在看指控的时候出现以下报错:
> pcovid_sn_1<-VlnPlot(covid_sn_1, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), ncol = 3)
Warning message:
In SingleExIPlot(type = type, data = data[, x, drop = FALSE], idents = idents, :
All cells have the same value of percent.mt.
搜到两篇解决的:Seurat 计算线粒体基因比例时,基因非MT-开头 - 简书 (jianshu.com)
单细胞测序分析R包Seurat质量控制小提琴图QC VlnPlot --关于MT的问题 - 简书 (jianshu.com)
Seurat可以利用PercentageFeatureSet计算线粒体基因比例并添加到meta.data,但是我们在使用
sce[["percent.mt"]] = PercentageFeatureSet(sce, pattern = "^MT-")
计算线粒体比例时,会遇到结果为0的情况。
其可能是由于比对时使用的gtf文件线粒体基因为非MT-开头。
image
image
那么,如何在seurat_object添加线粒体比例呢?
方案一:
#这里线粒体基因的名字可以查看你用的gtf文件里是哪些
MT <- c("COX1","COX2","COX3","ND1","ND2","ND3","ND4L","ND4","ND5","ND6","CYTB","ATP6","ATP8")
##table(grepl("^MT-",rownames(sce)))
#根据PercentageFeatureSet的function()源码做了修改
sce[["percent.mt"]] = colSums(x = GetAssayData(object = sce,
assay = "RNA", slot = "counts")[MT, , drop = FALSE])/sce[[paste0("nCount_","RNA")]] * 100
方案二:
在cellranger制备参考基因组前,把gtf文件里的线粒体基因添加“MT-”前缀。
作者:zhangsiyu
链接:https://www.jianshu.com/p/953692edb712
来源:简书
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