R/convert_units.R

In jdreyf/sybilxf: R package for integration of Seahorse extracellular flux (XF) data with metabolic modeling.

#' @title Convert pmol/min/ug_protein or pmol/min/ug_DNA to mmol/gDw/hr, the units of the metabolic model
#' @author Alfred Ramirez
#' @description This function takes the matrix returned by \code{\link{sample_seahorse}} and multiplies it by a factor
#' @param x A matrix
#' @param mwr Macromolecular weight ratio
#' @details The macromolecular weight ratio is the relationship between the initial normalization 
#' (typically DNA or protein) and total dry weight. It can vary substantially depending on cell type. By default,
#' mwr = 0.706, which is the estimated protein/dry_weight ratio from the biomass reaction in Recon 2. For adipocytes,
#' mwr = 0.026
#' @references Ramirez AK, Lynes MD, Shamsi F, Xue R, Tseng YH, Kahn CR, Kasif S, Dreyfuss JM. Integrating Extracellular 
#' Flux Measurements and Genome-Scale Modeling Reveals Differences between Brown and White Adipocytes. Cell Rep 2017 
#' Dec; 21(11): 3040-3048.
#' @export

convert_units <- function(x, mwr = 0.706){
  #Units are initially pmol/min/ug_macromolecule
  
  #Multiply by 1e-9 to convert from pmol to mmol
  c1 <- 1e-9
  
  #Multiply by 60 to convert from min to hrs
  c2 <- 60
  
  #Multiply by the mcr to convert from ug_macromolecule to ugDw
  c3 <- mwr
  
  #Multiply by 1e6 to from ugDw to gDw
  c4 <- 1e6
  
  y <- x*c1*c2*c3*c4
  y
}