R Package for Processing High Content Screening data

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Documentation for package ‘GladiaTOX’ version 1.3.0

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