prep_scATAC_seurat: prep_scATAC_seurat

In cinaR: A Computational Pipeline for Bulk 'ATAC-Seq' Profiles

prep_scATAC_seurat

Description

Prepare 10x scATAC data from a Seurat/Signac object for cinaR.

Usage

prep_scATAC_seurat(
  object,
  assay = NULL,
  slot = "counts",
  sample.col,
  group.col,
  cluster.col = NULL,
  peak.bed = NULL,
  min.cells = 20,
  verbose = TRUE
)

Arguments

object	Seurat object containing an ATAC assay (typically "peaks").
assay	assay name to use; defaults to Seurat::DefaultAssay(object).
slot	assay slot to pull counts from (default "counts").
sample.col	column name in [e-mail] indicating biological replicate.
group.col	column name in [e-mail] indicating condition/group.
cluster.col	optional column name for cell type/cluster.
peak.bed	optional data.frame with CHR/START/STOP columns for peaks.
min.cells	minimum number of cells required per sample (and per cluster if used).
verbose	logical, prints informative messages.

Value

list with elements 'bed', 'contrasts', and 'group.info', or a named list of such lists when cluster.col is provided.

Examples

## Not run: 
prep <- prep_scATAC_seurat(seurat_obj,
                           sample.col = "sample",
                           group.col = "group",
                           assay = "peaks")

## End(Not run)

cinaR documentation built on Feb. 4, 2026, 5:13 p.m.