DA_custom {ChromSCape}R Documentation

Differential Analysis in 'One vs Rest' mode

Description

Differential Analysis in 'One vs Rest' mode

Usage

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

Arguments

affectation

An annotation data.frame with cell_id and cell_cluster columns

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


[Package ChromSCape version 1.3.22 Index]