get_top_peak_gene_pairs — get_top_peak_gene

For peaks and genes with high abundance, construct candidate pairs where peaks are in close proximity to the gene.

Usage

get_top_peak_gene_pairs(
  obj,
  gene_top = 2000,
  peak_top = 20000,
  distance = 5e+05,
  gene_assay = "RNA",
  peak_assay = "peak"
)

obj: A Seurat object of single-cell multimodal data.
gene_top: Number of top highly expressed genes. Default to 2000.
peak_top: Number of top highly accessible peaks. Default to 20000.
distance: Distance threshold for peaks to be considered as possibly associated with genes. Default to 5e+05.
gene_assay: Name of the gene assay in Seurat object. Default to 'RNA'.
peak_assay: Name of the peak assay in Seurat object. Default to 'peak'.

A data frame of candidate peak-gene pairs.