cinaR (version 0.2.6)

prep_scATAC_seurat: 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
)

Value

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

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.

Examples

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