaEnhancers.bed"
res = runLOLA(userSets, userUniverse, regionDB, cores=1)
#> Calculating unit set overlaps...
#> Calculating universe set overlaps...
#> Calculating Fisher scores...
locResult = res[2,] extractEnrichmentOverlaps(locResult, userSets, regionDB)
#> GRanges object with 632 ranges and 0 metadata columns: #> seqnames ranges strand #> <Rle> <IRanges> <Rle> #> [1] chr1 [18229570, 19207602] * #> [2] chr1 [35350878, 35351854] * #> [3] chr1 [38065507, 38258622] * #> [4] chr1 [38499473, 39306315] * #> [5] chr1 [42611485, 42611691] * #> ... ... ... ... #> [628] chrX [125299245, 125300436] * #> [629] chrX [136032577, 138821238] * #> [630] chrX [139018365, 148549454] * #> [631] chrX [154066672, 154251301] * #> [632] chrY [ 2880166, 7112793] * #> ------- #> seqinfo: 69 sequences from an unspecified genome; no seqlengths
writeCombinedEnrichment(locResult, "temp_outfolder")
#> Overwriting temp_outfolder/allEnrichments.tsv...
userSetsRedefined = redefineUserSets(userSets, userUniverse) resRedefined = runLOLA(userSetsRedefined, userUniverse, regionDB, cores=1)
#> Calculating unit set overlaps...
#> Calculating universe set overlaps...
#> Calculating Fisher scores...
g = plotTopLOLAEnrichments(resRedefined)