man-roxygen/TF_peak.connectionTypes.R

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

#' @param TF_peak.connectionTypes Character vector. Default \code{all}. TF-peak connection types to consider. The special keyword \code{all} denotes all connection types (e.g., \code{expression} and \code{TFActivity}) that are found in the \code{\linkS4class{GRN}} object. By default, only \code{expression} is present in the object, so \code{all} and \code{expression} are usually equivalent unless calculation of TF-peak links based on TF activity has also been enabled.