Seurat的FindAllMarkers方法

轉自：https://scrnaseq-course.cog.sanger.ac.uk/website/seurat-chapter.html#finding-differentially-expressed-genes-cluster-biomarkers

https://satijalab.org/seurat/archive/v3.1/pbmc3k_tutorial.html

https://www.rdocumentation.org/packages/Seurat/versions/1.4.0/topics/FindAllMarkers

1.FindAllMarkers

FindAllMarkers(object, ident.1, ident.2 = NULL, genes.use = NULL,
  thresh.use = 0.25, test.use = "bimod", min.pct = 0.1,
  min.diff.pct = 0.05, print.bar = TRUE, only.pos = FALSE,
  max.cells.per.ident = Inf, return.thresh = 0.01, do.print = FALSE,
  random.seed = 1)

參數：

• only.pos：Only return positive markers ；

• min.pct：只測試在兩個cluster中檢測到至少在min.pct%中表達的基因。通過不測試那些很少表達的基因來加快速度。

• thresh.use：將測試限制在顯示兩組細胞之間平均至少x倍差異(對數尺度)的基因上。 增大它加速運算，但可能會錯過較弱的信號。  

教程中提供：

pbmc.markers <- FindAllMarkers(object = pbmc, only.pos = TRUE, min.pct = 0.25, thresh.use = 0.25)