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 1.2.62 Index]