R/RSAtransform.r

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

#' Set up RSA (relative specific amount) profiles for constrained proportional assignment
#'
#' @param NSA A matrix giving the specific amount or normalized specific amount
#'           profiles, either marker profiles from 'cpaSetup' (which requires
#'           normalized specific amounts as input), or a list of many protein profiles
#' @param NstartMaterialFractions Number of differential fractions, typically 6, for N, M, L1, L2, P, and S
#' @param totProt Total protein counts in each of the differential and nycodenz fractions; this is necessary to compute RSA's
#' @return Acup profiles
#'   amount of given protein in fraction / amount of that given protein in starting material
#' @examples
#' data(protNSA_test)
#' data(totProtAT5)
#' protAcup <- AcupFromNSA(protNSA_test[,seq_len(9)], NstartMaterialFractions = 9, totProt=totProtAT5)
#' protRSA <- RSAfromAcup(protAcup, NstartMaterialFractions = 9, totProt=totProtAT5)
#' protNSA <- NSAfromRSA(protRSA)
#' all.equal(protNSA, protNSA_test[,seq_len(9)] )
#' protRSA2 <- RSAfromNSA(protNSA_test[,seq_len(9)], NstartMaterialFractions = 9, totProt=totProtAT5)
#' all.equal(protRSA, protRSA2)
#' @export

AcupFromNSA <- function(NSA, NstartMaterialFractions,
                               totProt=NULL) {
  if (ncol(NSA) != length(totProt)) {
    cat("Error from relAmtTransform: no. of rows of NSA must match length of totProt\n")
  }

  startMaterialFractions <- NSA[,seq_len(NstartMaterialFractions)]  # just differential fractions
  nTotFractions <- length(totProt)    # number of all fractions
  NSAfractions <- NSA[,seq_len(nTotFractions)]  # columns with NSA amounts; excludes additional columns

  AA <- data.frame(sweep(NSAfractions, 2,totProt, "*"))
  names(AA) <- colnames(NSAfractions)

  # Compute amount of given protein in fraction / amount of given protein in starting material
  # use these values to create mixtures
  # these are in red in Excel spreadsheet
  Acup <- data.frame(t(apply(AA, 1, function(x) x/sum(x[seq_len(NstartMaterialFractions)]))))
  names(Acup) <- colnames(AA)

 Acup
}



#' Compute relative specific amount from relative amounts in protein fractions
#' @param Acup amount of given protein in fraction / amount of that given protein in starting material
#' @param NstartMaterialFractions Number of differential fractions, typically 6, for N, M, L1, L2, P, and S
#' @param totProt Total protein counts in each of the differential and nycodenz fractions; this is necessary to compute RSA's
#' @return rsa: relative specific amount
#' @examples
#' data(protNSA_test)
#' data(totProtAT5)
#' protAcup <- AcupFromNSA(protNSA_test[,seq_len(9)], NstartMaterialFractions = 9, totProt=totProtAT5)
#' protRSA <- RSAfromAcup(protAcup, NstartMaterialFractions = 9, totProt=totProtAT5)
#' protNSA <- NSAfromRSA(protRSA)
#' all.equal(protNSA, protNSA_test[,seq_len(9)] )
#' @export
RSAfromAcup <- function(Acup, NstartMaterialFractions, totProt=NULL) {

  if (ncol(Acup) != length(totProt)) {
    cat("Error from RSAfromAcup: no. of rows of Acup must match length of totProt\n")
  }
# # # # # # # #
# rename variables
# # # # # # # #

# Difp -> t.h
# propFrac -> t.cup

  t.h <- sum(totProt[seq_len(NstartMaterialFractions)])   # total protein in the differential fractions
  t.cup <- totProt/t.h  # proportion of protein in the differential fractions (9 component vector)

  rsa <- sweep(Acup, 2, 1/t.cup, "*")
  names(rsa) <- colnames(Acup)
  rsa <- as.data.frame(rsa)
  # The following, which standardizes rsa rows to sum to one, returns the original markerProfiles !!
  NSAfromRSA <- t(apply(rsa,1, function(x) x/sum(x)))  # this is deprecated; no need

  rsa
}





#' Directly compute relative specific activity from protProfileSummary (or from markerProfiles)
#' @param NSA A matrix giving the specific amount or normalized specific amount
#'           profiles, either marker profiles from 'cpaSetup' (which requires
#'           normalized specific amounts as input), or a list of many protein profiles
#' @param NstartMaterialFractions Number of differential fractions, typically 6, for N, M, L1, L2, P, and S
#' @param totProt Total protein counts in each of the fractions; this is necessary to compute RSA's
#'
#' @return rsa: relative specific activity
#' @examples
#' data(protNSA_test)
#' data(totProtAT5)
#' protAcup <- AcupFromNSA(protNSA_test[,seq_len(9)], NstartMaterialFractions = 9, totProt=totProtAT5)
#' protRSA <- RSAfromAcup(protAcup, NstartMaterialFractions = 9, totProt=totProtAT5)
#' protNSA <- NSAfromRSA(protRSA)
#' all.equal(protNSA, protNSA_test[,seq_len(9)] )
#' @importFrom stats complete.cases
#' @export

