Man pages for protViz/prozor
Minimal Protein Set Explaining Peptide Spectrum Matches
| annotateAHO | annotate peptides using AhoCorasickTrie |
| annotatePeptides | Annotate peptides with protein ids |
| bcd | Data frame as produced by COMET-MS search engine |
| 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_parsimony | given matrix (columns protein rows peptides), compute minimal... |
| greedyRes2Matrix | converts result of greedy_parsimony function to a matrix with... |
| hardconstrain | tests hard constraints |
| loadContaminantsFasta2019 | load list of contaminant sequences FGCZ 2019 |
| loadContaminantsFasta2021 | load list of contaminant sequences FGCZ 2021 |
| loadContaminantsFGCZ2022 | load list of contaminant sequences FGCZ 2022 |
| load_special_prot_2024 | load special prot |
| load_universal_contaminants_2024 | load universal contaminants |
| make_fasta_summary | make db summary which includes number of sequences, and amino... |
| 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... |
| objectiveMS1Function | compute the deviation from optimum: equal number of MS1 per... |
| 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... |
| removeSignalPeptide | remove signal peptides from main chain |
| reverseSeq | create rev sequences to fasta list |
| writeFasta | write fasta lists into file |
