## ----libraries, echo=FALSE, message=FALSE, warning=FALSE----------------------
suppressPackageStartupMessages({
library(RcisTarget)
})

## -----------------------------------------------------------------------------
packageVersion("RcisTarget")

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

## ----eval=FALSE---------------------------------------------------------------
#  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

## ----eval=FALSE---------------------------------------------------------------
#  dbRegionsLoc <- getDbRegionsLoc(featherFilePath)

## ----eval=FALSE---------------------------------------------------------------
#  # 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)

