mixtureAreaError: Compute area-based error for mixture of two compartment...

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

Description

Compute area-based error for mixture of two compartment profiles

Usage

mixtureAreaError(
  mixProtiProtjCPA,
  NstartMaterialFractions = 6,
  Loc1,
  Loc2,
  increment.prop = 0.1
)

Arguments

mixProtiProtjCPA	data frame of CPA estimated proportions for each mixture
NstartMaterialFractions	Number of fractions that comprise the starting material
Loc1	row number of subcellular location 1 of mixture
Loc2	row number of subcellular location 2 of mixture
increment.prop	increment for computation; default is 0.1

Value

error, the area between predicted and observed curves

Examples

data(protNSA_test)
data(markerListJadot)
data(totProtAT5)
refLocationProfilesNSA <- locationProfileSetup(profile=protNSA_AT5tmtMS2,
                                               markerList=markerListJadot, numDataCols=9)
round(refLocationProfilesNSA, digits=3)
# Convert NSA reference profiles to Acup to prepare for forming mixtures
refLocationProfilesAcup <- AcupFromNSA(NSA=refLocationProfilesNSA, NstartMaterialFractions=6,
                                       totProt=totProtAT5)
round(refLocationProfilesAcup, digits=4)
# Compute mixtures
mixCytoLysoAcup <- proteinMix(AcupRef=refLocationProfilesAcup,
                              increment.prop=0.1,
                              Loc1=1, Loc2=4)
# Convert to relative specific amoounts
mixCytoLysoRSA <- RSAfromAcup(Acup=mixCytoLysoAcup,
                              NstartMaterialFractions=6, totProt=totProtAT5)
# Find RSA transformed reference profiles
refLocationProfilesRSA <- RSAfromNSA(refLocationProfilesNSA, NstartMaterialFractions=6,
                                     totProt=totProtAT5)
# Find constrained proportional values
mixCytoLysoCPAfromRSA <- fitCPA(profile=mixCytoLysoRSA,
                                refLocationProfiles=refLocationProfilesRSA,
                                numDataCols=9)
# calculate the mixture error
mixtureAreaError(mixProtiProtjCPA=mixCytoLysoCPAfromRSA,
            NstartMaterialFractions=6, Loc1=1, Loc2=4,
            increment.prop=0.1)

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