visualization and annotation of isotopic enrichment patterns of
peptides and metabolites with stable isotope labeling from
proteomics and metabolomics
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Documentation for package ‘Aerith’ version 0.99.11
Help Pages
| AAspectra-class | AAspectra S4 class for annotated mass spectra |
| annotatePSM | annotatePSM |
| BYion_peak_calculator_DIY | BY Ion Peak Calculator with User-Defined Isotopic Distribution |
| calBYAtomCountAndBaseMass | Simple calculator of C H O N P S atom count and mass without isotope of B Y ions |
| calPepAtomCount | Simple calculator of C H O N P S atom count of peptide |
| calPepNeutronMass | Simple calculator neutron mass by average delta mass of each isotope |
| calPepPrecursorMass | Simple calculator of peptide precursor mass by binomial NP |
| cal_isotope_numbers | Calculate Isotope Numbers in natural abundance |
| cal_isotope_numbers_SIP | Calculate Isotope Numbers for SIP |
| cal_isotope_peaks_fft | Calculate Isotope Peaks using FFT |
| denoiseOneMS2ScanHasCharge | denoise one MS2 scan has charge |
| extractPSMfeatures | extractPSMfeatures extract featueres of top PSMs from multiple .Spe2Pep.txt files |
| extractPSMfeaturesTargetAndDecoy | extractPSMfeaturesTargetAndDecoy extract featueres of top PSMs from target and decoy .Spe2Pep.txt files |
| extractPSMfeaturesTargetAndDecoytoPercolatorPin | extractPSMfeaturesTargetAndDecoytoPercolatorPin extract featueres of top PSMs from target and decoy .Spe2Pep.txt files to pecorlator pin format |
| generateCFGs | generateCFGs |
| generateOneCFG | generateOneCFG |
| getFilterThreshold | getFilterThreshold |
| getFilterThresholdTopPSMs | getFilterThresholdTopPSMs get filter threshold of top PSMs of each scan from multiple .sip file |
| getFilterThresholdTopPSMsSpe2Pep | getFilterThresholdTopPSMsSpe2Pep get filter threshold of top PSMs of each scan from multiple .sip file |
| getMZ | add MZ to spectra data.frame |
| getPrecursorSpectra | Get AAspectra object of precursor from AA sequence with natural SIP abundance |
| getRealScan | Convert one scan with charges=1 normalized by highest peak in scans list of ft file to AAspectra class |
| getRealScanFromList | Convert one scan in list format to AAspectra class |
| getRealScans | Get real scans from a scans list of one FT file with charges converted to 1 and intensities normalized by the highest peak. |
| getRealScansWithCharges | get real scans with real charges and raw intensities from scans list of one ft file |
| getRealScanWithCharge | Convert one scan in scans with real charges and raw intensities from list of scans of ft file to AAspectra class |
| getRetentionTimeAndPrecursorInfo | get retention time and precursor mass from scans list of ft file |
| getSipBYionSpectra | Get AAspectra object of B and Y ions from AA sequence with labeled SIP abundance |
| getSipPrecursorSpectra | Get AAspectra object of precursor from AA sequence with labeled SIP abundance |
| getTIC | get TIC and retention time from scans list of ft file |
| getUnfilteredPeptides | getUnfilteredPeptides |
| getUnfilteredPSMs | getUnfilteredPSMs |
| plot-method | Plot an AAspectra object |
| plotFilteredPCTIntensitySummary | Plot decoy-filtered PSMs' PCT and intensity summary by each input file |
| plotMolecularFFTisotopes | Plot Molecular isotopes without fine structure by FFT algorithm |
| plotMolecularIsotopes | Plot Molecular Isotopes with fine structure by Montecarlo algorithm |
| plotPrecursorMzFrequency | Plot precursor MZ frequency per 5 per minute of MS2 |
| plotProSipPct | plot the distribution of SIP percent of proteins |
| plotPSMannotation | plot PSM annotation |
| plotPSMs | plot PSMs from FT2 files and PSM results |
| plotPSMsipPCT | Plot the distribution of SIP percent for PSMs |
| plotRealScan | plot real scan layer under the B Y ion peaks |
| plotScanFrequency | Plot scan frequency |
| plotScanFrequencyMS2 | Plot scan frequency layer of MS2 |
| plotScoreDistribution | plot the score of PSMs at different charge and mass error |
| plotSipBYionLabel | Draw AAspectra MS plot with B Y ion Labels |
| plotSIPfilteredPCTIntensityBySample | Plot SIP-filtered PCT and intensity summary by each input file |
| plotTIC | Plot TIC of MS1 or MS2 |
| precursor_peak_calculator | Precursor Peak Calculator |
| precursor_peak_calculator_DIY | Precursor Peak Calculator with User-Defined Isotopic Distribution |
| precursor_peak_calculator_DIY_averagine | Simple peak calculator of user defined isotopic distribution of one peptide by averagine |
| rankyfify | rankify numeric vector via ftFileWriter |
| readAllScanMS1 | read MS1 scans with scanNumber as index |
| readAllScanMS2 | read MS2 scans with scanNumber as index |
| readFilesScansTopPSMs | readFilesScansTopPSMs |
| readFilesScansTopPSMsFromOneFT2 | readFilesScansTopPSMsFromOneFT2 read each scan's top PSMs from multiple .sip files of one .FT2 file |
| readFTheader | read FT file header |
| readMgf | Read spectra from .mgf file |
| readMzmlMS1 | Read MS1 spectra from .mzML file |
| readMzmlMS2 | Read MS2 spectra from .mzML file |
| readOneScanMS1 | readOneScanMS1 |
| readOneScanMS2 | readOneScanMS2 |
| readPepXMLtable | Read PSM table from .pepXML file |
| readPSMtsv | Read PSM TSV File |
| readScansMS1 | read MS1 scans with scanNumber as index in a range |
| readScansMS1Vector | read MS1 scans with scanNumber as index in a vector |
| readScansMS2 | read MS2 scans with scanNumber as index in a range |
| readScansMS2Vector | read MS2 scans with scanNumber as index in a vector |
| readSip | readSip |
| readSips | readSips |
| readSpe2Pep | readSpe2Pep |
| readSpe2PepFilesScansTopPSMs | readSpe2PepFilesScansTopPSMs read each scan's top PSMs from multiple .Spe2Pep.txt files |
| readSpe2PepFilesScansTopPSMsFromEachFT2Parallel | readSpe2PepFilesScansTopPSMsFromEachFT2Parallel read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 file |
| readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParallel | readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParalle read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 file |
| readSpe2PepFilesScansTopPSMsFromOneFT2 | readSpe2PepFilesScansTopPSMsFromOneFT2 read each scan's top PSMs from multiple .Spe2PepFile.txt files of one .FT2 file |
| readSpe2Peps | readSpe2Peps |
| residue_peak_calculator_DIY | Simple residue peak calculator of user defined isotopic distribution of one residue |
| scoreIntensity | scoreIntensity |
| scoreIntensityByCE | scoreIntensityByCrossEntropy |
| scorePSM | scorePSM |
| scorePSMsimple | scorePSMsimple Score a PSM without isotopic envelope shape modeling |
| summaryPSMsipPCT | Summarize SIP percent for PSMs |
| writeAllScanMS1 | write all MS1 scans has charge |
| writeAllScanMS2 | write all MS2 scans has charge |
| writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel | writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 file and write them to one tsv file |