GetTFGeneCorrelation: Get TF gene correlation

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

Get TF gene correlation

Description

This function will compute the correlation between TF binding activity and gene expression along the trajectory.

Usage

GetTFGeneCorrelation(
  object,
  tf.use = NULL,
  gene.use = NULL,
  tf.assay = "chromvar",
  gene.assay = "RNA",
  atac.assay = "ATAC",
  trajectory.name = "Trajectory",
  groupEvery = 1
)

Arguments

object	A Seurat object
tf.use	A string list to specify which TFs to use for correlation computation
gene.use	A string list to specify which genes to use for correlation computation
tf.assay	Assay that includes TF activity data. Default: "chromvar"
gene.assay	Assay that includes gene expression activity data. Default: "RNA"
atac.assay	Assay that includes peaks data. Default: "ATAC"
trajectory.name	Trajectory name
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.

Value

A matrix containing TF-gene correlation

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