R/helpers.R

In saezlab/dorothea: Collection Of Human And Mouse TF Regulons

#' Construction of dorothea regulons for viper analysis
#'
#' This function converts DoRothEA's regulons that are stored in a table to the
#' format required by the \code{\link[viper]{viper}} function.
#'
#' @param df A regulon table from dorothea package.
#'
#' @return Regulons in the \code{viper} format.
#'
#' @export
#' @examples
#' # acessing (human) dorothea regulons
#' # for mouse regulons: data(dorothea_mm, package = "dorothea")
#' data(dorothea_hs, package = "dorothea")
#' # convert to the format required by viper
#' viper_regulons = df2regulon(dorothea_hs)
df2regulon <- function(df) {
  regulon_list = split(df, df$tf)

  viper_regulons = lapply(regulon_list, function(regulon) {
    tfmode = stats::setNames(regulon$mor, regulon$target)
    list(tfmode = tfmode, likelihood = rep(1, length(tfmode)))
    })

  return(viper_regulons)
}