R/getallele.r

In paularstrpo/GeTalleleR: A method for integrative analysis and visualization of DNA and RNA allele frequencies

#' Run GeTallele Vpr segmentation pipeline
#'
#' @param pos Integer or Numeric vector with genomic positions (within the same chromosome) to segment.
#' @param vaf Numeric vector of VAF (variant allele frequencies) for a given layer. Must correspond to sites in pos.
#' @param seg_start Where to start segmentation? Default is 1.
#' @param seg_end Where to end segmentation? Default is the maximum value of `pos`.
#' @param sensitivity Parameter for segmentation via findchangepoints
#' @param models_cdf cumulative density for a VAF model generated by gen_ideal_hist
#' @return a DF or list with the information: chromosome | layer_name | seg_start |  seg_end | genomic_length | num_sites | merged_window_idx | merged_window_start | merged_window_end | V(pr)

GeTallele <- function(){

    # TODO: create wrapper to run entire pipeline on all chromosomes

}