AAspectra-class         AAspectra S4 class for annotated mass spectra
BYion_peak_calculator_DIY
                        BY Ion Peak Calculator with User-Defined
                        Isotopic Distribution
annotatePSM             annotatePSM
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
getRealScanWithCharge   Convert one scan in scans with real charges and
                        raw intensities from list of scans of ft file
                        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
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
getUnfilteredPSMs       getUnfilteredPSMs
getUnfilteredPeptides   getUnfilteredPeptides
plot,AAspectra,missing-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
plotPSMannotation       plot PSM annotation
plotPSMs                plot PSMs from FT2 files and PSM results
plotPSMsipPCT           Plot the distribution of SIP percent for PSMs
plotPrecursorMzFrequency
                        Plot precursor MZ frequency per 5 per minute of
                        MS2
plotProSipPct           plot the distribution of SIP percent of
                        proteins
plotRealScan            plot real scan layer under the B Y ion peaks
plotSIPfilteredPCTIntensityBySample
                        Plot SIP-filtered PCT and intensity summary by
                        each input file
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
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
readFTheader            read FT file header
readFilesScansTopPSMs   readFilesScansTopPSMs
readFilesScansTopPSMsFromOneFT2
                        readFilesScansTopPSMsFromOneFT2 read each
                        scan's top PSMs from multiple .sip files of one
                        .FT2 file
readMgf                 Read spectra from .mgf file
readMzmlMS1             Read MS1 spectra from .mzML file
readMzmlMS2             Read MS2 spectra from .mzML file
readOneScanMS1          readOneScanMS1
readOneScanMS2          readOneScanMS2
readPSMtsv              Read PSM TSV File
readPepXMLtable         Read PSM table from .pepXML 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
