R语言DEDeq2包进行RNA-seq分析总结

最近在学习DESeq2包进行RNA-seq分析，并画火山图，分析代码总结如下：

rm(list = ls())
options(stringsAsFactors = F)

## 读入counts数据
exprSet <- read.csv("./DEGs_spleen.csv", header = T, row.names = 1)
exprSet <- exprSet[,-1]
View(exprSet)

## DESeq2进行差异分析
suppressMessages(library(DESeq2))
exprSet=ceiling(exprSet)
group_list <- factor(c('ctrl', 'ctrl', 'treat','treat'))       #设置分组
colData <- data.frame(row.names=colnames(exprSet), group_list=group_list)
dds <- DESeqDataSetFromMatrix(countData = exprSet,
                              colData = colData,
                              design = ~ group_list)  #构建dds
dds <- DESeq(dds)   #差异分析

plotDispEsts(dds, main="Dispersion plot")


res <- results(dds, contrast=c("group_list","treat" , "ctrl"))  #提取差异分析结果
resOrdered <- res[order(res$padj),]
DEG=as.data.frame(resOrdered)
write.csv(DEG,