Add Hemoglobin percentages — Add

Add hemoglobin percentages to meta.data slot of Seurat Object or cell.data/cellMeta slot of Liger object

Add_Hemo(object, ...)

# S3 method for liger
Add_Hemo(
  object,
  species,
  hemo_name = "percent_hemo",
  hemo_pattern = NULL,
  hemo_features = NULL,
  ensembl_ids = FALSE,
  overwrite = FALSE,
  list_species_names = FALSE,
  ...
)

# S3 method for Seurat
Add_Hemo(
  object,
  species,
  hemo_name = "percent_hemo",
  hemo_pattern = NULL,
  hemo_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, rhesus macaque, or chicken (name or abbreviation) are provided the function will automatically generate hemo_pattern values.
hemo_name: name to use for the new meta.data column containing percent hemoglobin counts. Default is "percent_hemo".
hemo_pattern: A regex pattern to match features against for hemoglobin genes (will set automatically if species is mouse or human; marmoset features list saved separately).
hemo_features: A list of hemoglobin gene names to be used instead of using regex pattern.
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 hemo_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.
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

if (FALSE) {
# Liger
liger_object <- Add_Hemo(object = liger_object, species = "human")
}

if (FALSE) {
# Seurat
seurat_object <- Add_Hemo(object = seurat_object, species = "human")
}