DEGs筛选代码

setwd("F:/转录组下游分析")
library("DESeq2")
A <- read.table("C:/Users/DELL/Desktop/DEGs.txt", header = TRUE,row.names = 1 )
B <- as.matrix(A)
coldata <- read.table("C:/Users/DELL/Desktop/group.txt", header = TRUE,row.names = 1)
coldata$condition <- factor(coldata$condition)

dds <- DESeqDataSetFromMatrix(countData = B, 
                              colData = coldata, 
                              design = ~ condition);
dds <- DESeq(dds)
res <- results(dds, contrast = c("condition", "H", "S")) 
sum(res$pvalue < 0.01,na.rm = TRUE)    
plotMA(res, alpha = 0.05, colSig = 'red', colLine = 'skyblue')
filter_up <- subset(res, pvalue < 0.01 & log2FoldChange > 2) #过滤上调基因
filter_down <- subset(res, pvalue < 0.01 & log2FoldChange < -2) #过滤下调基因
print(paste('差异上调基因数量: ', nrow(filter_up)))  #打印上调基因数量
print(paste('差异下调基因数量: ', nrow(filter_down)))  #打印下调基因数量

write.table(as.data.frame(res), file = "./DEGsHvsS.txt") #log2FoldChange + pvalue + padj
write.table(filter_up, file="./HvsSup_gene.txt", quote = F)  
write.table(filter_up, file="./HvsSdown_gene.txt", quote = F)