Grab the filename for a a single region set from a database specified by filename.

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)