# #——图书馆,呼应= FALSE,消息= FALSE,警告= FALSE ---------------------- suppressPackageStartupMessages({库(RcisTarget)图书馆(RcisTarget.hg19.motifDBs.cisbpOnly.500bp)图书馆(DT)库(data.table) #需要(visNetwork ) }) ## ----------------------------------------------------------------------------- packageVersion(“RcisTarget ") ## ----------------------------------------------------------------------------- # 基因分析:txtFile < -粘贴(file.path(系统。file('examples'， package='RcisTarget'))，"hypoxiaGeneSet.txt"， sep="/") geneSets <- list(hypoxia=read. txt)table(txtFile, stringsAsFactors=FALSE)[，1]) #背景:txtFile <- paste(file.path(system. path(system. path))file('examples'， package='RcisTarget'))，"randomGeneSet.txt"， sep="/") #对于玩具示例，我们将使用一些随机基因background <- read。表(txtFile stringsAsFactors = FALSE), 1 ] ## ----------------------------------------------------------------------------- # 背景:添加< -独特(c(美元geneSets缺氧、背景))# B:相交# geneSets缺氧< -相交(美元geneSets缺氧、背景)# #——无花果。身高= 3,fig.width = 3 ------------------------------------------------ gplots::维恩(列表(背景=背景,geneLists = unlist (geneSets ))) ## ---- eval = FALSE --------------------------------------------------------------- # dbPath < -“~ /数据库/ hg19 - 500 bp species.mc9nr——上游- 10。羽毛“# #——eval = FALSE --------------------------------------------------------------- # 库(RcisTarget) # rankingsDb < - importRankings (dbPath、列=背景)# bgRanking < - reRank (rankingsDb) # # - eval = FALSE --------------------------------------------------------------- # motifEnrichmentTable < - cisTarget (geneSets bgRanking # aucMaxRank = 0.03 * getNumColsInDB (bgRanking), # geneErnMaxRank = getNumColsInDB (bgRanking),# geneErnMethod = " icistarget ") ## ---- eval = FALSE --------------------------------------------------------------- # showLogo (motifEnrichmentTable)