# Getting Started with LOLA

#### Nathan Sheffield

#### 2017-04-24

# Getting started with LOLA

In this vignette, you’ll use small example datasets that come with the LOLA package to get a first look at the most common functions in a LOLA workflow.

You need 3 things to run a LOLA analysis:

1. A region database.
2. userSets: Regions of interest (at least 1 set of regions as a GRanges object, or multiple sets of regions of interest as a GRangesList object)
3. userUniverse: The set of regions tested for inclusion in your sets of regions of interest (a single GRanges object)

Let’s load an example regionDB with `loadRegionDB()`. Here’s a small example that comes with LOLA. The database location should point to a folder that contains collection subfolders:

    library("LOLA")
    dbPath = system.file("extdata", "hg19", package="LOLA")
    regionDB = loadRegionDB(dbPath)

    ## Reading collection annotations:

    ##  ucsc_example: found collection annotation:C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpMlovYq/Rinst23402e8f6ebb/LOLA/extdata/hg19/ucsc_example/collection.txt

    ## Reading region annotations...

    ## Warning in readRegionSetAnnotation(dbLocation, collections): You don't have simpleCache installed, so you won't be able to cache the
    ## regionDB after reading it in. Install simpleCache to speed up later database
    ## loading.

    ## C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpMlovYq/Rinst23402e8f6ebb/LOLA/extdata/hg19//ucsc_example/regions

    ##  In 'ucsc_example', found index file:C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpMlovYq/Rinst23402e8f6ebb/LOLA/extdata/hg19/ucsc_example/index.txt

    ## Warning in `[.data.table`(indexDT, , `:=`(col, as.character(NA)), with
    ## = FALSE): with=FALSE together with := was deprecated in v1.9.4 released
    ## Oct 2014. Please wrap the LHS of := with parentheses; e.g., DT[,
    ## (myVar):=sum(b),by=a] to assign to column name(s) held in variable myVar.
    ## See ?':=' for other examples. As warned in 2014, this is now a warning.

    ## Warning in `[.data.table`(indexDT, , `:=`(col, as.character(NA)), with
    ## = FALSE): with=FALSE together with := was deprecated in v1.9.4 released
    ## Oct 2014. Please wrap the LHS of := with parentheses; e.g., DT[,
    ## (myVar):=sum(b),by=a] to assign to column name(s) held in variable myVar.
    ## See ?':=' for other examples. As warned in 2014, this is now a warning.

    ## Warning in `[.data.table`(indexDT, , `:=`(col, as.character(NA)), with
    ## = FALSE): with=FALSE together with := was deprecated in v1.9.4 released
    ## Oct 2014. Please wrap the LHS of := with parentheses; e.g., DT[,
    ## (myVar):=sum(b),by=a] to assign to column name(s) held in variable myVar.
    ## See ?':=' for other examples. As warned in 2014, this is now a warning.

    ## Warning in `[.data.table`(indexDT, , `:=`(col, as.character(NA)), with
    ## = FALSE): with=FALSE together with := was deprecated in v1.9.4 released
    ## Oct 2014. Please wrap the LHS of := with parentheses; e.g., DT[,
    ## (myVar):=sum(b),by=a] to assign to column name(s) held in variable myVar.
    ## See ?':=' for other examples. As warned in 2014, this is now a warning.

    ## Warning in `[.data.table`(indexDT, , `:=`(col, as.character(NA)), with
    ## = FALSE): with=FALSE together with := was deprecated in v1.9.4 released
    ## Oct 2014. Please wrap the LHS of := with parentheses; e.g., DT[,
    ## (myVar):=sum(b),by=a] to assign to column name(s) held in variable myVar.
    ## See ?':=' for other examples. As warned in 2014, this is now a warning.

    ## Collection: ucsc_example. Creating size file...

    ## ucsc_example

    ## Reading 5 files...

    ## 1: C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpMlovYq/Rinst23402e8f6ebb/LOLA/extdata/hg19/ucsc_example/regions/cpgIslandExt.bed

    ## 2: C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpMlovYq/Rinst23402e8f6ebb/LOLA/extdata/hg19/ucsc_example/regions/laminB1Lads.bed

    ## 3: C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpMlovYq/Rinst23402e8f6ebb/LOLA/extdata/hg19/ucsc_example/regions/numtSAssembled.bed

    ## 4: C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpMlovYq/Rinst23402e8f6ebb/LOLA/extdata/hg19/ucsc_example/regions/vistaEnhancers.bed

