R/getHRDScore.R

In maxwell-lab/HRDex:

#' get the standard HRD score
#' 
#' @param seq.dat the preprocessed sequencing data
#' @param CN.dat the copy number data
#' @param scaleTotal optional: rescale the total to range of 0-100
#' @param type optional: type of score to return, one of "sum" or "average"
#' 
#' @details calculates the 'standard' HRD score: the sum of LST, LOH, and NTAI, all normalized. Can optionally
#' return the HRD score rescaled to a range of 0 - 100.
#' 
#' @return a numeric value representing the HRD score
#' 
#' @examples
#'seq.dat <- preprocessHRD( sub01.segments )
#'
#'CN.dat <- getCNT( seq.dat )
#'HRD <- getHRD.Score( seq.dat, CN.dat, scaleTotal = FALSE)
#' @export

# ------------------------------- getHRD.Score ---------------------------------- #
# function to get the total HRD score. this is a simple summation of LST, NTAI, and LOH.
# this is the 'standard' HRD score most commonly seen in publication. this function is
# implemented to automatically calculate this score- eg, select the proper mean/raw criteria
getHRD.Score <- function( seq.dat, CN.dat, scaleTotal = FALSE, type = "sum" )
  # input: seq.dat, (data.frame) with chromosome, start.pos, end.pos, CNt, alleleA, alleleB;
  #         ploidy.dat (data.frame), the ploidy data
  #         CN.dat (data.frame), copy number data
  #         min.seg.size (integer), minimum segment size used in TAI calculations
  #         scaleTotal (boolean), rescale HRD total to 0-100
  # output: HRD.Score (integer), the total HRD Score
{
  HRD.Score <- getLOH(  seq.dat ) + getLST(  seq.dat ) + getNTAI.norm( seq.dat, CN.dat )
  
  if( !(type %in% c("average", "sum")))
  {
    stop("'type' must be one of 'average' or 'sum")
  }
  
  if( type == "average" )
  {
    HRD.Score <- HRD.Score / 3
  }
  
  # rescale HRD total to 0-100
  if( scaleTotal == TRUE )
  {
    library(scales)
    HRD.Score <- round( rescale(HRD.Score, to = c(0,100), from = range(HRD.Score)), 2 )
  }
  
  return(HRD.Score)
  
  
}
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