Add Mito and Ribo percentages — Add_Mito_Ribo

Add Mito, Ribo, & Mito+Ribo percentages to meta.data slot of Seurat Object

Add_Mito_Ribo_Seurat(
  seurat_object,
  species,
  mito_name = "percent_mito",
  ribo_name = "percent_ribo",
  mito_ribo_name = "percent_mito_ribo",
  mito_pattern = NULL,
  ribo_pattern = NULL,
  mito_features = NULL,
  ribo_features = NULL,
  ensembl_ids = FALSE,
  assay = NULL,
  overwrite = FALSE,
  list_species_names = FALSE
)

Arguments

seurat_object: object name.
species: Species of origin for given Seurat Object. If mouse, human, marmoset, zebrafish, rat, drosophila, or rhesus macaque (name or abbreviation) are provided the function will automatically generate mito_pattern and ribo_pattern values.
mito_name: name to use for the new meta.data column containing percent mitochondrial counts. Default is "percent_mito".
ribo_name: name to use for the new meta.data column containing percent ribosomal counts. Default is "percent_ribo".
mito_ribo_name: name to use for the new meta.data column containing percent mitochondrial+ribosomal counts. Default is "percent_mito_ribo".
mito_pattern: A regex pattern to match features against for mitochondrial genes (will set automatically if species is mouse or human; marmoset features list saved separately).
ribo_pattern: A regex pattern to match features against for ribosomal genes (will set automatically if species is mouse, human, or marmoset).
mito_features: A list of mitochondrial gene names to be used instead of using regex pattern. Will override regex pattern if both are present (including default saved regex patterns).
ribo_features: A list of ribosomal gene names to be used instead of using regex pattern. Will override regex pattern if both are present (including default saved regex patterns).
ensembl_ids: logical, whether feature names in the object are gene names or ensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).
assay: Assay to use (default is the current object default assay).
overwrite: Logical. Whether to overwrite existing meta.data columns. Default is FALSE meaning that function will abort if columns with any one of the names provided to mito_name ribo_name or mito_ribo_name is present in meta.data slot.
list_species_names: returns list of all accepted values to use for default species names which contain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, and rhesus macaque). Default is FALSE.

Value

A Seurat Object

Examples

if (FALSE) {
obj <- Add_Mito_Ribo_Seurat(seurat_object = obj, species = "human")
}