Import externally derived TF Activity data. EXPERIMENTAL.

We do not yet provide full support for this function. It is currently being tested. Use at our own risk.

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. When set to cyclicLoess, the csaw package is required (as it is listed under Suggests, it may not be installed).

forceRerun

TRUE or FALSE. Default FALSE. Force execution, even if the GRN object already contains the result. Overwrites the old results.

Value

An updated GRN object, with added data from this function.