fCPAone: Carry out constrained proportional assignment for protein i;...

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

Description

Carry out constrained proportional assignment for protein i; service function for fitCPA

Usage

fCPAone(
  profile,
  refLocationProfiles,
  numDataCols,
  startProps = NULL,
  maxit = 10000,
  showProgress = TRUE,
  ind.vary = NULL,
  minVal = FALSE
)

Arguments

profile	data frame of one protein name (row name) and relative abundance levels for that protein
refLocationProfiles	A matrix giving the abundance level profiles of the subcellular locations
numDataCols	Number of channels of abundance levels
startProps	starting valuese for proportional assignements; set equal if this is null (default)
maxit	maximum number of iterations (default is 10000)
ind.vary	if not NULL, indexes of proportions allowed to vary
minVal	default is false. If true, return minimum value of goodness of fit

Value

assignProbsOut Data frame of proportionate assignments of each protein to compartments. also nspectra and npeptides if in profile input If ind.vary specified, only the referenced proportion cpa estimates are returned

Examples

data(protNSA_test)
data(markerListJadot)
nTestProts <- nrow(protNSA_test)
refLocationProfilesNSA <- locationProfileSetup(profile=protNSA_test,
    markerList=markerListJadot, numDataCols=9)
protCPAfromNSA_test <- fCPAone(profile=protNSA_markTLN1[1,],
                              refLocationProfiles=refLocationProfilesNSA,
                              numDataCols=9, startProps=NULL,
                              maxit=10000,
                              ind.vary=NULL, minVal=FALSE)

mooredf22/protlocassign0p1p1 documentation built on Feb. 7, 2022, 1:55 a.m.