Aerith-package	Aerith-package
.onLoad	dot-onLoad
.onUnload	dot-onUnload
AAspectra-class	AAspectra-class
Aerith	Aerith-package
aerith	Aerith-package
annotatePrecursor	annotatePrecursor
annotatePSM	annotatePSM
BYion_peak_calculator_DIY	BYion_peak_calculator_DIY
calBYAtomCountAndBaseMass	calBYAtomCountAndBaseMass
calPepAtomCount	calPepAtomCount
calPepNeutronMass	calPepNeutronMass
calPepPrecursorMass	calPepPrecursorMass
cal_isotope_numbers	cal_isotope_numbers
cal_isotope_numbers_SIP	cal_isotope_numbers_SIP
cal_isotope_peaks_fft	cal_isotope_peaks_fft
denoiseOneMS2ScanHasCharge	denoiseOneMS2ScanHasCharge
extractPSMfeatures	extractPSMfeatures
extractPSMfeaturesTargetAndDecoy	extractPSMfeaturesTargetAndDecoy
extractPSMfeaturesTargetAndDecoytoPercolatorPin	extractPSMfeaturesTargetAndDecoytoPercolatorPin
generateCFGs	generateCFGs
generateOneCFG	generateOneCFG
getFilterThreshold	getFilterThreshold
getFilterThresholdTopPSMs	getFilterThresholdTopPSMs
getFilterThresholdTopPSMsSpe2Pep	getFilterThresholdTopPSMsSpe2Pep
getMZ	getMZ
getPrecursorSpectra	getPrecursorSpectra
getRealScan	getRealScan
getRealScanFromList	getRealScanFromList
getRealScans	getRealScans
getRealScansWithCharges	getRealScansWithCharges
getRealScanWithCharge	getRealScanWithCharge
getRetentionTimeAndPrecursorInfo	getRetentionTimeAndPrecursorInfo
getSipBYionSpectra	getSipBYionSpectra
getSipPrecursorSpectra	getSipPrecursorSpectra
getTIC	getTIC
getUnfilteredPeptides	getUnfilteredPeptides
getUnfilteredPSMs	getUnfilteredPSMs
plot,AAspectra,missing-method	plot-AAspectra
plot,AAspectra-method	plot-AAspectra
plotFilteredPCTIntensitySummary	plotFilteredPCTIntensitySummary
plotMolecularFFTisotopes	plotMolecularFFTisotopes
plotMolecularIsotopes	plotMolecularIsotopes
plotPrecursorAnnotation	plotPrecursorAnnotation
plotPrecursorMzFrequency	plotPrecursorMzFrequency
plotProSipPct	plotProSipPct
plotPSMannotation	plotPSMannotation
plotPSMs	plotPSMs
plotPSMsipPCT	plotPSMsipPCT
plotRealScan	plotRealScan
plotScanFrequency	plotScanFrequency
plotScanFrequencyMS2	plotScanFrequencyMS2
plotScoreDistribution	plotScoreDistribution
plotSipBYionLabel	plotSipBYionLabel
plotSIPfilteredPCTIntensityBySample	plotSIPfilteredPCTIntensityBySample
plotTIC	plotTIC
precursor_peak_calculator	precursor_peak_calculator
precursor_peak_calculator_DIY	precursor_peak_calculator_DIY
precursor_peak_calculator_DIY_averagine	precursor_peak_calculator_DIY_averagine
rankyfify	rankyfify
readAllScanMS1	readAllScanMS1
readAllScanMS2	readAllScanMS2
readFilesScansTopPSMs	readFilesScansTopPSMs
readFilesScansTopPSMsFromOneFT2	readFilesScansTopPSMsFromOneFT2
readFTheader	readFTheader
readMgf	readMgf
readMzmlMS1	readMzmlMS1
readMzmlMS2	readMzmlMS2
readOneScanMS1	readOneScanMS1
readOneScanMS2	readOneScanMS2
readPepXMLtable	readPepXMLtable
readPSMtsv	readPSMtsv
readScansMS1	readScansMS1
readScansMS1Vector	readScansMS1Vector
readScansMS2	readScansMS2
readScansMS2Vector	readScansMS2Vector
readSip	readSip
readSips	readSips
readSpe2Pep	readSpe2Pep
readSpe2PepFilesScansTopPSMs	readSpe2PepFilesScansTopPSMs
readSpe2PepFilesScansTopPSMsFromEachFT2Parallel	readSpe2PepFilesScansTopPSMsFromEachFT2Parallel
readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParallel	readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParallel
readSpe2PepFilesScansTopPSMsFromOneFT2	readSpe2PepFilesScansTopPSMsFromOneFT2
readSpe2Peps	readSpe2Peps
residue_peak_calculator_DIY	residue_peak_calculator_DIY
scoreIntensity	scoreIntensity
scoreIntensityByCE	scoreIntensityByCE
scorePSM	scorePSM
scorePSMsimple	scorePSMsimple
summaryPSMsipPCT	summaryPSMsipPCT
writeAllScanMS1	writeAllScanMS1
writeAllScanMS2	writeAllScanMS2
writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel	writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel
