Minimal Protein Set Explaining Peptide Spectrum Matches

Documentation for package ‘prozor’ version 0.2.3

prozor-package	Minimal Protein set Explaining Peptides
annotateAHO	annotate peptides using AhoCorasickTrie
annotatePeptides	Annotate peptides with protein ids
annotateVec	annotate vector of petpide sequences against fasta file (Deprecated)
createDecoyDB	create db with decoys and contaminants
filterSequences	Filter for specific residues
greedy	given matrix (columns protein rows peptides), compute minimal protein set using greedy algorithm
greedyRes2Matrix	converts result of greedy function to a matrix with 3 columns - peptide - charge and protein
loadContaminantsFasta	load list of contaminant sequences
loadContaminantsNoHumanFasta	load list of contaminant without human sequences
loadHomoSapiensSignalPeptides	load human signal peptides
loadMusMusculusSignalPeptides	load mus musculus signal peptides
makeID	make id for chain in format sp\|P30443\|1A01_HUMANs25
makeIDUnip	make id for chain compatible with uniprot
pepprot	Table containing peptide information
prepareMatrix	given table of peptide protein assigments generate matrix
protpepmeta	Generated from pepprot using method annotatePeptides
protpepmetashort	Small version of pepprot dataset to speed up computation
prozor	Minimal Protein set Explaining Peptides
readPeptideFasta	wrapper setting the correct parameters
removeSignalPeptide	remove signal peptides from main chain
reverseSeq	create rev sequences to fasta list
writeFasta	write fasta lists into file