Add TF activity data to GRN object using a simplified procedure for estimating it. EXPERIMENTAL.

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

addData_TFActivity(
  GRN,
  normalization = "cyclicLoess",
  name = "TF_activity",
  forceRerun = FALSE
)

Arguments

GRN

Object of class GRN

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).

name

Name in object under which it should be stored. This corresponds to the connectionType afterwards that some functions iterate over.

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 (GRN@data$TFs[[name]] in particular, with name referring to the value of tje name parameter)