利用RNA-seq结果计算每个样本中线粒体Count比率

做过单细胞测序的都知道，Seurat包中有一个PercentageFeatureSet函数可以计算每个细胞中比对到线粒体的UMI/read Count比率。如果把组织当作一个细胞来看待，能不能计算这个样本的线粒体的read Count比率呢？
先将Count矩阵导入

matrix <-read.csv(myfiles[1],sep =",",header=T,row.names=1,check.names = F)

1 Seurat

drg <- CreateSeuratObject(matrix, project = "DRG", names.delim = "_")
features=c("ENSMUSG00000064341","ENSMUSG00000064345","ENSMUSG00000064351","ENSMUSG00000064354",
           "ENSMUSG00000064356","ENSMUSG00000064357","ENSMUSG00000064358","ENSMUSG00000064360",
           "ENSMUSG00000065947","ENSMUSG00000064363","ENSMUSG00000064367","ENSMUSG00000064368",
           "ENSMUSG00000064370")
drg[["percent.mt"]] <- PercentageFeatureSet(object = drg, features=features)
head(drg@meta.data)

#             orig.ident nCount_RNA nFeature_RNA percent.mt
#SRR11617449        DRG   42823530        18563  33.541305
#SRR11617450        DRG   39310982        18982  36.160760
#SRR11617451        DRG   23711965        18574  19.601733
#SRR11617452        DRG   19406721        17905  24.340614
#SRR11617453        DRG   21100439        18200  26.200886
#SRR11617454        DRG   17490800        17916  24.937516

drg@meta.data$group  <- c(rep("Ankle",6),rep("DRG",6),rep("spinal",6))
VlnPlot(object = drg, features = c("percent.mt"), ncol = 1,pt.size=0.3,group.by = "group")+
  xlab("") + ylab("Mitochondrial genes ratio") + ggtitle("")

2 自行计算

features=c("ENSMUSG00000064341","ENSMUSG00000064345","ENSMUSG00000064351","ENSMUSG00000064354",
           "ENSMUSG00000064356","ENSMUSG00000064357","ENSMUSG00000064358","ENSMUSG00000064360",
           "ENSMUSG00000065947","ENSMUSG00000064363","ENSMUSG00000064367","ENSMUSG00000064368",
           "ENSMUSG00000064370")
mt<-matrix[row.names(matrix)%in%features,]
pencent.mt=c()
for (i in 1:ncol(matrix)) {
  f=apply(mt,2,sum)[i]*100/apply(matrix,2,sum)[i];
  pencent.mt=append(e,f)
}
head(pencent.mt)

#SRR11617449 SRR11617450 SRR11617451 SRR11617452 SRR11617453 SRR11617454 SRR11617455 
#  33.541305   36.160760   19.601733   24.340614   26.200886   24.937516   25.409828

那么问题来呢，这个线粒体Count比率能不能成为衡量组织或细胞线粒体数量的一个指标？例如在白色脂肪的褐变过程中。

percent.mt.png