    ## 5: C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpMlovYq/Rinst23402e8f6ebb/LOLA/extdata/hg19/ucsc_example/regions/vistaEnhancers_colNames.bed

The regionDB is an R (list) object that has a few elements:

    names(regionDB)

    ## [1] "dbLocation"     "regionAnno"     "collectionAnno" "regionGRL"

- dbLocation: A string recording the location of the database folder you passed to `loadRegionDB()`.
- collectionAnno: A `data.table` annotating the collections, with rows corresponding to the rows in your `collection` annotation files in the database.
- regionAnno: A `data.table` annotating each region set, with rows corresponding to bed files in the database (there is also a `collection` column recording which collection each region set belongs to).
- regionGRL: A `GRangesList` object holding the actual regions, with one list element per region set, ordered as in `regionAnno`.

Now with the database loaded, let’s load up some sample data (the regions of interest, and the tested universe):

    data("sample_input", package="LOLA") # load userSets
    data("sample_universe", package="LOLA") # load userUniverse

Now we have a GRanges object called `userSets` and a GRanges object called `userUniverse`. This is all we need to run the enrichment calculation. `calcLocEnrichemnt()` will test the overlap between your userSets, and each region set in the regionDB.

    locResults = runLOLA(userSets, userUniverse, regionDB, cores=1)

    ## Calculating unit set overlaps...

    ## Calculating universe set overlaps...

    ## Calculating Fisher scores...

runLOLA tests for pairwise overlap between each user set and each region set in regionDB. It then uses a Fisher’s exact test to assess signficance of the overlap. The results are a `data.table` with several columns:

    colnames(locResults)

    ##  [1] "userSet"      "dbSet"        "collection"   "pValueLog"
    ##  [5] "logOddsRatio" "support"      "rnkPV"        "rnkLO"
    ##  [9] "rnkSup"       "maxRnk"       "meanRnk"      "b"
    ## [13] "c"            "d"            "description"  "cellType"
    ## [17] "tissue"       "antibody"     "treatment"    "dataSource"
    ## [21] "filename"     "qValue"       "size"

    head(locResults)

    ##    userSet dbSet   collection   pValueLog logOddsRatio support rnkPV rnkLO
    ## 1:    setB     2 ucsc_example 264.4863407    7.7578283     850     1     1
    ## 2:    setA     2 ucsc_example 254.6188080    8.6487312     632     1     1
    ## 3:    setB     1 ucsc_example  34.6073689    3.3494078    5747     2     2
    ## 4:    setA     4 ucsc_example   1.7169689    1.2377725     124     2     2
    ## 5:    setA     5 ucsc_example   1.7169689    1.2377725     124     2     2
    ## 6:    setA     3 ucsc_example   0.1877354    0.9135696       8     4     4
    ##    rnkSup maxRnk meanRnk     b    c     d                      description
    ## 1:      2      2    1.33   452 4981 20546                     ucsc_example
    ## 2:      2      2    1.33   670 2510 23017                     ucsc_example
    ## 3:      1      2    1.67 20018   84   980 CpG islands from UCSC annotation
    ## 4:      3      3    2.33   761 3018 22926                     ucsc_example
    ## 5:      3      3    2.33   761 3018 22926                     ucsc_example
    ## 6:      5      5    4.33    66 3134 23621                     ucsc_example
    ##    cellType tissue antibody treatment dataSource
    ## 1:       NA     NA       NA        NA         NA
    ## 2:       NA     NA       NA        NA         NA
    ## 3:       NA     NA       NA        NA         NA
    ## 4:       NA     NA       NA        NA         NA
    ## 5:       NA     NA       NA        NA         NA
    ## 6:       NA     NA       NA        NA         NA
    ##                       filename        qValue  size
    ## 1:             laminB1Lads.bed 3.263317e-264  1302
    ## 2:             laminB1Lads.bed 1.202713e-254  1302
    ## 3:            cpgIslandExt.bed  8.232086e-35 28691
    ## 4:          vistaEnhancers.bed  3.837612e-02  1339
    ## 5: vistaEnhancers_colNames.bed  3.837612e-02  1340
    ## 6:          numtSAssembled.bed  1.000000e+00    78

If you’re not familiar with how `data.table` works in R, it’s worth reading some of the documentation of this powerful package. Columns `userSet` and `dbSet` are indexes into the respective GRangeList objects, identifying each pairwise comparison. There are a series of columns describing the results of the statistical test, such as `pValueLog`, `logOdds`, and the actual values from the contingency table (`support` is the overlap, and `b`, `c`, and `d` complete the 2x2 table). Rank columns simply rank the tests by `pValueLog`, `logOdds`, or `support`; following these are a series of columns annotating the database regions, depending on how you populated the `index` table in the regionDB folder.

