差异性分析傻瓜版

path1输入你的第一个Excel

 

path2输入你的第二个Excel

 

DEG.dig <- function(path1,path2) {
  
  require(xlsx)
  
  require(tidyverse)
  
  require(limma)
  
  require(edgeR)
  
  E<- read.xlsx (path1,sheetIndex = 1,header = 1) %>% column_to_rownames(var ="NA." )
  
  type<- read.xlsx (path2,sheetIndex = 1,header = 1)  %>% select(type)
  
  type <- type$type
  
  type <- factor(type,levels = c(0,1),labels = c("tumor","normal")) 
  

  design <- model.matrix(~0+type)
  
  rownames(design) = colnames(E)
  
  colnames(design) = c("normal","tumor")
  

  
  dge <- DGEList(counts  = E)
  
  dge$E %>% dim
  

  keep_gene <- rowSums(cpm(dge) > 1) >= 2
  
  dge <- dge[keep_gene,,keep.lib.sizes=FALSE]
  
  dge$E %>% dim
  

  
  dge <- calcNormFactors( dge )
  
  dge$sample 
 
  pdf(file = "MDS.pdf")
  
  plotMDS(dge)
  
  dev.off()
  
  v <- voom(dge, design, plot = F, normalize = "quantile")
  
  fit <- lmFit(v, design)
  

  cont.matrix <- makeContrasts(tumorvsnormal=tumor-normal, levels = design)

  fit2 <- contrasts.fit(fit, cont.matrix)
  
  fit2 <- eBayes(fit2)
  
  nrDEG_limma_voom <- topTable(fit2, n = 100) %>%   na.omit() 
  
  head(nrDEG_limma_voom)
  
  write.csv(nrDEG_limma_voom,"结果.csv")
}