DA_custom: Differential Analysis Custom in 'One vs One' mode

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

Differential Analysis Custom in 'One vs One' mode

Description

Differential Analysis Custom in 'One vs One' mode

Usage

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

Arguments

affectation	An annotation data.frame with cell_id and
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 tables
block	Blocking feature
ref	If de_type is custom, the reference to compare (data.frame), must be a one-column data.frame with cell_clusters or sample_id as character in rows
group	If de_type is custom, the group to compare (data.frame), must be a one-column data.frame with cell_clusters or sample_id as character in rows
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.