You can explore these results in R by, for example, ranking with different orders:

    locResults[order(support, decreasing=TRUE),]

    ##     userSet dbSet   collection    pValueLog logOddsRatio support rnkPV
    ##  1:    setB     1 ucsc_example 3.460737e+01    3.3494078    5747     2
    ##  2:    setA     1 ucsc_example 2.818334e-02    0.8704355    3002     5
    ##  3:    setB     2 ucsc_example 2.644863e+02    7.7578283     850     1
    ##  4:    setA     2 ucsc_example 2.546188e+02    8.6487312     632     1
    ##  5:    setA     4 ucsc_example 1.716969e+00    1.2377725     124     2
    ##  6:    setA     5 ucsc_example 1.716969e+00    1.2377725     124     2
    ##  7:    setB     4 ucsc_example 0.000000e+00    0.3489379      80     4
    ##  8:    setB     5 ucsc_example 0.000000e+00    0.3489379      80     4
    ##  9:    setA     3 ucsc_example 1.877354e-01    0.9135696       8     4
    ## 10:    setB     3 ucsc_example 9.184826e-06    0.2052377       4     3
    ##     rnkLO rnkSup maxRnk meanRnk     b    c     d
    ##  1:     2      1      2    1.67 20018   84   980
    ##  2:     5      1      5    3.67 22763  140   924
    ##  3:     1      2      2    1.33   452 4981 20546
    ##  4:     1      2      2    1.33   670 2510 23017
    ##  5:     2      3      3    2.33   761 3018 22926
    ##  6:     2      3      3    2.33   761 3018 22926
    ##  7:     3      3      4    3.33   805 5751 20193
    ##  8:     3      3      4    3.33   805 5751 20193
    ##  9:     4      5      5    4.33    66 3134 23621
    ## 10:     5      5      5    4.33    70 5827 20928
    ##                          description cellType tissue antibody treatment
    ##  1: CpG islands from UCSC annotation       NA     NA       NA        NA
    ##  2: CpG islands from UCSC annotation       NA     NA       NA        NA
    ##  3:                     ucsc_example       NA     NA       NA        NA
    ##  4:                     ucsc_example       NA     NA       NA        NA
    ##  5:                     ucsc_example       NA     NA       NA        NA
    ##  6:                     ucsc_example       NA     NA       NA        NA
    ##  7:                     ucsc_example       NA     NA       NA        NA
    ##  8:                     ucsc_example       NA     NA       NA        NA
    ##  9:                     ucsc_example       NA     NA       NA        NA
    ## 10:                     ucsc_example       NA     NA       NA        NA
    ##     dataSource                    filename        qValue  size
    ##  1:         NA            cpgIslandExt.bed  8.232086e-35 28691
    ##  2:         NA            cpgIslandExt.bed  1.000000e+00 28691
    ##  3:         NA             laminB1Lads.bed 3.263317e-264  1302
    ##  4:         NA             laminB1Lads.bed 1.202713e-254  1302
    ##  5:         NA          vistaEnhancers.bed  3.837612e-02  1339
    ##  6:         NA vistaEnhancers_colNames.bed  3.837612e-02  1340
    ##  7:         NA          vistaEnhancers.bed  1.000000e+00  1339
    ##  8:         NA vistaEnhancers_colNames.bed  1.000000e+00  1340
    ##  9:         NA          numtSAssembled.bed  1.000000e+00    78
    ## 10:         NA          numtSAssembled.bed  1.000000e+00    78

You can order by one of the rank columns:

    locResults[order(maxRnk, decreasing=TRUE),]

