estimateExpressionChange: Expression shift magnitudes per cluster between conditions

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

Expression shift magnitudes per cluster between conditions

Description

Expression shift magnitudes per cluster between conditions

Usage

estimateExpressionChange(
  cm.per.type,
  sample.groups,
  cell.groups,
  sample.per.cell,
  dist = NULL,
  dist.type = c("shift", "total", "var"),
  verbose = FALSE,
  ref.level = NULL,
  n.permutations = 1000,
  p.adjust.method = "BH",
  top.n.genes = NULL,
  gene.selection = "wilcox",
  n.pcs = NULL,
  trim = 0.2,
  n.cores = 1,
  ...
)

Arguments

cm.per.type	List of normalized count matrices per cell type
sample.groups	Named factor with cell names indicating condition/sample, e.g., ctrl/disease
cell.groups	Named clustering/annotation factor with cell names
dist	what distance measure to use: 'JS' - Jensen-Shannon divergence (default), 'cor' - Pearson's linear correlation on log transformed values
verbose	(default=FALSE)
n.cores	number of cores (default=1)

Value

List of distances per cell type, distance matrices, sample groups, cell types, pvalues, and adjusted p-values.

kharchenkolab/cacoa documentation built on May 10, 2022, 3:42 a.m.