AddDuckModuleScore — duckModuleScore • scSpotlight

A modified version of Seurat::AddModuleScore() function querying expression data from duckdb backend

Usage

duckModuleScore(
  con,
  features,
  pool = NULL,
  nbin = 24,
  ctrl = 100,
  assay = "RNA",
  name = "Cluster",
  seed = 1,
  search = FALSE,
  slot = "data",
  ...
)

Arguments

con: duckdb connection object
features: A list of vectors of features for expression programs; each entry should be a vector of feature names
pool: List of features to check expression levels against, defaults to rownames(x = object)
nbin: Number of bins of aggregate expression levels for all analyzed features
ctrl: Number of control features selected from the same bin per analyzed feature
assay: Name of assay to use
name: Name for the expression programs; will append a number to the end for each entry in features (eg. if features has three programs, the results will be stored as name1, name2, name3, respectively)
seed: Set a random seed. If NULL, seed is not set.
search: Search for symbol synonyms for features in features that don't match features in object? Searches the HGNC's gene names database; see UpdateSymbolList for more details
slot: Slot to calculate score values off of. Defaults to data slot (i.e log-normalized counts)
...: Extra parameters passed to UpdateSymbolList

Value

A dataframe with a single column of module score, using cells as rownames