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"getFilterThresholdTopPSMsSpe2Pep", "title": "getFilterThresholdTopPSMsSpe2Pep get filter threshold of top PSMs of each scan from multiple .sip file", "topics": [ "getFilterThresholdTopPSMsSpe2Pep" ] }, { "page": "getMZ", "title": "add MZ to spectra data.frame", "topics": [ "getMZ" ] }, { "page": "getPrecursorSpectra", "title": "Get AAspectra object of precursor from AA sequence with natural SIP abundance", "topics": [ "getPrecursorSpectra" ] }, { "page": "getRealScan", "title": "Convert one scan with charges=1 normalized by highest peak in scans list of ft file to AAspectra class", "topics": [ "getRealScan" ] }, { "page": "getRealScanFromList", "title": "Convert one scan in list format to AAspectra class", "topics": [ "getRealScanFromList" ] }, { "page": "getRealScans", "title": "Get real scans from a scans list of one FT file with charges converted to 1 and intensities normalized by the highest peak.", "topics": [ "getRealScans" ] }, { "page": "getRealScansWithCharges", "title": "get real scans with real charges and raw intensities from scans list of one ft file", "topics": [ "getRealScansWithCharges" ] }, { "page": "getRealScanWithCharge", "title": "Convert one scan in scans with real charges and raw intensities from list of scans of ft file to AAspectra class", "topics": [ "getRealScanWithCharge" ] }, { "page": "getRetentionTimeAndPrecursorInfo", "title": "get retention time and precursor mass from scans list of ft file", "topics": [ "getRetentionTimeAndPrecursorInfo" ] }, { "page": "getSipBYionSpectra", "title": "Get AAspectra object of B and Y ions from AA sequence with labeled SIP abundance", "topics": [ "getSipBYionSpectra" ] }, { "page": "getSipPrecursorSpectra", "title": "Get AAspectra object of precursor from AA sequence with labeled SIP abundance", "topics": [ "getSipPrecursorSpectra" ] }, { "page": "getTIC", "title": "get TIC and retention time from scans list of ft file", "topics": [ "getTIC" ] }, { "page": "getUnfilteredPeptides", "title": "getUnfilteredPeptides", "topics": [ "getUnfilteredPeptides" ] }, { "page": "getUnfilteredPSMs", "title": "getUnfilteredPSMs", "topics": [ "getUnfilteredPSMs" ] }, { "page": "plot-AAspectra", "title": "Plot an AAspectra object", "topics": [ "plot,AAspectra,missing-method", "plot,AAspectra-method" ] }, { "page": "plotFilteredPCTIntensitySummary", "title": "Plot decoy-filtered PSMs' PCT and intensity summary by each input file", "topics": [ "plotFilteredPCTIntensitySummary" ] }, { "page": "plotMolecularFFTisotopes", "title": "Plot Molecular isotopes without fine structure by FFT algorithm", "topics": [ "plotMolecularFFTisotopes" ] }, { "page": "plotMolecularIsotopes", "title": "Plot Molecular Isotopes with fine structure by Montecarlo algorithm", "topics": [ "plotMolecularIsotopes" ] }, { "page": "plotPrecursorAnnotation", "title": "plot precursor annotation", "topics": [ "plotPrecursorAnnotation" ] }, { "page": "plotPrecursorMzFrequency", "title": "Plot precursor MZ frequency per 5 per minute of MS2", "topics": [ "plotPrecursorMzFrequency" ] }, { "page": "plotProSipPct", "title": "plot the distribution of SIP percent of proteins", "topics": [ "plotProSipPct" ] }, { "page": "plotPSMannotation", "title": "plot PSM annotation", "topics": [ "plotPSMannotation" ] }, { "page": "plotPSMs", "title": "plot PSMs from FT2 files and PSM results", "topics": [ "plotPSMs" ] }, { "page": "plotPSMsipPCT", "title": "Plot the distribution of SIP percent for PSMs", "topics": [ "plotPSMsipPCT" ] }, { "page": "plotRealScan", "title": "plot real scan layer under the B Y ion peaks", "topics": [ "plotRealScan" ] }, { "page": "plotScanFrequency", "title": "Plot scan frequency", "topics": [ "plotScanFrequency" ] }, { "page": "plotScanFrequencyMS2", "title": "Plot scan frequency layer of MS2", "topics": [ "plotScanFrequencyMS2" ] }, { "page": "plotScoreDistribution", "title": "plot the score of PSMs at different charge and mass error", "topics": [ "plotScoreDistribution" ] }, { "page": "plotSipBYionLabel", "title": "Draw AAspectra MS plot with B Y ion Labels", "topics": [ "plotSipBYionLabel" ] }, { "page": "plotSIPfilteredPCTIntensityBySample", "title": "Plot SIP-filtered PCT and intensity summary by each input file", "topics": [ "plotSIPfilteredPCTIntensityBySample" ] }, { "page": "plotTIC", "title": "Plot TIC of MS1 or MS2", "topics": [ "plotTIC" ] }, { "page": "precursor_peak_calculator", "title": "Precursor Peak Calculator", "topics": [ "precursor_peak_calculator" ] }, { "page": "precursor_peak_calculator_DIY", "title": "Precursor Peak Calculator with User-Defined Isotopic Distribution", "topics": [ "precursor_peak_calculator_DIY" ] }, { "page": "precursor_peak_calculator_DIY_averagine", "title": "Simple peak calculator of user defined isotopic distribution of one peptide by averagine", "topics": [ "precursor_peak_calculator_DIY_averagine" ] }, { "page": "rankyfify", "title": "rankify numeric vector via ftFileWriter", "topics": [ "rankyfify" ] }, { "page": "readAllScanMS1", "title": "read MS1 scans with scanNumber as index", "topics": [ "readAllScanMS1" ] }, { "page": "readAllScanMS2", "title": "read MS2 scans with scanNumber as index", "topics": [ "readAllScanMS2" ] }, { "page": "readFilesScansTopPSMs", "title": "readFilesScansTopPSMs", "topics": [ "readFilesScansTopPSMs" ] }, { "page": "readFilesScansTopPSMsFromOneFT2", "title": "readFilesScansTopPSMsFromOneFT2 read each scan's top PSMs from multiple .sip files of one .FT2 file", "topics": [ "readFilesScansTopPSMsFromOneFT2" ] }, { "page": "readFTheader", "title": "read FT file header", "topics": [ "readFTheader" ] }, { "page": "readMgf", "title": "Read spectra from .mgf file", "topics": [ "readMgf" ] }, { "page": "readMzmlMS1", "title": "Read MS1 spectra from .mzML file", "topics": [ "readMzmlMS1" ] }, { "page": "readMzmlMS2", "title": "Read MS2 spectra from .mzML file", "topics": [ "readMzmlMS2" ] }, { "page": "readOneScanMS1", "title": "readOneScanMS1", "topics": [ "readOneScanMS1" ] }, { "page": "readOneScanMS2", "title": "readOneScanMS2", "topics": [ "readOneScanMS2" ] }, { "page": "readPepXMLtable", "title": "Read PSM table from .pepXML file", "topics": [ "readPepXMLtable" ] }, { "page": "readPSMtsv", "title": "Read PSM TSV File", "topics": [ "readPSMtsv" ] }, { "page": "readScansMS1", "title": "read MS1 scans with scanNumber as index in a range", "topics": [ "readScansMS1" ] }, { "page": "readScansMS1Vector", "title": "read MS1 scans with scanNumber as index in a vector", "topics": [ "readScansMS1Vector" ] }, { "page": "readScansMS2", "title": "read MS2 scans with scanNumber as index in a range", "topics": [ "readScansMS2" ] }, { "page": "readScansMS2Vector", "title": "read MS2 scans with scanNumber as index in a vector", "topics": [ "readScansMS2Vector" ] }, { "page": "readSip", "title": "readSip", "topics": [ "readSip" ] }, { "page": "readSips", "title": "readSips", "topics": [ "readSips" ] }, { "page": "readSpe2Pep", "title": "readSpe2Pep", "topics": [ 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