calculate_Uscore: Calculate rankings and scores for query data and given...

In carmonalab/UCell: Rank-based signature enrichment analysis for single-cell data

Calculate rankings and scores for query data and given signature set

Description

Calculate rankings and scores for query data and given signature set

Usage

calculate_Uscore(
  matrix,
  features,
  maxRank = 1500,
  chunk.size = 100,
  BPPARAM = NULL,
  ncores = 1,
  w_neg = 1,
  ties.method = "average",
  storeRanks = FALSE,
  force.gc = FALSE,
  name = "_UCell"
)

Arguments

matrix	Input data matrix
features	List of signatures
maxRank	Rank cutoff (1500)
chunk.size	Cells per sub-matrix (100)
BPPARAM	A BioParallel object to instruct UCell how to parallelize
ncores	Number of cores to use for parallelization
w_neg	Weight on negative signatures
ties.method	How to break ties, for data.table::frankv method ("average")
storeRanks	Store ranks? (FALSE)
force.gc	Force garbage collection? (FALSE)
name	Suffix for metadata columns ("_UCell")

Value

A list of signature scores

carmonalab/UCell documentation built on Nov. 4, 2024, 5:32 p.m.