Add Multiple Cell Quality Control Values with Single Function

Add Mito/Ribo %, Cell Complexity (log10GenesPerUMI), Top Gene Percent with single function call

Add_Cell_QC_Metrics(
  seurat_object,
  add_mito_ribo = TRUE,
  add_complexity = TRUE,
  add_top_pct = TRUE,
  add_MSigDB = TRUE,
  add_IEG = TRUE,
  add_cell_cycle = TRUE,
  species,
  mito_name = "percent_mito",
  ribo_name = "percent_ribo",
  mito_ribo_name = "percent_mito_ribo",
  complexity_name = "log10GenesPerUMI",
  top_pct_name = NULL,
  oxphos_name = "percent_oxphos",
  apop_name = "percent_apop",
  dna_repair_name = "percent_dna_repair",
  ieg_name = "percent_ieg",
  mito_pattern = NULL,
  ribo_pattern = NULL,
  mito_features = NULL,
  ribo_features = NULL,
  ensembl_ids = FALSE,
  num_top_genes = 50,
  assay = NULL,
  overwrite = FALSE
)

Arguments

seurat_object: object name.
add_mito_ribo: logical, whether to add percentage of counts belonging to mitochondrial/ribosomal genes to object (Default is TRUE).
add_complexity: logical, whether to add Cell Complexity to object (Default is TRUE).
add_top_pct: logical, whether to add Top Gene Percentages to object (Default is TRUE).
add_MSigDB: logical, whether to add percentages of counts belonging to genes from of mSigDB hallmark gene lists: "HALLMARK_OXIDATIVE_PHOSPHORYLATION", "HALLMARK_APOPTOSIS", and "HALLMARK_DNA_REPAIR" to object (Default is TRUE).
add_IEG: logical, whether to add percentage of counts belonging to IEG genes to object (Default is TRUE).
add_cell_cycle: logical, whether to addcell cycle scores and phase based on CellCycleScoring. Only applicable if species = "human". (Default is TRUE).
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".
complexity_name: name to use for new meta data column for Add_Cell_Complexity_Seurat. Default is "log10GenesPerUMI".
top_pct_name: name to use for new meta data column for Add_Top_Gene_Pct_Seurat. Default is "percent_topXX", where XX is equal to the value provided to num_top_genes.
oxphos_name: name to use for new meta data column for percentage of MSigDB oxidative phosphorylation counts. Default is "percent_oxphos".
apop_name: name to use for new meta data column for percentage of MSigDB apoptosis counts. Default is "percent_apop".
dna_repair_name: name to use for new meta data column for percentage of MSigDB DNA repair counts. Default is "percent_dna_repair"..
ieg_name: name to use for new meta data column for percentage of IEG counts. Default is "percent_ieg".
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).
num_top_genes: An integer vector specifying the size(s) of the top set of high-abundance genes. Used to compute the percentage of library size occupied by the most highly expressed genes in each cell.
assay: assay to use in calculation. Default is "RNA". Note This should only be changed if storing corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).
overwrite: Logical. Whether to overwrite existing an meta.data column. Default is FALSE meaning that function will abort if column with name provided to meta_col_name is present in meta.data slot.

Value

A Seurat Object

Examples

if (FALSE) {
obj <- Add_Cell_QC_Metrics(seurat_object = obj, species = "Human")
}