Cdsw-class              Compute dynamic swath windows
annotateAHO             annotate peptides using AhoCorasickTrie
annotatePeptides        Annotate peptides with protein ids
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
readPeptideFasta        wrapper setting the correct parameters
                        seqinr::read.fasta for reading peptide
                        sequences
readjustWindows         Readjust windows so that boundaries in regions
                        of few peaks.
removeSignalPeptide     remove signal peptides from main chain
reverseSeq              create rev sequences to fasta list
writeFasta              write fasta lists into file
