# #设置,回声= FALSE,结果=“隐藏 "---------------------------------------- knitr: opts_chunk美元集(整洁= FALSE,缓存= TRUE, dev =“png”,消息= FALSE,错误= FALSE,警告= TRUE) # #——bioC eval = FALSE --------------------------------------------------------- # ## 试试http://如果不支持https:// url #(!需要(“BiocManager”))# install.packages (BiocManager) # BiocManager::安装(“NBSplice version = "重击 ") ## ---- expMat建成,eval = FALSE ------------------------------------------------- # 文件名< - c(粘贴(代表(“C1R”,4),1:4,”/丰富。tsv”,9 = " "),#粘贴(代表(“C2R”,4),1:4,”/丰富。tsv"， sep="")) # # myInfo<-lapply(seq_along(fileNames)， function(x){# quant<-read.delim(fileNames[x]， header = TRUE) # expression<-quant[，"est_counts"] # return(expression) #}) # #添加isoform IDS作为行名# isoform_id<-read.delim(fileNames[x]， header = TRUE)[，"target_id"] # expressionMatrix<-(do. delm)调用(cbind myInfo)) # rownames (expressionMatrix) < -isoform_id # #添加样品名称列名称# colnames (expressionMatrix) < - c(粘贴(代表(“C1R”,4),1:4,9 = " "),#粘贴(代表(“C2R”,4),1:4,9月 ="")) ## ---- expMat eval = TRUE -------------------------------------------------------- 数据(isoCounts包=“NBSplice”)负责人(isoCounts)暗(isoCounts) # #——geneIsoMat eval = TRUE ---------------------------------------------------- 数据(geneIso,包=“NBSplice”)负责人(geneIso)暗(geneIso) # #——designMat eval = TRUE ----------------------------------------------------- designMatrix < -data.frame(示例= c(粘贴(代表(“C1R”,4),1:4,9 = " "),粘贴(代表(“C2R”,4),1:4,9 = " ")),条件=因子(c(代表(“正常”,4),代表(“肿瘤”,4)),水平= c(“正常”、“肿瘤”)))rownames (designMatrix) < -designMatrix[,“sample”]designMatrix colData # #,eval = TRUE ------------------------------------------------------- colName < -“条件”(designMatrix [colName水平 ]) ## ---- objectBuild eval = TRUE --------------------------------------------------- 库(NBSplice) myIsoDataSet < -IsoDataSet (isoCounts、designMatrix colName, geneIso) # #——objectInsp eval = TRUE ---------------------------------------------------- 显示(myIsoDataSet)头(isoCounts (myIsoDataSet )) ## ---- lowExp,eval = TRUE -------------------------------------------------------- myIsoDataSet < -buildLowExpIdx (myIsoDataSet colName ratioThres = 0.01, countThres = 1) # #——电视台,eval = TRUE -------------------------------------------------------- myDSResults < -NBTest (myIsoDataSet、colName、测试= " F ") ## ---- 对象loading2、回声= FALSE eval = TRUE,结果= "隐藏 "------------------- 数据(myDSResults、包= " NBSplice ") ## ---- 资金占用,eval = TRUE --------------------------------------------------------- 头(lowExpIndex (myDSResults)) (myDSResults)头(结果(myDSResults形成鲜明对比 )) ## ---- lowExpRes eval = TRUE ----------------------------------------------------- (结果(myDSResults过滤器= FALSE )) ## ---- getDSGe,eval = TRUE ------------------------------------------------------- mySignificantRes < -GetDSResults (myDSResults)头(mySignificantRes)暗(mySignificantRes) myDSGenes < -GetDSGenes (myDSResults)头(myDSGenes)长度(myDSGenes) # #——plotD eval = TRUE --------------------------------------------------------- plotRatiosDisp (myDSResults) # #——plotv eval = TRUE --------------------------------------------------------- plotVolcano (myDSResults) # #——plotGene,eval = TRUE ------------------------------------------------------ ## 选择第一个不同拼接基因基因< -GetDSGenes (myDSResults) [1] GetGeneResults (myDSResults、基因)plotGeneResults (myDSResults、基因)# #——plotGene2 eval = TRUE ----------------------------------------------------- ## 保持non-reliable和非重要亚型plotGeneResults (myDSResults基因,filterLowExpIso = FALSE, filterNotSignificant = FALSE) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()