R Package for Processing High Content Screening data

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Documentation for package ‘GladiaTOX’ version 1.25.3

• 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
glCheckInput	Check validity of input file
glComputeToxInd	Create toxicological indicator values for all chemicals in input
glLoadInput	Check validity of input file
glPlotPie	Pie chart for Minimal Effective Concentrations (MEC) and AC50 plot
glPlotPieLogo	plot package logo
glPlotPosCtrl	Box plot for positive control check
glPlotPosCtrlMEC	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