Get TF gene correlation

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

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