    ##     userSet dbSet   collection    pValueLog logOddsRatio support rnkPV
    ##  1:    setA     3 ucsc_example 1.877354e-01    0.9135696       8     4
    ##  2:    setA     1 ucsc_example 2.818334e-02    0.8704355    3002     5
    ##  3:    setB     3 ucsc_example 9.184826e-06    0.2052377       4     3
    ##  4:    setB     4 ucsc_example 0.000000e+00    0.3489379      80     4
    ##  5:    setB     5 ucsc_example 0.000000e+00    0.3489379      80     4
    ##  6:    setA     4 ucsc_example 1.716969e+00    1.2377725     124     2
    ##  7:    setA     5 ucsc_example 1.716969e+00    1.2377725     124     2
    ##  8:    setB     2 ucsc_example 2.644863e+02    7.7578283     850     1
    ##  9:    setA     2 ucsc_example 2.546188e+02    8.6487312     632     1
    ## 10:    setB     1 ucsc_example 3.460737e+01    3.3494078    5747     2
    ##     rnkLO rnkSup maxRnk meanRnk     b    c     d
    ##  1:     4      5      5    4.33    66 3134 23621
    ##  2:     5      1      5    3.67 22763  140   924
    ##  3:     5      5      5    4.33    70 5827 20928
    ##  4:     3      3      4    3.33   805 5751 20193
    ##  5:     3      3      4    3.33   805 5751 20193
    ##  6:     2      3      3    2.33   761 3018 22926
    ##  7:     2      3      3    2.33   761 3018 22926
    ##  8:     1      2      2    1.33   452 4981 20546
    ##  9:     1      2      2    1.33   670 2510 23017
    ## 10:     2      1      2    1.67 20018   84   980
    ##                          description cellType tissue antibody treatment
    ##  1:                     ucsc_example       NA     NA       NA        NA
    ##  2: CpG islands from UCSC annotation       NA     NA       NA        NA
    ##  3:                     ucsc_example       NA     NA       NA        NA
    ##  4:                     ucsc_example       NA     NA       NA        NA
    ##  5:                     ucsc_example       NA     NA       NA        NA
    ##  6:                     ucsc_example       NA     NA       NA        NA
    ##  7:                     ucsc_example       NA     NA       NA        NA
    ##  8:                     ucsc_example       NA     NA       NA        NA
    ##  9:                     ucsc_example       NA     NA       NA        NA
    ## 10: CpG islands from UCSC annotation       NA     NA       NA        NA
    ##     dataSource                    filename        qValue  size
    ##  1:         NA          numtSAssembled.bed  1.000000e+00    78
    ##  2:         NA            cpgIslandExt.bed  1.000000e+00 28691
    ##  3:         NA          numtSAssembled.bed  1.000000e+00    78
    ##  4:         NA          vistaEnhancers.bed  1.000000e+00  1339
    ##  5:         NA vistaEnhancers_colNames.bed  1.000000e+00  1340
    ##  6:         NA          vistaEnhancers.bed  3.837612e-02  1339
    ##  7:         NA vistaEnhancers_colNames.bed  3.837612e-02  1340
    ##  8:         NA             laminB1Lads.bed 3.263317e-264  1302
    ##  9:         NA             laminB1Lads.bed 1.202713e-254  1302
    ## 10:         NA            cpgIslandExt.bed  8.232086e-35 28691

And finally, record the results to file like this:

4. Write out results:

    writeCombinedEnrichment(locResults, outFolder= "lolaResults")

    ## lolaResults/userSet_setA.tsv

    ## lolaResults/userSet_setB.tsv

By default, this function will write the entire table to a tsv file. I recommend using the includeSplits parameter, which tells the function to also print out additional tables that are subsetted by userSet, so that each region set you test has its own result table. It just makes it a little easier to explore the results.

    writeCombinedEnrichment(locResults, outFolder= "lolaResults", includeSplits=TRUE)

    ## Overwriting lolaResults/userSet_setA.tsv...

    ## Overwriting lolaResults/userSet_setB.tsv...

    ## Overwriting lolaResults/allEnrichments.tsv...

# Exploring LOLA Results

Say you’d like to know which regions are responsible for the enrichment we see; or, in other words, you’d like to extract the regions that are actually overlapping a particular database. For this, you can use the function `extractEnrichmentOverlaps()`:

    oneResult = locResults[2,]
    extractEnrichmentOverlaps(oneResult, 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

# Extracting certain region sets from a database

If you have a large database, you may be interested in using the LOLA database format for other projects, or for additional follow-up analysis. In this case, you may be interested in just a single region set within a database, or perhaps just a few of them. LOLA provides a function to extract certain region sets from either a loaded or an unloaded database.

