Man pages for philipmorrisintl/GladiaTOX
R Package for Processing High Content Screening data
| assay_funcs | Functions for loading assay information |
| assignDefaultMthds | Assign default processing methods |
| blineShift | Shift the baseline to 0 |
| buildAssayTab | Prepare assay table mapping info |
| config_funcs | 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 |
| flareFunc | Calculate the weighted mean of a square to detect plate... |
| glCheckInput | Check validity of input file |
| glComputeToxInd | Create toxicological indicator values for all chemicals in... |
| glLoadInput | Check validity of input file |
| glPlotPie | Pie chart for Minimal Effective Concentrations (MEC) and AC50... |
| 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... |
| glPlotToxInd | Plot toxicological indicator values for all chemicals in... |
| gtoxAddModel | Draw a gtox Model onto an exisiting plot |
| gtoxAICProb | Calculate the AIC probabilities |
| gtoxAppend | Append rows to a table |
| gtoxCalcVmad | Calculate and update the assay endpoint cutoff values |
| gtoxCascade | Do a cascading delete on gtox screening data |
| gtoxCode2CASN | Convert chemical code to CAS Registry Number |
| gtoxDelete | Delete rows from gtox databases |
| gtoxFit | Fit the data with the constant, hill, and gain-loss models |
| gtoxImportThermoDB | Import data from ThermoDB by study ID |
| gtoxListFlds | Load the field names for a table |
| gtoxLoadApid | Load assay plate information |
| gtoxLoadChem | Load sample/chemical information |
| gtoxLoadClib | Load chemical library information |
| gtoxLoadData | Load gtox data |
| gtoxLoadUnit | Load response units for assay endpoints |
| gtoxLoadVehicle | Load vehicle information |
| gtoxLoadVmad | Load cutoff values for assay endpoints |
| gtoxLoadWaid | Load well annotation information |
| gtoxMakeAeidPlts | Create a .pdf with dose-response plots |
| 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 |
| gtoxReport | Generate a report |
| gtoxRun | Perform data processing |
| gtoxSetWllq | Change the well quality for a vector of lvl 0 IDs |
| gtoxSubsetChid | Subset level 5 data to a single sample per chemical |
| gtoxWriteData | Write screening data into the gtox databases |
| hill_utils | Functions to solve the Hill model |
| interlaceFunc | Calculate the weighted mean of a square to detect interlace... |
| is.odd | Check for odd numbers |
| loadAnnot | Register the annotations provided by GUI |
| lu | Abbreviation for 'length(unique(x))' |
| lw | Abbreviation for 'length(which(x))' |
| mc1 | Perform level 1 multiple-concentration processing |
| mc2 | Perform level 2 multiple-concentration processing |
| MC2_Methods | List of level 2 multiple-concentration correction functions |
| mc3 | Perform level 3 multiple-concentration processing |
| MC3_Methods | List of level 3 multiple-concentration normalization methods |
| mc4 | Perform level 4 multiple-concentration processing |
| mc5 | Perform level 5 multiple-concentration processing |
| MC5_Methods | Load list of level 5 multiple-concentration cutoff methods |
| mc6 | Perform level 6 multiple-concentration processing |
| MC6_Methods | Load list of level 6 multiple-concentration flag methods |
| Models | Model objective functions |
| mthd_funcs | Functions for managing processing methods |
| prepareDatForDB | Assign default processing methods |
| query_funcs | Wrappers for sending queries and fetching results |
| registerMthd | Add a new analysis method |
| rgstr_funcs | Functions for registering & updating annotation information |
| sc1 | Perform level 1 single-concentration processing |
| SC1_Methods | List of level 1 single-concentration normalization functions |
| sc2 | Perform level 2 single-concentration processing |
| SC2_Methods | List of level 2 single-concentration hit-call functions |
| sink_reset | Reset all sinks |
