canprot (version 1.0.0)

recomp: Recompute Protein Compositions

Description

Recompute compositional metrics given the existing output of one of the pdat_ functions.

Usage

recomp(pdat, basis = "rQEC")

Arguments

pdat

list, result from a pdat_ function

basis

character, keyword for basis species to use

Details

This function recomputes a pdat object for a different basis. This avoids the need to regenerate the list of UniProt IDs and search for amino acid compositions. It was previously used to speed up the processing of the vignettes.

Examples

# NOT RUN {
# process the first dataset for prostate cancer using the QEC basis species
datasets <- pdat_prostate()
pdat <- pdat_prostate(datasets[1], basis = "QEC")
# recompute the compositions using the rQEC values
pdat2 <- recomp(pdat, "rQEC")
# compare the results
nH2O_QEC <- pdat$pcomp$residue.basis[, "H2O"]
nH2O_rQEC <- pdat2$pcomp$residue.basis[, "H2O"]
plot(nH2O_QEC, nH2O_rQEC)
# the slower way (not that it makes much difference for this example)
pdat2.slow <- pdat_prostate(datasets[1], basis = "rQEC")
stopifnot(identical(pdat2, pdat2.slow))
# }