DA_pairwise: Run differential analysis in Pairwise mode

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Run differential analysis in Pairwise mode

Description

Run differential analysis in Pairwise mode

Usage

DA_pairwise(
  affectation,
  by,
  counts,
  method,
  feature,
  block,
  progress = NULL,
  BPPARAM = BiocParallel::bpparam()
)

Arguments

affectation	An annotation data.frame with cell_cluster and cell_id columns
by	= A character specifying the column of the object containing the groups of cells to compare.
counts	Count matrix
method	DA method, Wilcoxon or edgeR
feature	Feature data.frame
block	Blocking feature
progress	A shiny Progress instance to display progress bar.
BPPARAM	BPPARAM object for multiprocessing. See bpparam for more informations. Will take the default BPPARAM set in your R session.

Value

A list of results, groups compared and references

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.