fCPAsubsets: Restricted CPA

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

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.