fCPAsubsets | R Documentation |
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
fCPAsubsets(
profile,
refLocationProfiles,
numDataCols,
startProps = NULL,
showProgress = TRUE,
maxit = 10000,
nCPAcomparts = 2
)
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 |
Data frame with CPA estimates for every combination ordered by value, with best fit listed first
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)
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