SelectTFs: Select TFs for GRN inference

In CostaLab/scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference

Select TFs for GRN inference

Description

Select TFs for GRN inference

Usage

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

CostaLab/scMEGA documentation built on Sept. 25, 2024, 6:11 a.m.