# R Package for Processing High Content Screening data

## Documentation for package ‘GladiaTOX’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

assignDefaultMthds | Assign default processing methods
buildAssayTab | Prepare assay table mapping info
Configure functions | Functions for configuring the gtox package
deleteStudy | Completely remove all data for a study
exportResultForToxpiGUI | Create the result table for the asi in input
exportResultTable | Create the result table for the asi in input
glComputeToxInd | Create toxicological indicator values for all chemicals in input
glPlotPie | Pie chart for Minimal Effective Concentrations (MEC) and AC50 plot
glPlotPieLogo | plot package logo
glPlotPosCtrl | Box plot for positive control check
glPlotStat | Box plot for Minimal Effective Concentrations (MEC) and AC50 plot
glPlotToxInd | Plot toxicological indicator values for all chemicals in input
gtoxAddModel | Draw a gtox Model onto an exisiting plot
gtoxAICProb | Calculate the AIC probabilities
gtoxCalcVmad | Calculate and update the assay endpoint cutoff values
gtoxCode2CASN | Convert chemical code to CAS Registry Number
gtoxConf | Functions for configuring the gtox package
gtoxConfDefault | Functions for configuring the gtox package
gtoxConfList | Functions for configuring the gtox package
gtoxConfLoad | Functions for configuring the gtox package
gtoxConfReset | Functions for configuring the gtox package
gtoxConfSave | Functions for configuring the gtox package
gtoxFit | Fit the data with the constant, hill, and gain-loss models
gtoxHillACXX | Functions to solve the Hill model
gtoxHillConc | Functions to solve the Hill model
gtoxHillVal | Functions to solve the Hill model
gtoxImportThermoDB | Import data from ThermoDB by study ID
gtoxListFlds | Load the field names for a table
gtoxLoadAcid | Functions for loading assay information
gtoxLoadAeid | Functions for loading assay information
gtoxLoadAid | Functions for loading assay information
gtoxLoadApid | Load assay plate information
gtoxLoadAsid | Functions for loading assay information
gtoxLoadChem | Load sample/chemical information
gtoxLoadClib | Load chemical library information
gtoxLoadData | Load gtox data
gtoxLoadVehicle | Load vehicle information
gtoxLoadVmad | Load cutoff values for assay endpoints
gtoxLoadWaid | Load well annotation information
gtoxMakeAeidPlts | Create a .pdf with dose-response plots
gtoxMthdAssign | Functions for managing processing methods
gtoxMthdClear | Functions for managing processing methods
gtoxMthdList | Functions for managing processing methods
gtoxMthdLoad | Functions for managing processing methods
gtoxObjCnst | Model objective functions
gtoxObjGnls | Model objective functions
gtoxObjHill | Model objective functions
gtoxPlotErrBar | Create error bar plots
gtoxPlotFitc | Plot the fit category tree
gtoxPlotFits | Plot summary fits based on fit and dose-response data
gtoxPlotM4ID | Plot fit summary plot by m4id
gtoxPlotPie | Create piechart plots
gtoxPlotPieLgnd | Create piechart plot legend
gtoxPlotPlate | Plot plate heatmap
gtoxPlotWin | Create winning curve plots
gtoxPrepOtpt | Map assay/chemcial ID values to annotation information
gtoxQuery | Wrappers for sending queries and fetching results
gtoxRegister | Functions for registering & updating annotation information
gtoxReport | Generate a report
gtoxRun | Perform data processing
gtoxSendQuery | Wrappers for sending queries and fetching results
gtoxSetWllq | Change the well quality for a vector of lvl 0 IDs
gtoxSubsetChid | Subset level 5 data to a single sample per chemical
gtoxUpdate | Functions for registering & updating annotation information
gtoxWriteData | Write screening data into the gtox databases
Hill model utilites | Functions to solve the Hill model
Load assay information | Functions for loading assay information
loadAnnot | Register the annotations provided by GUI
lu | Abbreviation for 'length(unique(x))'
lw | Abbreviation for 'length(which(x))'
Method functions | Functions for managing processing methods
Models | Model objective functions
prepareDatForDB | Assign default processing methods
Query functions | Wrappers for sending queries and fetching results
Register/update annotation | Functions for registering & updating annotation information