prep_scATAC_seurat — prep_scATAC

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 object@meta.data indicating biological replicate.
group.col: column name in object@meta.data 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

if (FALSE) { # \dontrun{
prep <- prep_scATAC_seurat(seurat_obj,
                           sample.col = "sample",
                           group.col = "group",
                           assay = "peaks")
} # }