RSAfromNSA <- function(NSA, NstartMaterialFractions,
                      totProt=NULL) {

  missing.rows <- NSA[!complete.cases(NSA),]

  if (ncol(NSA) != length(totProt)) {
     cat("Error from rsaDirect: no. of rows of NSA must match length of totProt\n")
  }

  startMaterialFractions <- NSA[,seq_len(NstartMaterialFractions)]   # first columns of NSA
  nTotFractions <- length(totProt)    # number of all fractions
  NSAfractions <- NSA[,seq_len(nTotFractions)]  # columns with NSA amounts; excludes additional columns


  protAbund <- AcupFromNSA(NSAfractions,NstartMaterialFractions=NstartMaterialFractions,
                               totProt=totProt)
  Acup <- protAbund
  rsa <- RSAfromAcup(Acup, NstartMaterialFractions=NstartMaterialFractions, totProt=totProt)

  rsa
}

#' convert RSA to NSA
#' @param RSA relative specific activity
#' @return NSA A matrix giving the specific amount or normalized specific amount
#'           profiles, either marker profiles from 'cpaSetup' (which requires
#'           normalized specific amounts as input), or a list of many protein profiles
#' @examples
#' data(protNSA_test)
#' data(totProtAT5)
#' protAcup <- AcupFromNSA(protNSA_test[,seq_len(9)], NstartMaterialFractions = 9, totProt=totProtAT5)
#' protRSA <- RSAfromAcup(protAcup, NstartMaterialFractions = 9, totProt=totProtAT5)
#' protNSA <- NSAfromRSA(protRSA)
#' all.equal(protNSA, protNSA_test[,seq_len(9)] )
#' @export
NSAfromRSA <- function(RSA) {
  NSA <- data.frame(t(apply(RSA, 1, function(x) x/sum(x))))
  NSA
}

#' Compute relative specific amount from relative amounts in protein fractions
#' @param Acup amount of given protein in fraction / amount of that given protein in starting material
#' @param NstartMaterialFractions Number of differential fractions, typically 6, for N, M, L1, L2, P, and S
#' @param totProt Total protein counts in each of the differential and nycodenz fractions; this is necessary to compute RSA's
#' @return NSA: normalized specific amount
#' @examples
#' data(protNSA_test)
#' data(totProtAT5)
#' protAcup <- AcupFromNSA(protNSA_test[,seq_len(9)], NstartMaterialFractions = 9, totProt=totProtAT5)
#' protNSA <- NSAfromAcup(protAcup, NstartMaterialFractions = 9, totProt=totProtAT5)
#' all.equal(protNSA, protNSA_test[,seq_len(9)])
#' @export
NSAfromAcup <- function(Acup, NstartMaterialFractions,
                        totProt=NULL) {
  RSA <- RSAfromAcup(Acup, NstartMaterialFractions=NstartMaterialFractions,
                      totProt=totProt)
  NSA <- NSAfromRSA(RSA)
  NSA
}

#' Compute relative specific amount from relative amounts in protein fractions
#' @param RSA amount of given protein in fraction / amount of that given protein in starting material
#' @param NstartMaterialFractions Number of differential fractions, typically 6, for N, M, L1, L2, P, and S
#' @param totProt Total protein counts in each of the differential and nycodenz fractions; this is necessary to compute RSA's
#' @return Acup: relative amount
#' @examples
#' data(protNSA_test)
#' data(totProtAT5)
#' protAcup <- AcupFromNSA(protNSA_test[,seq_len(9)], NstartMaterialFractions = 9, totProt=totProtAT5)
#' protRSA <- RSAfromAcup(protAcup, NstartMaterialFractions = 9, totProt=totProtAT5)
#' protNSA <- NSAfromRSA(protRSA)
#' all.equal(protNSA, protNSA_test[,seq_len(9)] )
#' @export
AcupFromRSA <- function(RSA, NstartMaterialFractions,
                        totProt=NULL) {
       NSA <- NSAfromRSA(RSA)
       Acup <- AcupFromNSA(NSA, NstartMaterialFractions=NstartMaterialFractions,
                           totProt=totProt)
       Acup
}