Entering edit mode
4.5 years ago
mikysyc2016
▴
120
Hi all, I need to define control features (genes) - ERCC spike-ins and mitochondrial genes when I do single cell RNA-seq analysis. while isSpike in SingleCellExperiment package defunct now.
isSpike(umi, "ERCC") <- grepl("^ERCC-", rownames(umi))
isSpike(umi, "MT") <- rownames(umi) %in%
c("ENSG00000198899", "ENSG00000198727", "ENSG00000198888",
"ENSG00000198886", "ENSG00000212907", "ENSG00000198786",
"ENSG00000198695", "ENSG00000198712", "ENSG00000198804",
"ENSG00000198763", "ENSG00000228253", "ENSG00000198938",
"ENSG00000198840")
Did anyone know how I can do this step in R now? Thanks in advance!
