# # # R代码从装饰图案来源的小插曲ChIPXpress /本月/ doc / ChIPXpress。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:ChIPXpress。Rnw: 51-54 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(ChIPXpress)数据(Oct4ESC_ChIPgenes)头(Oct4ESC_ChIPgenes) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:ChIPXpress。Rnw: 58 - 62 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(ChIPXpressData)库(bigmemory)路径< -系统。文件(“extdata”,包=“ChIPXpressData”) DB_GPL1261 <——attach.big.matrix (“DB_GPL1261.bigmemory.desc”,路径(路径)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:ChIPXpress。Rnw: 68 - 71 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #输出<——ChIPXpress (TFID = " 18999 ",芯片= Oct4ESC_ChIPgenes EntrezID美元,DB = DB_GPL1261)头(输出[[1]])头(输出[[2]])# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:ChIPXpress。Rnw: 77 - 82 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # GeneNames < - Oct4ESC_ChIPgenes美元注释(匹配(名字(输出[[1]]),Oct4ESC_ChIPgenes EntrezID美元)]结果< - data.frame(1:长度(输出[[1]]),GeneNames,名字(输出[[1]]),输出[[1]])colnames(结果)< - c(“等级”、“GeneNames”,“EntrezID”、“ChIPXpressScore”)负责人(结果)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:ChIPXpress。Rnw: 107 - 117 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(bigmemory) # #库(biganalytics) # #库(ChIPXrpess) # #库(GEOquery) # #库(affy) # #库(frma)图书馆(mouse4302frmavecs) # # # # # # DB <——buildDatabase (GPL_id = GPL1261, SaveDir = tempdir()) # # # #确保已经创建的保存目录和空!# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:ChIPXpress。Rnw: 122 - 125 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # GSM_ids < - c (“GSM24056”、“GSM24058”、“GSM24060”、“GSM24061”, # #“GSM94856”、“GSM94857”、“GSM94858”、“GSM94859”) # # DB <——buildDatabase (GSMfiles = GSM_ids SaveDir = tempdir()) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:ChIPXpress。Rnw: 132 - 135 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(mouse4302.db) # # EntrezID < - mget (as.character (rownames (DB)), mouse4302ENTREZID) # # rownames (DB) <——as.character (EntrezID) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:ChIPXpress。Rnw: 141 - 146 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # cleanDB < - cleanDatabase (DB, SaveFile = " newDB_GPL1261。bigmemory”, # # SavePath = tempdir (cleanDB)负责人())# # # # # # # cleanDB包含完成数据库准备ChIPXpress # # # # #输入。# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:ChIPXpress。Rnw:150-153 (eval = FALSE) ################################################### ## out <- ChIPXpress(TFID="18999",ChIP=Oct4ESC_ChIPgenes,DB=cleanDB) ## head(out[[1]]) ## head(out[[2]]) ################################################### ### code chunk number 10: ChIPXpress.Rnw:158-160 (eval = FALSE) ################################################### ## cleanDB <- attach.big.matrix("newDB_GPL1261.bigmemory.desc",path=tempdir()) ## head(cleanDB)