fitCPA: Carry out constrained proportional assignment on all proteins

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

Description

Carry out constrained proportional assignment on all proteins

Usage

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

Arguments

profile	a data frame of protein names (row names) and relative abundance levels.
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)
showProgress	print out progress if TRUE, the default
ind.vary	if not NULL, indexes of parameters to allow 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

Examples

data(protNSA_test)
data(markerListJadot)
refLocationProfilesNSA <- locationProfileSetup(profile=protNSA_test, markerList=markerListJadot, numDataCols=9)
protCPAfromNSA_test <- fitCPA(profile=protNSA_markTLN1,
                              refLocationProfiles=refLocationProfilesNSA,
                              numDataCols=9)

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