Man pages for GladiaTOX
R Package for Processing High Content Screening data

assay_funcsFunctions for loading assay information
assignDefaultMthdsAssign default processing methods
blineShiftShift the baseline to 0
buildAssayTabPrepare assay table mapping info
config_funcsFunctions for configuring the gtox package
deleteStudyCompletely remove all data for a study
exportResultForToxpiGUICreate the result table for the asi in input
exportResultTableCreate the result table for the asi in input
flareFuncCalculate the weighted mean of a square to detect plate...
glComputeToxIndCreate toxicological indicator values for all chemicals in...
glPlotPiePie chart for Minimal Effective Concentrations (MEC) and AC50...
glPlotPieLogoplot package logo
glPlotPosCtrlBox plot for positive control check
glPlotStatBox plot for Minimal Effective Concentrations (MEC) and AC50...
glPlotToxIndPlot toxicological indicator values for all chemicals in...
gtoxAddModelDraw a gtox Model onto an exisiting plot
gtoxAICProbCalculate the AIC probabilities
gtoxAppendAppend rows to a table
gtoxCalcVmadCalculate and update the assay endpoint cutoff values
gtoxCascadeDo a cascading delete on gtox screening data
gtoxCode2CASNConvert chemical code to CAS Registry Number
gtoxDeleteDelete rows from gtox databases
gtoxFitFit the data with the constant, hill, and gain-loss models
gtoxImportThermoDBImport data from ThermoDB by study ID
gtoxListFldsLoad the field names for a table
gtoxLoadApidLoad assay plate information
gtoxLoadChemLoad sample/chemical information
gtoxLoadClibLoad chemical library information
gtoxLoadDataLoad gtox data
gtoxLoadUnitLoad response units for assay endpoints
gtoxLoadVehicleLoad vehicle information
gtoxLoadVmadLoad cutoff values for assay endpoints
gtoxLoadWaidLoad well annotation information
gtoxMakeAeidPltsCreate a .pdf with dose-response plots
gtoxPlotErrBarCreate error bar plots
gtoxPlotFitcPlot the fit category tree
gtoxPlotFitsPlot summary fits based on fit and dose-response data
gtoxPlotM4IDPlot fit summary plot by m4id
gtoxPlotPieCreate piechart plots
gtoxPlotPieLgndCreate piechart plot legend
gtoxPlotPlatePlot plate heatmap
gtoxPlotWinCreate winning curve plots
gtoxPrepOtptMap assay/chemcial ID values to annotation information
gtoxReportGenerate a report
gtoxRunPerform data processing
gtoxSetWllqChange the well quality for a vector of lvl 0 IDs
gtoxSubsetChidSubset level 5 data to a single sample per chemical
gtoxWriteDataWrite screening data into the gtox databases
hill_utilsFunctions to solve the Hill model
interlaceFuncCalculate the weighted mean of a square to detect interlace...
is.oddCheck for odd numbers
loadAnnotRegister the annotations provided by GUI
luAbbreviation for 'length(unique(x))'
lwAbbreviation for 'length(which(x))'
mc1Perform level 1 multiple-concentration processing
mc2Perform level 2 multiple-concentration processing
MC2_MethodsList of level 2 multiple-concentration correction functions
mc3Perform level 3 multiple-concentration processing
MC3_MethodsList of level 3 multiple-concentration normalization methods
mc4Perform level 4 multiple-concentration processing
mc5Perform level 5 multiple-concentration processing
MC5_MethodsLoad list of level 5 multiple-concentration cutoff methods
mc6Perform level 6 multiple-concentration processing
MC6_MethodsLoad list of level 6 multiple-concentration flag methods
ModelsModel objective functions
mthd_funcsFunctions for managing processing methods
prepareDatForDBAssign default processing methods
query_funcsWrappers for sending queries and fetching results
registerMthdAdd a new analysis method
rgstr_funcsFunctions for registering & updating annotation information
sc1Perform level 1 single-concentration processing
SC1_MethodsList of level 1 single-concentration normalization functions
sc2Perform level 2 single-concentration processing
SC2_MethodsList of level 2 single-concentration hit-call functions
sink_resetReset all sinks
GladiaTOX documentation built on Nov. 15, 2020, 2:07 a.m.