R: Minimal Protein Set Explaining Peptide Spectrum Matches

# Minimal Protein Set Explaining Peptide Spectrum Matches

## Documentation for package ‘prozor’ version 0.3.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

annotateAHO | annotate peptides using AhoCorasickTrie
annotatePeptides | Annotate peptides with protein ids
Cdsw | Compute dynamic swath windows
Cdsw-class | Compute dynamic swath windows
computeFDR | Compute FDR given a score
computeFDRwithID | Compute FDR given a score
createDecoyDB | Create db with decoys and contaminants
create_fgcz_fasta_db | create fasta db from one or more fasta files
fdrSample | Data frame score and proteinID
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
loadContaminantsFasta2019 | load list of contaminant sequences FGCZ 2019
loadContaminantsFasta2021 | load list of contaminant sequences FGCZ 2021
makeID | make id for chain in format sp|P30443|1A01_HUMANs25
makeIDUnip | make id for chain compatible with uniprot
masses | MS masses A dataset containing approx 150000 MS1 precursor masses
objectiveMS1Function | compute the deviation from optimum: equal number of MS1 per bin
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
readjustWindows | Readjust windows so that boundaries in regions of few peaks.
readPeptideFasta | wrapper setting the correct parameters seqinr::read.fasta for reading peptide sequences
removeSignalPeptide | remove signal peptides from main chain
reverseSeq | create rev sequences to fasta list
writeFasta | write fasta lists into file