assignCPAloc: Assign to single subcellular location

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

Assign to single subcellular location

Description

Assign proteins to the most prevalent subcellular location (meeting a specific cutoff) using CPA estimates, with minimum value being 0.5.

Usage

assignCPAloc(assignLocProps, cutoff = 0.5, Locations)

Arguments

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

Value

Single compartment where most of protein resides, undefined if largest CPA value is <0.5

Examples

data(protNSA_test)
data(markerListJadot)
data(refLocProfNSA)
protCPAfromNSA_test <- fitCPA(profile=protNSA_test,
         refLocationProfiles=refLocProfNSA,
         numDataCols=9)
Locations <- unique(markerListJadot$referenceCompartment)

# write table listing predominant CPA assignment of each protein in data set
table(apply(protCPAfromNSA_test[,1:8],1,assignCPAloc,
         cutoff=0.5, Locations=Locations))

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