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NAMESPACE
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useDynLib(TargetSearch, .registration = TRUE, .fixes = "c_")
import("methods")
import("stats")
importFrom("graphics",
"abline",
"axis",
"box",
"boxplot",
"grid",
"image",
"layout",
"lcm",
"legend",
"matlines",
"matplot",
"mtext",
"par",
"plot.new",
"points",
"rect",
"strheight",
"strwidth",
"text",
"title"
)
importFrom("grDevices", "colorRamp", "dev.off", "pdf", "gray", "rgb")
importFrom("utils",
"combn",
"head",
"read.delim",
"setTxtProgressBar",
"txtProgressBar",
"write.table"
)
importFrom("ncdf4", "nc_open", "nc_close", "ncvar_get", "ncvar_put",
"ncatt_get", "ncatt_put", "ncdim_def", "ncvar_def", "nc_create")
importFrom("assertthat",
"assert_that",
"is.count",
"is.flag",
"is.number",
"is.scalar",
"is.string",
"noNA",
"on_failure<-"
)
exportClasses(
"tsLib",
"tsRim",
"tsSample",
"tsMSdata",
"tsProfile"
)
exportMethods(
"rimMass",
"rimMass<-",
"rimLimits",
"rimLimits<-",
"rimStandard",
"rimStandard<-",
"CDFfiles",
"CDFfiles<-",
"RIfiles",
"RIfiles<-",
"CDFpath",
"CDFpath<-",
"RIpath",
"RIpath<-",
"sampleData",
"sampleData<-",
"sampleNames",
"sampleNames<-",
"sampleDays",
"sampleDays<-",
"refLib",
"libId",
"medRI",
"medRI<-",
"selMass",
"selMass<-",
"topMass",
"topMass<-",
"quantMass",
"quantMass<-",
"spectra",
"spectra<-",
"libName",
"libName<-",
"libRI",
"libRI<-",
"libData",
"libData<-",
"RIdev",
"RIdev<-",
"retIndex",
"retIndex<-",
"retTime",
"retTime<-",
"Intensity",
"Intensity<-",
"profileInfo",
"profileInfo<-",
"profileInt",
"profileInt<-",
"profileRI",
"profileRI<-",
"profileRT",
"profileRT<-",
"fileFormat",
"fileFormat<-",
"show",
"tsUpdate",
"ncdf4Convert"
)
S3method("as.list", "tsMSdata")
S3method("as.list", "tsProfile")
export(
"baseline",
"baselineCorrection",
"baselineCorrectionQuant",
"bin2text",
"checkRimLim",
"FAMEoutliers",
"FindAllPeaks",
"FindPeaks",
"fixRI",
"fixRIcorrection",
"ImportFameSettings",
"ImportLibrary",
"ImportLibrary.msp",
"ImportLibrary.tab",
"ImportSamples",
"ImportSamplesFromDir",
"makeIndex",
"medianRILib",
"ncdf4_convert",
"ncdf4_convert_from_path",
"ncdf4_data_extract",
"ncdf4_plot_peak",
"ncdf4_update_ri",
"NetCDFPeakFinding",
"peakCDFextraction",
"peakFind",
"plotAllRIdev",
"plotAllSpectra",
"plotFAME",
"plotPeak",
"plotPeakRI",
"plotPeakSimple",
"plotRefSpectra",
"plotRIdev",
"plotSpectra",
"Profile",
"ProfileCleanUp",
"quantMatrix",
"ri2rt",
"RIcorrect",
"riMatrix",
"ri_data_extract",
"ri_plot_peak",
"rt2ri",
"sampleRI",
"TargetSearchGUI",
"text2bin",
"updateRI",
"Write.Results",
"writeLibText",
"writeMSP"
)