Seurat4.0 系列教程9：差异表达检测

我们使用通过SeuratData[1]包提供的 2，700个 PBMC 来演示。

library(Seurat)
pbmc3k_final <- readRDS("G:/practice/single cell/pbmc3k/pbmc3k_final.rds")
pbmc=pbmc3k_final

#执行默认差异表达检测 Seurat 的大部分差异表达功能可以通过FindMarkers()功能访问。默认Seurat 执行Wilcoxon rank sum test。要测试两个特定细胞组之间的差异表达，可指定ident参数。

# list options for groups to perform differential expression on
levels(pbmc)

## [1] "Naive CD4 T"  "Memory CD4 T" "CD14+ Mono"   "B"            "CD8 T"       
## [6] "FCGR3A+ Mono" "NK"           "DC"           "Platelet"

# Find differentially expressed features between CD14+ and FCGR3A+ Monocytes
monocyte.de.markers <- FindMarkers(pbmc, ident.1 = "CD14+ Mono", ident.2 = "FCGR3A+ Mono")
# view results
head(monocyte.de.markers)

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