Select TFs for GRN inference

Select TFs for GRN inference

SelectTFs(
  object,
  tf.assay = "chromvar",
  rna.assay = "RNA",
  atac.assay = "ATAC",
  trajectory.name = "Trajectory",
  groupEvery = 1,
  p.cutoff = 0.01,
  cor.cutoff = 0.3,
  return.heatmap = TRUE
)

Arguments

object

A Seurat object

tf.assay

The assay name for TF activity. Default: "chromvar"

rna.assay

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

atac.assay

The assay name for Peaks. Default: "ATAC"

trajectory.name

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

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.

p.cutoff

A cutoff of p-values. Default: 0.01

cor.cutoff

A cutoff of correlation. Default: 0.3

return.heatmap

Whether or not return the heatmap for visualization

Value

A list containing a dataframe of TF activity and expression correlation and a heatmap