assignCPAloc: assign proteins to a subcellular location using CPA estimates

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

Description

assign proteins to a subcellular location using CPA estimates

Usage

assignCPAloc(assignLocProps, cutoff = 0.8, Locations)

Arguments

assignLocProps	matrix of proportion estimates for each protein
cutoff	cutoff for assigning a protein to a location
Locations	list of subcellular locations

Value

protLoc assigned location of protein

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)
Locations <- unique(markerListJadot$referenceCompartment)
table(apply(protCPAfromNSA_test[,1:8],1,assignCPAloc, cutoff=0.8, Locations=Locations))

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