# Motif enrichment in genomic regions

Abstract

Example using RcisTarget to analyze genomic regions (instead of genes).

This tutorial requires RcisTarget >= 1.11

    packageVersion("RcisTarget")

    ## [1] '1.24.0'

### 1. Prepare/download the input regions

    # download.file("https://gbiomed.kuleuven.be/apps/lcb/i-cisTarget/examples/input_files/human/peaks/Encode_GATA1_peaks.bed", "Encode_GATA1_peaks.bed")
    txtFile <- paste(file.path(system.file('examples', package='RcisTarget')),"Encode_GATA1_peaks.bed", sep="/")
    regionsList <- rtracklayer::import.bed(txtFile)
    regionSets <- list(GATA1_peaks=regionsList)

### 2. Load the RcisTarget databases

This analysis requires the region-based databases (for the appropriate organism): - Region-based motif rankings - Motif-TF annotations (same for region- & gene-based analysis) - Region location (i.e. conversion from region ID to genomic location)

The databases can be downloaded from: https://resources.aertslab.org/cistarget/

Note: This example uses an old version of the database (mc9nr), we recommend to use the latest version (v10_clus).

    library(RcisTarget)
    # Motif rankings
    featherFilePath <- "~/databases/hg19-regions-9species.all_regions.mc9nr.feather"

    ## Motif - TF annotation:
    data(motifAnnotations_hgnc_v9) # human TFs (for motif collection 9)
    motifAnnotation <- motifAnnotations_hgnc_v9

    # Regions location *
    data(dbRegionsLoc_hg19)
    dbRegionsLoc <- dbRegionsLoc_hg19

- Note: The region location is only needed for human and mouse databases. For drosophila, the region ID contains the location, and can be obtained with:

    dbRegionsLoc <- getDbRegionsLoc(featherFilePath)

### 3. Run the analysis

The main difference with a gene-based analysis is that the regions need to be converted to the database IDs first, and the parameter `aucMaxRank` should be adjusted:

- For Human: `aucMaxRank= 0.005`
- For Mouse: `aucMaxRank= 0.005`
- For Fly: `aucMaxRank= 0.01`

    # Convert regions
    regionSets_db <- lapply(regionSets, function(x) convertToTargetRegions(queryRegions=x, targetRegions=dbRegionsLoc))

    # Import rankings
    allRegionsToImport <- unique(unlist(regionSets_db)); length(allRegionsToImport)
    motifRankings <- importRankings(featherFilePath, columns=allRegionsToImport)

    # Run RcisTarget
    motifEnrichmentTable <- cisTarget(regionSets_db, motifRankings, aucMaxRank=0.005*getNumColsInDB(motifRankings))

    # Show output:
    showLogo(motifEnrichmentTable)