fCPAsubsets: Carry out constrained proportional assignment for protein...

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

Description

Carry out constrained proportional assignment for protein number i in profile with constraint being the number of compartments that are allowed to vary freely; other compartment proportions are fixed at zero

Usage

fCPAsubsets(
  profile,
  refLocationProfiles,
  numDataCols,
  startProps = NULL,
  showProgress = TRUE,
  maxit = 10000,
  nCPAcomparts = 2
)

Arguments

profile	one-row data frame of a protein name (in the row name) and relative abundance levels. Nspectra and Npep, if present, will be removed
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)
showProgress	default is T
maxit	maximum number of iterations (default is 10000)
nCPAcomparts	number of compartments to fit restricted CPA; remaining proportions are fixed at zero

Value

list with components: resultAll: Data frame of CPA estimates of each protein to compartments. resultMin: CPA estimates of minimum (best) fit resultAvg: mean of "quint" of the best fitting CPA estimates; default is the best 0.25 of estimates

Examples

data(protNSA_test)
data(markerListJadot)
nTestProts <- nrow(protNSA_test)
refLocationProfilesNSA <- locationProfileSetup(profile=protNSA_test,
    markerList=markerListJadot, numDataCols=9)
protCPAfromNSA_test <- fCPAsubsets(profile=protNSA_markTLN1[1,],
                              refLocationProfiles=refLocationProfilesNSA,
                              numDataCols=9, startProps=NULL, nCPAcomparts=2)

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