library(DESeq2)
library(dplyr)
# 读取表达矩阵
mycounts <- read.csv("Input File Format/mycounts.csv",row.names = 1)
# 查看读入的表达矩阵
head(mycounts)
dim(mycounts)
# 去除表达量全为0的行
mycounts_1 <- mycounts[rowSums(mycounts) != 0,]
#查看去除后的剩余的基因数目
dim(mycounts_1)
# 读取分组文件
mymeta <- read.csv("Input File Format/mymeta.csv",stringsAsFactors = T)
mymeta
colnames(mycounts_1) == mymeta$id
dds <- DESeqDataSetFromMatrix(countData = mycounts_1, colData = mymeta,design = ~dex)
dds <- DESeq(dds)
res <- results(dds)
head(res)
res_1 <- data.frame(res)
head(res_1)
res_1 %>%
mutate(group = case_when(
log2FoldChange >= 1 & pvalue <= 0.05 ~ "UP",
log2FoldChange <= -1 & pvalue <= 0.05 ~ "DOWN",
TRUE ~ "NOT_CHANGE"
)) -> res_2
table(res_2$group)
write.csv(res_2, file = "diff_expr_result.csv", quote = F)
Demo Data csv:
2025060214542848 2025060214542958
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