# Generated by roxygen2: do not edit by hand

export(BYion_peak_calculator_DIY)
export(annotatePSM)
export(calBYAtomCountAndBaseMass)
export(calPepAtomCount)
export(calPepNeutronMass)
export(calPepPrecursorMass)
export(cal_isotope_numbers)
export(cal_isotope_numbers_SIP)
export(cal_isotope_peaks_fft)
export(denoiseOneMS2ScanHasCharge)
export(extractPSMfeatures)
export(extractPSMfeaturesTargetAndDecoy)
export(extractPSMfeaturesTargetAndDecoytoPercolatorPin)
export(generateCFGs)
export(generateOneCFG)
export(getFilterThreshold)
export(getFilterThresholdTopPSMs)
export(getFilterThresholdTopPSMsSpe2Pep)
export(getMZ)
export(getPrecursorSpectra)
export(getRealScan)
export(getRealScanFromList)
export(getRealScanWithCharge)
export(getRealScans)
export(getRealScansWithCharges)
export(getRetentionTimeAndPrecursorInfo)
export(getSipBYionSpectra)
export(getSipPrecursorSpectra)
export(getTIC)
export(getUnfilteredPSMs)
export(getUnfilteredPeptides)
export(plotFilteredPCTIntensitySummary)
export(plotMolecularFFTisotopes)
export(plotMolecularIsotopes)
export(plotPSMannotation)
export(plotPSMs)
export(plotPSMsipPCT)
export(plotPrecursorMzFrequency)
export(plotProSipPct)
export(plotRealScan)
export(plotSIPfilteredPCTIntensityBySample)
export(plotScanFrequency)
export(plotScanFrequencyMS2)
export(plotScoreDistribution)
export(plotSipBYionLabel)
export(plotTIC)
export(precursor_peak_calculator)
export(precursor_peak_calculator_DIY)
export(precursor_peak_calculator_DIY_averagine)
export(rankyfify)
export(readAllScanMS1)
export(readAllScanMS2)
export(readFTheader)
export(readFilesScansTopPSMs)
export(readFilesScansTopPSMsFromOneFT2)
export(readMgf)
export(readMzmlMS1)
export(readMzmlMS2)
export(readOneScanMS1)
export(readOneScanMS2)
export(readPSMtsv)
export(readPepXMLtable)
export(readScansMS1)
export(readScansMS1Vector)
export(readScansMS2)
export(readScansMS2Vector)
export(readSip)
export(readSips)
export(readSpe2Pep)
export(readSpe2PepFilesScansTopPSMs)
export(readSpe2PepFilesScansTopPSMsFromEachFT2Parallel)
export(readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParallel)
export(readSpe2PepFilesScansTopPSMsFromOneFT2)
export(readSpe2Peps)
export(residue_peak_calculator_DIY)
export(scoreIntensity)
export(scoreIntensityByCE)
export(scorePSM)
export(scorePSMsimple)
export(summaryPSMsipPCT)
export(writeAllScanMS1)
export(writeAllScanMS2)
export(writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel)
exportClasses(AAspectra)
exportMethods(plot)
import(data.table)
import(ggplot2)
import(stringr)
importFrom(dplyr,group_by)
importFrom(dplyr,n)
importFrom(dplyr,summarise)
importFrom(ggplot2,aes)
importFrom(ggplot2,geom_freqpoly)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,scale_y_log10)
importFrom(ggrepel,geom_text_repel)
importFrom(scales,log_breaks)
importFrom(stringr,str_detect)
useDynLib(Aerith, .registration = TRUE)
