Add percentage of mitochondrial and ribosomal transcripts.

Source: R/addPercentMtRibo.R

Get percentage of transcripts of gene list compared to all transcripts per cell.

addPercentMtRibo(object, assay = "RNA", organism, gene_nomenclature)

Arguments

object

Seurat object.
assay

Assay to pull counts from; defaults to 'RNA'. Only relevant in Seurat v3.0 or higher since the concept of assays wasn't implemented before.
organism

Organism, can be either human ('hg') or mouse ('mm'). Genes need to annotated as gene symbol, e.g. MKI67 (human) / Mki67 (mouse).
gene_nomenclature

Define if genes are saved by their name ('name'), ENSEMBL ID ('ensembl') or GENCODE ID ('gencode_v27', 'gencode_vM16').

Value

Seurat object with two new meta data columns containing the percentage of mitochondrial and ribosomal gene expression for each cell.

Examples

pbmc <- readRDS(system.file("extdata/v1.3/pbmc_seurat.rds",
  package = "cerebroApp"))
pbmc <- addPercentMtRibo(
  object = pbmc,
  assay = 'RNA',
  organism = 'hg',
  gene_nomenclature = 'name'
)

#> [17:53:22] No mitochondrial genes found in data set.
#> [17:53:22] Calculate percentage of 1 ribosomal transcript(s) present in the data set...