addPercentMtRibo: Add percentage of mitochondrial and ribosomal transcripts.

In romanhaa/cerebroApp: Interactive visualization of scRNA-seq data with Cerebro

Description

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

Usage

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'
)

romanhaa/cerebroApp documentation built on Nov. 25, 2021, 5:29 p.m.