Add Hemoglobin percentages — Add_Hemo (original) (raw)

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")
}