greedy_parsimony: given matrix (columns protein rows peptides), compute minimal...
In protViz/prozor: Minimal Protein Set Explaining Peptide Spectrum Matches

greedy_parsimony

R Documentation

given matrix (columns protein rows peptides), compute minimal protein set using greedy algorithm

Description

given matrix (columns protein rows peptides), compute minimal protein set using greedy algorithm

Usage

greedy_parsimony(pepprot)

Arguments

pepprot

matrix as returned by prepareMatrix

Value

list of peptide protein assignment

Examples

#library(prozor)

data(protpepmetashort)
colnames(protpepmetashort)
dim(unique(protpepmetashort[,4]))
xx = prepareMatrix(protpepmetashort, peptideID = "peptideModSeq")
dim(xx)
stopifnot(dim(xx)[1] == dim(unique(protpepmetashort[,4]))[1])

es = greedy(xx)
debug(prozor:::.greedy2)
stopifnot(length(unique(names(es))) == dim(unique(protpepmetashort[,4]))[1])

protViz/prozor documentation built on Oct. 17, 2023, 6:39 p.m.