Add_Mito_Ribo {scCustomize} | R Documentation |
Add Mito and Ribo percentages
Description
Add Mito, Ribo, & Mito+Ribo percentages to meta.data slot of Seurat Object or cell.data slot of Liger object
Usage
Add_Mito_Ribo(object, ...)
## S3 method for class 'liger'
Add_Mito_Ribo(
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,
overwrite = FALSE,
list_species_names = FALSE,
...
)
## S3 method for class 'Seurat'
Add_Mito_Ribo(
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
object |
Seurat or LIGER object |
... |
Arguments passed to other methods |
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). |
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 |
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. |
assay |
Assay to use (default is the current object default assay). |
Value
An object of the same class as object
with columns added to object meta data.
Examples
## Not run:
# Liger
liger_object <- Add_Mito_Ribo(object = liger_object, species = "human")
## End(Not run)
## Not run:
# Seurat
seurat_object <- Add_Mito_Ribo(object = seurat_object, species = "human")
## End(Not run)