protPepProfile: Interlace protein profiles and component peptide profiles

In mooredf22/protlocassign: Estimation of protein distribution from quantitative subcellular fractionation experiments using a constrained proportional assignment model

Interlace protein profiles and component peptide profiles

Description

Interlace profiles of proteins and their component peptides into a single data frame.

Usage

protPepProfile(flagPeps, numRefCols, numDataCols, protProfileData)

Arguments

flagPeps	data frame containing profiles for all spectra, information mapping these to proteins and peptides, and outlier indicators for spectra and peptides
numRefCols	number of reference columns
numDataCols	number of data columns
protProfileData	data frame containing protein profiles

Value

Data frame containing protein and peptide profiles

Examples

set.seed(17356)
eps <- 0.029885209
data(spectraNSA_test)
flagSpectraBox <- outlierFind(protClass=spectraNSA_test,
                    outlierLevel='peptide', numRefCols=5, numDataCols=9,
                    outlierMeth='boxplot', range=3, eps=eps,
                    randomError=TRUE)
                    
 #examine numbers of spectra that are outliers
table(flagSpectraBox$outlier.num.spectra)
# find peptide-level profiles
pepProfiles <- profileSummarize(protsCombineCnew=flagSpectraBox,
      numRefCols=6, numDataCols=9, refColsKeep=c(1,2,4),eps=eps,
      GroupBy="peptideId", outlierExclude="spectra")
      
 # find oulier peptides
flagPepsBox <- outlierFind(protClass=pepProfiles,
      outlierLevel="protein",
      numRefCols=3, numDataCols=9, eps=eps)
      str(flagPepsBox, strict.width="cut", width=65)
      
 # combine the two types of outliers into one
flagSpectraPeps <- merge(x=flagSpectraBox,
      y=flagPepsBox[,c(4,17)], by="pepId")
      
 # create protein profile from component peptide and spectra
protNSA_1 <-
      profileSummarize(protsCombineCnew=flagSpectraPeps,
      numRefCols=7, numDataCols=9, eps=eps, GroupBy="protId",
      outlierExclude="spectraAndPeptide")
      
# combine protein and peptide profiles
protPepProfileNSA <- protPepProfile(flagPeps=flagPepsBox,
      numRefCols=4, numDataCols=9,
      protProfileData=protNSA_1)
str(protPepProfileNSA, strict.width="cut", width=65)
  # See Vignette 6 for a full explanation

mooredf22/protlocassign documentation built on Sept. 13, 2023, 3:57 p.m.