R/protPepProfile.r

In mooredf22/protsummarize2:

protPepProfile.i <- function(i, flagPeps, numRefCols, numDataCols, protProfileData) {
                            #byProtein, eps) {
  # flagPeps:  one row per peptide
  #   col 1:  prot
  #   col 2:  peptide
  #   col numRefCols + 1:  N   (followed by M, L1, L2, ... for numDataCols columns)
  # protProfileData:  one row per protein; must match proteins in flagPeps
  #   col 1: prot
  #   col 2: N, M, L1, L2, ...
  # This program will insert a copy of the protein in "peptide" after prot
  #

  #  testing:
  #flagPeps <- tannousflagPeps
  #protProfileData <- tannousprotProfileData
  #i=1

  prot.i <- protProfileData$prot[i]

  Npep <- 1   # always only one peptide for the peptide-level data
  protDataNarrow.i <- protProfileData[protProfileData$prot == prot.i,]  # original form for protein data
  #blankInsert <- cbind(rep(0, Nspectra),
  #                             matrix(NA, nrow=nSpectra, numDataCols=(numRefCols-3)))
 #  Create a one-row matrix of protein data; put protein name first
  #  (for "prot" slot) and second (for "peptide" slot)
  # This will allow for using the second column for row names later
  # protData.i is formatted to combine with pepData.i
  protData.i <- data.frame(rep(protDataNarrow.i[1],2), matrix(NA, ncol=(numRefCols-2), nrow=1), protDataNarrow.i[2:(1+numDataCols+2)])



  # drop protId and pepId columns
  pepData.i <- flagPeps[flagPeps$prot == prot.i, -((numRefCols + numDataCols + 3):(numRefCols + numDataCols + 4)) ]
  Nspectra <- nrow(pepData.i)
  #pepMatInsert <- data.frame(matrix(NA, nrow=Nspectra, numDataCols=2))
  #names(pepMatInsert) <- c("Nspectra.Pep", "Npep.Pep")
  #pepData.i <- data.frame(pepDataT.i, pepMatInsert)

  names(protData.i) <- names(pepData.i)

  protPepData.i <- rbind(protData.i, pepData.i)
  protPepData.i
  }

protPepProfile <- function(flagPeps, numRefCols, numDataCols, protProfileData) {
                             #byProtein, eps) {
  # flagPeps:  one row per peptide
  #   col 1:  prot
  #   col 2:  peptide
  #   col numRefCols + 1:  N   (followed by M, L1, L2, ... for numDataCols columns)
  # protProfileData:  one row per protein; must match proteins in flagPeps
  #   col 1: prot
  #   col 2: N, M, L1, L2, ...
  # This program will insert a copy of the protein in "peptide" after prot
  n.prots <- nrow(protProfileData)
  protPepData <- NULL
  for (i in 1:n.prots) {
    protPepData.i <- protPepProfile.i(i, flagPeps, numRefCols, numDataCols, protProfileData)
                                                 # byProtein, eps)
    protPepData <- rbind(protPepData, protPepData.i)

  }
  protPepData
}