Select genes

Select genes

SelectGenes(
  object,
  atac.assay = "ATAC",
  rna.assay = "RNA",
  var.cutoff.gene = 0.9,
  trajectory.name = "Trajectory",
  distance.cutoff = 2000,
  groupEvery = 1,
  cor.cutoff = 0,
  fdr.cutoff = 1e-04,
  return.heatmap = TRUE,
  labelTop1 = 10,
  labelTop2 = 10,
  genome = "hg38"
)

Arguments

object

A Seurat object

atac.assay

The assay name for chromatin accessibility. Default: "ATAC"

rna.assay

The assay name for gene expression. Default: "RNA"

var.cutoff.gene

The cutoff of variation to select genes. Default: 0.9

trajectory.name

The trajectory name used for computing correlation between TF binding activity and TF expression

distance.cutoff

The minimum distance between cis-regulatory elements and genes

groupEvery

The number of sequential percentiles to group together when generating a trajectory. This is similar to smoothing via a non-overlapping sliding window across pseudo-time.

cor.cutoff

The cutoff of peak-to-gene correlation. Default: 0

fdr.cutoff

The cutoff of peak-to-gene p-value Default: 1e-04

return.heatmap

Whether or not return the heatmap for visualization

labelTop1

Number of labels for row names

labelTop2

Number of labels for row names

Value

A list containing a dataframe of peak-to-gene links and a heatmap