## ----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 annotations # data("motifAnnotations_hgnc") # motifAnnotation <- motifAnnotations_hgnc # # # 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: # resultsToShow <- addLogo(motifEnrichmentTable) # DT::datatable(resultsToShow[,-c("enrichedGenes", "TF_lowConf"), with=FALSE], # escape = FALSE, # To show the logo # filter="top", options=list(pageLength=5))