Man pages for prozor
Minimal Protein Set Explaining Peptide Spectrum Matches

annotateAHOannotate peptides using AhoCorasickTrie
annotatePeptidesAnnotate peptides with protein ids
annotateVecannotate vector of petpide sequences against fasta file...
computeFDRCompute FDR given a score
computeFDRwithIDCompute FDR given a score
createDecoyDBCreate db with decoys and contaminants
fdrSampleData frame score and proteinID
filterSequencesFilter for specific residues
greedygiven matrix (columns protein rows peptides), compute minimal...
greedyRes2Matrixconverts result of greedy function to a matrix with 3 columns...
loadContaminantsFastaload list of contaminant sequences
loadContaminantsNoHumanFastaload list of contaminant without human sequences
makeIDmake id for chain in format sp|P30443|1A01_HUMANs25
makeIDUnipmake id for chain compatible with uniprot
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
readPeptideFastawrapper setting the correct parameters
removeSignalPeptideremove signal peptides from main chain
reverseSeqcreate rev sequences to fasta list
writeFastawrite fasta lists into file
prozor documentation built on May 2, 2019, 8:18 a.m.