> setwd("C:\\renalcancer\\sygy\\08.diffFilter") #设置工作目录
> inputFile="uniq.symbol.txt" #输入文件
> pFilter=0.05 #p值临界值
> logFCfilter=1 #logFC临界值
> conNum=32 #normal组样品数目
> treatNum=375 #tumor组样品数目
>
> #读取输入文件
> outTab=data.frame()
> grade=c(rep(1,conNum),rep(2,treatNum))
> data=read.table(inputFile,sep="\t",header=T,check.names=F,row.names=1)
> data=as.matrix(data)
>
> #差异分析
> for(i in 1){
+ geneName=unlist(strsplit(i,"\\|",))[1]
+ geneName=gsub("\\/", "_", geneName)
+ rt=rbind(expression=data[i,],grade=grade)
+ rt=as.matrix(t(rt))
+ wilcoxTest<-wilcox.test(expression ~ grade, data=rt)
+ pvalue=wilcoxTest$p.value
+ conGeneMeans=mean(data[i,1:conNum])
+ treatGeneMeans=mean(data[i,(conNum+1):ncol(data)])
+ logFC=log2(treatGeneMeans)-log2(conGeneMeans)
+ conMed=median(data[i,1:conNum])
+ treatMed=median(data[i,(conNum+1):ncol(data)])
+ diffMed=treatMed-conMed
+ if( ((logFC>0) & (diffMed>0)) | ((logFC<0) & (diffMed<0)) ){
+ outTab=rbind(outTab,cbind(gene=i, conMean=conGeneMeans, treatMean=treatGeneMeans,logFC=logFC,pValue=pvalue))
> }
错误: 意外的'}' in "}"
> }
错误: 意外的'}' in " }"
>
> #输出所有基因的差异情况
> write.table(outTab,file="all.xls",sep="\t",row.names=F,quote=F)
>
> #输出差异表格
> outDiff=outTab[( abs(as.numeric(as.vector(outTab$logFC)))>logFCfilter & as.numeric(as.vector(outTab$pValue))<pFilter),]
> write.table(outDiff,file="diff.xls",sep="\t",row.names=F,quote=F)
>
> #输出差异基因表达
> heatmap=rbind(ID=colnames(data[as.vector(outDiff[,1]),]),data[as.vector(outDiff[,1]),])
Error in `[.data.frame`(outDiff, , 1) : 选择了未定义的列
> write.table(heatmap,file="diffGeneExp.txt",sep="\t",col.names=F,quote=F)


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