Add_Hemo: Add Hemoglobin percentages

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Add Hemoglobin percentages

Description

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

Usage

Add_Hemo(object, ...)

## S3 method for class '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 class '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

## Not run: 
# Liger
liger_object <- Add_Hemo(object = liger_object, species = "human")

## End(Not run)

## Not run: 
# Seurat
seurat_object <- Add_Hemo(object = seurat_object, species = "human")

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.