# Minimal Protein Set Explaining Peptide Spectrum Matches

## Documentation for package ‘prozor’ version 0.2.11

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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)
computeFDR | Compute FDR given a score
computeFDRwithID | Compute FDR given a score
createDecoyDB | Create db with decoys and contaminants
fdrSample | Data frame score and proteinID
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
makeID | make id for chain in format sp|P30443|1A01_HUMANs25
makeIDUnip | make id for chain compatible with uniprot
pepprot | Table containing peptide information
plotFDR | plot FDR
predictScoreFDR | Predict score given FDR
prepareMatrix | given table of peptide protein assigments generate matrix
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