# #——图书馆,呼应= FALSE,消息= FALSE,警告= FALSE ---------------------- suppressPackageStartupMessages({库(RcisTarget ) }) ## ----------------------------------------------------------------------------- packageVersion(“RcisTarget ") ## ----------------------------------------------------------------------------- download.file (" https://gbiomed.kuleuven.be/apps/lcb/i-cisTarget/examples/input_files/human/peaks/Encode_GATA1_peaks。床”、“Encode_GATA1_peaks.bed”)regionsList < - rtracklayer:: import.bed(“Encode_GATA1_peaks.bed”)regionSets < -列表(GATA1_peaks = regionsList) # # - eval = FALSE --------------------------------------------------------------- # 库(RcisTarget) # #主题排名# featherFilePath <——“~ / / hg19-regions-9species.all_regions.mc9nr数据库。羽毛“# # # # Motif-TF注释数据(“motifAnnotations_hgnc”)# motifAnnotation < - motifAnnotations_hgnc位置* # # # #区域数据(dbRegionsLoc_hg19) # dbRegionsLoc < - dbRegionsLoc_hg19 # # - eval = FALSE --------------------------------------------------------------- # dbRegionsLoc < - getDbRegionsLoc (featherFilePath) # # - eval = FALSE --------------------------------------------------------------- # # 转换区域# regionSets_db < -拉普(regionSetsfunction(x) convertToTargetRegions(queryRegions=x, targetRegions=dbRegionsLoc)) # # #导入排名# allRegionsToImport <- unique(unlist(regionSets_db));length(allRegionsToImport) # motifRankings <- importRankings(featherFilePath, columns=allRegionsToImport) # # #运行RcisTarget # motifgradimenttable <- cisTarget(regionSets_db, motifRankings, aucMaxRank=0.005*getNumColsInDB(motiffrankings)) # # #显示输出:# showLogo(motifgradimenttable)