diffCellDensity: Estimate differential cell density

In kharchenkolab/cacoa: Case-Control Analysis Tools for Single-Cell RNA-Seq

Estimate differential cell density

Description

Estimate differential cell density

Usage

diffCellDensity(
  density.mat,
  sample.groups,
  ref.level,
  target.level,
  type = "subtract"
)

Arguments

density.mat	estimated cell density matrix with estimateCellDensity
sample.groups	A two-level factor on the sample names describing the conditions being compared (default: stored vector)
ref.level	Reference sample group, e.g., ctrl, healthy, or untreated. (default: stored value)
target.level	target/disease level for sample.group vector
type	method to calculate differential cell density of each bin; subtract: target density minus ref density; entropy: estimated kl divergence entropy between sample groups ; t.test: zscore of t-test, global variance is setting for t.test

kharchenkolab/cacoa documentation built on Nov. 8, 2024, 6:06 a.m.