fCPAsubsets: Restricted CPA

View source: R/fCPAsubsets.R

fCPAsubsetsR Documentation

Restricted CPA

Description

Carry out constrained proportional assignment for protein i, restricting the number of compartments that are allowed to vary freely and fixing the CPA values of the others at 0

Usage

fCPAsubsets(
  profile,
  refLocationProfiles,
  numDataCols,
  startProps = NULL,
  showProgress = TRUE,
  maxit = 10000,
  nCPAcomparts = 2
)

Arguments

profile

a vector containing a specified protein (row name) profile ‘Nspectra’ and ‘Npep’, if present, will be removed

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)

showProgress

default is TRUE

maxit

maximum number of iterations (default is 10000)

nCPAcomparts

number of compartments to fit restricted CPA; remaining proportions are fixed at zero

Value

Data frame with CPA estimates for every combination ordered by value, with best fit listed first

Examples

data(protRSA_test)
data(refLocProfRSA)
protCPAfromRSA_out2 <- fCPAsubsets(profile=protRSA_test[1,],
                         refLocationProfiles=refLocProfRSA,
                         numDataCols=9, startProps=NULL, nCPAcomparts=2)
round(head(protCPAfromRSA_out2), digits=4)

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