Man pages for prozor
Minimal Protein Set Explaining Peptide Spectrum Matches

annotateAHOannotate peptides using AhoCorasickTrie
annotatePeptidesAnnotate peptides with protein ids
Cdsw-classCompute dynamic swath windows
computeFDRCompute FDR given a score
computeFDRwithIDCompute FDR given a score
createDecoyDBCreate db with decoys and contaminants
create_fgcz_fasta_dbcreate fasta db from one or more fasta files
fdrSampleData frame score and proteinID
greedygiven matrix (columns protein rows peptides), compute minimal...
greedyRes2Matrixconverts result of greedy function to a matrix with 3 columns...
hardconstraintests hard constraints
loadContaminantsFasta2019load list of contaminant sequences FGCZ 2019
loadContaminantsFasta2021load list of contaminant sequences FGCZ 2021
makeIDmake id for chain in format sp|P30443|1A01_HUMANs25
makeIDUnipmake id for chain compatible with uniprot
massesMS masses A dataset containing approx 150000 MS1 precursor...
objectiveMS1Functioncompute the deviation from optimum: equal number of MS1 per...
pepprotTable containing peptide information
plotFDRplot FDR
predictScoreFDRPredict score given FDR
prepareMatrixgiven table of peptide protein assigments generate matrix
protpepmetashortSmall version of pepprot dataset to speed up computation
prozorMinimal Protein Set Explaining Peptides
readjustWindowsReadjust windows so that boundaries in regions of few peaks.
readPeptideFastawrapper setting the correct parameters seqinr::read.fasta for...
removeSignalPeptideremove signal peptides from main chain
reverseSeqcreate rev sequences to fasta list
writeFastawrite fasta lists into file
prozor documentation built on Dec. 11, 2021, 9:51 a.m.