1.读入文件

library(DESeq2) 
rm(list=ls())
#读入文件并修改行列名
countdata <- read.table("./hhh/hhh_WT_matrix.out", header=TRUE, row.names=1) #导入数据
head(countdata) 

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colnames(countdata) <- c("hhh-1","hhh-2","hhh-3","WT_1","WT_2","WT_3") # 修改列名,
head(countdata) 

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2.构建分组信息

condition <- factor(c("hhh","hhh","hhh","WT","WT","WT")) # 赋值因子，即变量
sample_Data <- data.frame(sampleID=colnames(countdata), condition) 

#设置因子，并确定顺序（一般突变体在后，这样最终结果是Mutant/WT）
sample_Data$condition=factor(sample_Data$condition,c("WT","hhh")) #设置分组顺序，最终差异结果是后面/前面，

sample_Data

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3.构建DESeq2中的dds对象

dds<- DESeqDataSetFromMatrix(countData = countdata, colData =sample_Data, design = ~condition)

#4.差异分析

dds<-DESeq(dds)

5.获得各组的size factors

sizefactor<-sizeFactors(dds)

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6.获得比较组

resultsNames(dds)#list the coefficients,获得比较组

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7.提取差异结果 name根据前面resultsNames(dds)获得。

res<-results(dds,name="condition_hhh_vs_WT")

head(res)

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8.合并前面的Raw reads counts

final_data=merge(as.data.frame(res),countdata,by="row.names",sort=FALSE)

head(final_data)

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9.写入文件

write.table(final_data,"HAG704VSWT.out2.txt",sep="\t",quote=F,col.names = NA)