## ----libraries, echo=FALSE, message=FALSE, warning=FALSE---------------------- suppressPackageStartupMessages({ library(RcisTarget) library(rcistarget.hg19.motifdbs.cisbponly.500bp）库（dt）库（data.table）#require（visnetwork）}）## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------包装库（“ rcistarget”）## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------＃分析基因：txtfile < - 糊状（file.path（system.file（'示例'，package ='rcistArget'）），“ hypoxiageneset.txt”，sep =“/”）基因< - list（hypoxia = read.table（txtfile，stringsasfactors = false）[，1]）＃背景：txtfile < - paste（file.path（system.file（'示例'，package ='rcistarget'）），“ randogeneset.txt”，sep =“/”）＃for toy示例我们将使用几个随机基因背景< - read.table（txtfile，stringsasFactors = false）[，1] ## ------------------------------------------------------------------------------------------------------------------------------------------------------------＃a：添加背景< - unique（c（基因$缺氧，backgr）ound））＃b：Intersect＃基因$缺氧<-Intersect（Genesets $缺氧，背景）## -----图。------------------------------------ gplots::venn(list(background=background, geneLists=unlist（基因）））## ---- eval = false ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------“〜/database/hg19-500bp-upstream-10species.mc9nr.feather” ##---- eval = false -------------------------------------------------------------------------------------------------------------------------------------------------＃library（rcistarget）＃排名db < - Inportrankings（dbpath，columns = background）＃bgranking <-Rerank（RankingsDB）## -------eval = false -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # motifEnrichmentTable <- cisTarget(geneSets, bgRanking, # aucMaxRank=0.03*getNumColsInDB(bgRanking), # geneErnMaxRank=getNumColsInDB(bgRanking), # geneErnMethod = "icistarget") ## ----eval=FALSE--------------------------------------------------------------- # showLogo(motifEnrichmentTable)