GetFootprintData: Get footprinting data

In Signac: Analysis of Single-Cell Chromatin Data

Get footprinting data

Description

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.

Usage

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

Signac documentation built on Sept. 11, 2024, 9:30 p.m.