importTFData: Import externally derived TF Activity data. EXPERIMENTAL.

In chrarnold/GRaNIE: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

Import externally derived TF Activity data. EXPERIMENTAL.

Description

Import externally derived TF Activity data. EXPERIMENTAL.

Usage

importTFData(
  GRN,
  data,
  name,
  idColumn = "ENSEMBL",
  nameColumn = "TF.name",
  normalization = "none",
  forceRerun = FALSE
)

Arguments

GRN	Object of class GRN
data	Data frame. No default. Data with TF data.
name	Name in object under which it should be stored. This corresponds to the connectionType afterwards that some functions iterate over.
idColumn	Character. Default ENSEMBL. Name of the ID column. Must not be unique as some TFs may correspond to the same ID.
nameColumn	Character. Default TF.name. Must be unique for each TF / row.
normalization	Character. Default cyclicLoess. One of cyclicLoess, sizeFactors, quantile, or none. Normalization procedure.
forceRerun	TRUE or FALSE. Default FALSE. Force execution, even if the GRN object already contains the result. Overwrites the old results.

Value

The same GRN object, with added data from this function.

chrarnold/GRaNIE documentation built on April 28, 2022, 2:18 a.m.