mixtureAreaError: Area-based error of mixtures

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

Area-based error of mixtures

Description

Compute area-based error for accuracy of CPA estimates for sets of simulated proteins distributed between two compartments.

Usage

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

Arguments

mixProtiProtjCPA	data frame of CPA estimates for each set of two compartment mixtures
NstartMaterialFractions	Number of fractions that reconstitute the starting material, e.g., a complete set of differential centrifugation fractions. For experiment AT5, it is 6 ( N, M, L1, L2, P, and S).
Loc1	row number of subcellular location 1 of mixture
Loc2	row number of subcellular location 2 of mixture
increment.prop	increments in proportion residing in Loc1 (from 0 to 1); Default is 0.1

Value

The area between predicted and observed curves

Examples

data(refLocProfAcup)
data(refLocProfNSA)
data(totProtAT5)

# Compute relative amount of each theoretical protein that resides 
#    in each fraction in a mixture set
mixCytoLysoAcup <- proteinMix(AcupRef=refLocProfAcup,
                              increment.prop=0.1,
                              Loc1=1, Loc2=4)
                              
# Convert theoretical protein profiles to NSA
mixCytoLysoNSA <- NSAfromAcup(Acup=mixCytoLysoAcup,
                           NstartMaterialFractions=6, totProt=totProtAT5)
                              
# Find constrained proportional values
mixCytoLysoCPAfromNSA <- fitCPA(profile=mixCytoLysoNSA,
                                refLocationProfiles=refLocProfNSA,
                                numDataCols=9)
# calculate the mixture error
mixtureAreaError(mixProtiProtjCPA=mixCytoLysoCPAfromNSA,
            NstartMaterialFractions=6, Loc1=1, Loc2=4,
            increment.prop=0.1)

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