Differential Analysis in 'One vs Rest' mode

Source: R/diff_analysis_gene_set_enrichment.R

Differential Analysis in 'One vs Rest' mode

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