Given a single row from an enrichment table calculation, finds the set of overlaps between the user set and the test set. You can then use these, for example, to get sequences for those regions.

Given a single row from an enrichment table calculation, finds the set of overlaps between the user set and the test set. You can then use these, for example, to get sequences for those regions.

extractEnrichmentOverlaps(locResult, userSets, regionDB)

Arguments

locResult	Results from runLOLA function
userSets	User sets passed to the runLOLA function
regionDB	Region database used

Value

userSets overlapping the supplied database entry.

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)