fCPAone: CPA for protein i

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

CPA for protein i

Description

Carry out constrained proportional assignment for protein i; service function for fitCPA

Usage

fCPAone(
  profile,
  refLocationProfiles,
  numDataCols,
  startProps = NULL,
  maxit = 10000,
  ind.vary = NULL,
  minVal = FALSE
)

Arguments

profile	vector of a specified protein (row name) profile
refLocationProfiles	data frame of profiles for the reference compartments
numDataCols	number of fractions in each profile
startProps	starting values for proportional assignments; set equal if this is null (default)
maxit	maximum number of iterations (default is 10000)
ind.vary	if not NULL, indexes of proportions allowed to vary with others constrained to zero
minVal	default is FALSE. If TRUE, return minimum value of goodness of fit

Value

Vector of proportional assignments of each protein to compartments. Also returns variables 'nspectra' and 'npeptides' if they are included in the profile input. If 'ind.vary' is specified, only the referenced CPA estimates are returned.

Examples

data(protRSA_test)
data(refLocProfRSA)

protCPAfromRSA_i_out1 <- fCPAone(profile=protRSA_test[1,],
                          refLocationProfiles=refLocProfRSA,
                          numDataCols=9, startProps=NULL,
                          maxit=10000,
                         ind.vary=NULL, minVal=FALSE)
round(protCPAfromRSA_i_out1, digits=4)

protCPAfromRSA_i_out1b <- fCPAone(profile=protRSA_test[1,],
          refLocationProfiles=refLocProfRSA,
          numDataCols=9, startProps=NULL,
          maxit=10000,
          ind.vary=c(2,4), minVal=FALSE)
round(protCPAfromRSA_i_out1b, digits=4)

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