Function for writing output all at once: combinedResults is an table generated by "locationEnrichment()" or by rbinding category/location results. Writes all enrichments to a single file, and also spits out the same data divided into groups based on userSets, and Databases, just for convenience. disable this with an option.

Function for writing output all at once: combinedResults is an table generated by "locationEnrichment()" or by rbinding category/location results. Writes all enrichments to a single file, and also spits out the same data divided into groups based on userSets, and Databases, just for convenience. disable this with an option.

writeCombinedEnrichment(combinedResults, outFolder = NULL,
  includeSplits = TRUE)

Arguments

combinedResults	enrichment results object
outFolder	location to write results on disk
includeSplits	also include individual files for each user set and database?

Value

No return value.

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)