Say you just want an object with regions from the “vistaEnhancers” region set. You can grab it from a loaded database like this:

    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   [ 3190581,  3191428]      *
    ##      2     chr1   [ 8130439,  8131887]      *
    ##      3     chr1   [10593123, 10594209]      *
    ##      4     chr1   [10732070, 10733118]      *
    ##      5     chr1   [10757664, 10758631]      *
    ##    ...      ...                    ...    ...
    ##   1335     chrX [139380916, 139382199]      *
    ##   1336     chrX [139593502, 139594774]      *
    ##   1337     chrX [139674499, 139675403]      *
    ##   1338     chrX [147829016, 147830159]      *
    ##   1339     chrX [150407692, 150409052]      *
    ##
    ## -------
    ## seqinfo: 69 sequences from an unspecified genome; no seqlengths

Or, if you haven’t already loaded the database, you can just give the path to the database and LOLA will only load the specific region set(s) you are interested in. This can take more than one filename or collection:

    getRegionSet(dbPath, collections="ucsc_example", filenames="vistaEnhancers.bed")

    ## Reading collection annotations: ucsc_example

    ##  ucsc_example: found collection annotation:C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpMlovYq/Rinst23402e8f6ebb/LOLA/extdata/hg19/ucsc_example/collection.txt

    ## Reading region annotations...

    ## Warning in readRegionSetAnnotation(dbLocation, collections): You don't have simpleCache installed, so you won't be able to cache the
    ## regionDB after reading it in. Install simpleCache to speed up later database
    ## loading.

    ## C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpMlovYq/Rinst23402e8f6ebb/LOLA/extdata/hg19//ucsc_example/regions

    ##  In 'ucsc_example', found index file:C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpMlovYq/Rinst23402e8f6ebb/LOLA/extdata/hg19/ucsc_example/index.txt

    ## Warning in `[.data.table`(indexDT, , `:=`(col, as.character(NA)), with
    ## = FALSE): with=FALSE together with := was deprecated in v1.9.4 released
    ## Oct 2014. Please wrap the LHS of := with parentheses; e.g., DT[,
    ## (myVar):=sum(b),by=a] to assign to column name(s) held in variable myVar.
    ## See ?':=' for other examples. As warned in 2014, this is now a warning.

    ## Warning in `[.data.table`(indexDT, , `:=`(col, as.character(NA)), with
    ## = FALSE): with=FALSE together with := was deprecated in v1.9.4 released
    ## Oct 2014. Please wrap the LHS of := with parentheses; e.g., DT[,
    ## (myVar):=sum(b),by=a] to assign to column name(s) held in variable myVar.
    ## See ?':=' for other examples. As warned in 2014, this is now a warning.

    ## Warning in `[.data.table`(indexDT, , `:=`(col, as.character(NA)), with
    ## = FALSE): with=FALSE together with := was deprecated in v1.9.4 released
    ## Oct 2014. Please wrap the LHS of := with parentheses; e.g., DT[,
    ## (myVar):=sum(b),by=a] to assign to column name(s) held in variable myVar.
    ## See ?':=' for other examples. As warned in 2014, this is now a warning.

    ## Warning in `[.data.table`(indexDT, , `:=`(col, as.character(NA)), with
    ## = FALSE): with=FALSE together with := was deprecated in v1.9.4 released
    ## Oct 2014. Please wrap the LHS of := with parentheses; e.g., DT[,
    ## (myVar):=sum(b),by=a] to assign to column name(s) held in variable myVar.
    ## See ?':=' for other examples. As warned in 2014, this is now a warning.

    ## Warning in `[.data.table`(indexDT, , `:=`(col, as.character(NA)), with
    ## = FALSE): with=FALSE together with := was deprecated in v1.9.4 released
    ## Oct 2014. Please wrap the LHS of := with parentheses; e.g., DT[,
    ## (myVar):=sum(b),by=a] to assign to column name(s) held in variable myVar.
    ## See ?':=' for other examples. As warned in 2014, this is now a warning.

    ## Collection: ucsc_example. Creating size file...

    ## Reading 1 files...

    ## 1: C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpMlovYq/Rinst23402e8f6ebb/LOLA/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   [ 3190581,  3191428]      *
    ##      2     chr1   [ 8130439,  8131887]      *
    ##      3     chr1   [10593123, 10594209]      *
    ##      4     chr1   [10732070, 10733118]      *
    ##      5     chr1   [10757664, 10758631]      *
    ##    ...      ...                    ...    ...
    ##   1335     chrX [139380916, 139382199]      *
    ##   1336     chrX [139593502, 139594774]      *
    ##   1337     chrX [139674499, 139675403]      *
    ##   1338     chrX [147829016, 147830159]      *
    ##   1339     chrX [150407692, 150409052]      *
    ##
    ## -------
    ## seqinfo: 23 sequences from an unspecified genome; no seqlengths

Now that you have a basic idea of what the functions are, you can follow some other vignettes, such as Using LOLA Core, to see how this works on a realistic dataset.