Get footprinting data

Source: R/footprinting.R

Extract footprint data for a set of transcription factors or metafeatures. This function will pull accessibility data for a given feature (eg, a TF), and perform background normalization for each identity class. This is the data that's used to create TF footprinting plots with the PlotFootprint function.

GetFootprintData(
  object,
  features,
  assay = NULL,
  group.by = NULL,
  idents = NULL
)

Arguments

object

A Seurat object

features

A vector of features to extract data for

assay

Name of assay to use

group.by

A grouping variable

idents

Set of identities to group cells by

Value

Returns a data.frame with the following columns:

  • group: Cell group (determined by group.by parameter

  • position: Position relative to motif center

  • count: Normalized Tn5 insertion counts at each position

  • norm.value: Normalized Tn5 insertion counts at each position (same as count)

  • feature: Name of the footprinted motif

  • class: observed or expected