SelectGenes: Select genes

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

Select genes

Description

Select genes

Usage

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

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