R/proteinMix.r

In mooredf22/protlocassign0p1p1: Compute constrained proportional assignments for fractionated protein abundance

#' compute a mixture of proteins in two compartments
#' @param AcupRef amount of given protein in fraction / amount of given protein in starting material
#' @param Loc1  row number of one compartment
#' @param Loc2  row number of other compartment
#' @param increment.prop fraction increment from 0 to 1
#' @return mixAmount relative amounts of proteins in the fractions
#' @examples
#' data(protNSA_test)
#' data(markerListJadot)
#' data(totProtAT5)
#' refLocationProfilesNSA <- locationProfileSetup(profile=protNSA_test,
#'                                                markerList=markerListJadot, numDataCols=9)
#' round(refLocationProfilesNSA, digits=3)
#' # Convert NSA reference profiles to Acup to prepare for forming mixtures
#' refLocationProfilesAcup <- AcupFromNSA(NSA=refLocationProfilesNSA, NstartMaterialFractions=6,
#'                                        totProt=totProtAT5)
#' round(refLocationProfilesAcup, digits=4)
#' # Compute mixtures
#' mixCytoLysoAcup <- proteinMix(AcupRef=refLocationProfilesAcup,
#'                               increment.prop=0.1,
#'                               Loc1=1, Loc2=4)
#' @export
proteinMix <- function(AcupRef, Loc1, Loc2, increment.prop=0.10) {
  # replace mix.df with input.prop throughout
  # replace relAmount with Acup througout
  nrowRef <- nrow(AcupRef)
  if (Loc1 > Loc2) {
    Loc1orig <- Loc1
    Loc2orig <- Loc2
    Loc1 <- Loc2orig
    Loc2 <- Loc1orig
  }
  if (Loc2 > nrowRef) cat("Error, not enough rows\n")
  LocNames <- row.names(AcupRef)
  prop.vec <- seq(0,1,increment.prop)
  qrop.vec <- 1 - prop.vec
  nrow.out <- length(prop.vec)
  Acup <- NULL
  mixProtNames <- NULL

  for (i in seq_len(nrow.out)) {
    Acup.i <- prop.vec[i]*AcupRef[Loc1,] + qrop.vec[i]*AcupRef[Loc2,]
    Acup <- rbind(Acup, Acup.i)
    mixProtNames.i <- paste(prop.vec[i],"_", LocNames[Loc1], ":", qrop.vec[i], "_",LocNames[Loc2], sep='')
    mixProtNames <- c(mixProtNames, mixProtNames.i)

  }

 # mixMat <- matrix(0, nrow=nrow.out, ncol=nrow(Acup))  # matrix of mixtures
  # each row is a "protein" with mixed residence
  # each column is a subcellular location, with the proportioal assignment
 # mixMat[,Loc1] <- prop.vec
 # mixMat[,Loc2] <- qrop.vec
 # input.prop <- data.frame(mixMat)
 # names(input.prop) <- row.names(Acup)
 # rownames(input.prop) <- mixProtNames

  row.names(Acup) <- mixProtNames
  #result <- list(Acup=Acup, input.prop=input.prop)
  #result
  Acup
}