├── ..Rcheck ├── 00install.out ├── Autotuner-manual.tex ├── Autotuner │ ├── DESCRIPTION │ ├── INDEX │ ├── LICENSE │ ├── Meta │ │ ├── Rd.rds │ │ ├── data.rds │ │ ├── features.rds │ │ ├── hsearch.rds │ │ ├── links.rds │ │ ├── nsInfo.rds │ │ └── package.rds │ ├── NAMESPACE │ ├── R │ │ ├── Autotuner │ │ ├── Autotuner.rdb │ │ └── Autotuner.rdx │ ├── application │ │ ├── app.R │ │ └── autotuner_parameters.csv │ ├── data │ │ ├── Rdata.rdb │ │ ├── Rdata.rds │ │ └── Rdata.rdx │ ├── help │ │ ├── AnIndex │ │ ├── Autotuner.rdb │ │ ├── Autotuner.rdx │ │ ├── aliases.rds │ │ └── paths.rds │ └── html │ │ ├── 00Index.html │ │ └── R.css └── tests │ ├── startup.Rs │ ├── testthat.R │ ├── testthat.Rout │ └── testthat │ ├── test_Autotuner.R │ └── test_loadingData.R ├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── Autotuner-class.R ├── EICParams.R ├── TIC_params.R ├── ThresholdingAlgo.R ├── checkBounds.R ├── checkEICFunctions.R ├── checkEICPeaks.R ├── data.R ├── dissectScans.R ├── extract_peaks.R ├── findPeakWidth.R ├── findTruePeaks.R ├── internal.R ├── isolatePeaks.R ├── peak_time_difference.R ├── peakwidth_est.R ├── peakwidth_table.R ├── plot_peaks.R ├── plot_signals.R └── returnParams.R ├── README.md ├── data ├── eicParamsEsts.rda ├── mzDb.rda └── observedPeak.rda ├── inst ├── extdata │ ├── Autotuner.rds │ ├── AutotunerObj.rds │ ├── eicParamsEsts.rds │ └── header.rds └── script │ ├── makeAutotunerTestData.R │ └── makeTestData.R ├── man ├── Autotuner-class.Rd ├── EICparams.Rd ├── TIC_params.Rd ├── ThresholdingAlgo.Rd ├── checkBounds.Rd ├── checkEICPeaks.Rd ├── createAutotuner.Rd ├── dissectScans.Rd ├── eicParamsEsts.Rd ├── estimatePPM.Rd ├── estimateSNThresh.Rd ├── extract_peaks.Rd ├── filterPeaksfromNoise.Rd ├── filterPpmError.Rd ├── findPeakWidth.Rd ├── findTruePeaks.Rd ├── getAutoFactorCol.Rd ├── getAutoFile_col.Rd ├── getAutoFile_paths.Rd ├── getAutoIntensity.Rd ├── getAutoMetadata.Rd ├── getAutoPeak_difference.Rd ├── getAutoPeak_table.Rd ├── getAutoPeaks.Rd ├── getAutoTime.Rd ├── initialize-Autotuner-method.Rd ├── isolatePeaks.Rd ├── mzDb.Rd ├── observedPeak.Rd ├── peak_time_difference.Rd ├── peakwidth_est.Rd ├── peakwidth_table.Rd ├── plot_peaks.Rd ├── plot_signals.Rd ├── returnParams.Rd ├── setAutoFactorCol.Rd ├── setAutoFile_col.Rd ├── setAutoFile_paths.Rd ├── setAutoIntensity.Rd ├── setAutoMetadata.Rd ├── setAutoPeak_difference.Rd ├── setAutoPeak_table.Rd ├── setAutoPeaks.Rd └── setAutoTime.Rd ├── tests ├── testthat.R └── testthat │ ├── test_Autotuner.R │ ├── test_gettersSetters.R │ ├── test_loadingData.R │ └── test_paramSummary.R └── vignettes ├── .gitignore └── Autotuner.Rmd /..Rcheck/00install.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KujawinskiLaboratory/Autotuner/HEAD/..Rcheck/00install.out -------------------------------------------------------------------------------- /..Rcheck/Autotuner-manual.tex: 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