ESCC_GEO 数据库挖掘实战

2019-01-06 本文已影响0人陈宇乔

第一：转换ID两个数据包

library(hgu133a2.db)
ls("package:hgu133a2.db")
ids=toTable(hgu133a2SYMBOL)

理解ID转换

library(org.Hs.eg.db)
ls("package:org.Hs.eg.db")
g2s=toTable(org.Hs.egSYMBOL);head(g2s)
g2e=toTable(org.Hs.egENSEMBL);head(g2e)
tmp=merge(a,g2e,by='ensembl_id')
tmp=merge(tmp,g2s,by='gene_id')

第二：hclust

  colnames(exprSet)=paste(group_list,1:ncol(exprSet),sep='_')
  # Define nodePar
  nodePar <- list(lab.cex = 0.6, pch = c(NA, 19),
                  cex = 0.7, col = "blue")
  hc=hclust(dist(t(exprSet)))
  par(mar=c(5,5,5,10))
  png('hclust.png',res=120)
  plot(as.dendrogram(hc), nodePar = nodePar, horiz = TRUE) ######这里画图
  dev.off()