Man pages for tcpl
ToxCast Data Analysis Pipeline
| assay_funcs | Functions for loading assay information |
| blineShift | Shift the baseline to 0 |
| check_tcpl_db_schema | Function that checks if the most recent v3 table schema is... |
| config_funcs | Functions for configuring the tcpl package |
| dot-buildAssayQ | Generate query for assay information |
| dot-convertNames | Convert assay names to their abbreviations |
| dot-load6DR | Load data for tcpl6 |
| dot-plateHeat | Plot plate heatmap |
| dot-prepField | Paste appropriate table name to field name |
| flareFunc | Calculate the weighted mean of a square to detect plate... |
| hill_utils | Functions to solve the Hill model |
| interlaceFunc | Calculate the weighted mean of a square to detect interlace... |
| invitrodb_dd | Short descriptions of fields for different tables are stored... |
| is.odd | Check for odd numbers |
| load_data_columns | Lists of column names returned from tcplLoadData invitrodb... |
| 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 |
| MC4_Methods | List of level 4 multiple-concentration methods for... |
| 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 |
| mcdat | A subset of ToxCast data showing changes in the activity of... |
| mc_test | List of lists containing queries sent to tcplQuery associated... |
| mc_vignette | List with multi-concentration data for the vignette |
| Models | Model objective functions |
| mthd_funcs | Functions for managing processing methods |
| mthd_list_defaults | Lists of data frames returned from tcplMthdList invitrodb... |
| 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 |
| scdat | A subset of ToxCast data showing changes in transcription... |
| sc_test | List of lists containing queries sent to tcplQuery associated... |
| sc_vignette | List with single-concentration data for the vignette |
| sink.reset | Reset all sinks |
| tcplAddModel | Draw a tcpl Model onto an existing plot |
| tcplAICProb | Calculate the AIC probabilities |
| tcplAppend | Append rows to a table |
| tcplCascade | Do a cascading delete on tcpl screening data |
| tcplCode2CASN | Convert chemical code to CAS Registry Number |
| tcplCytoPt | Calculate the cytotoxicity point based on the "burst"... |
| tcpldbStats | Get summary statistics for the database |
| tcplDefine | Load data dictionary descriptions |
| tcplDelete | Delete rows from tcpl databases |
| tcplFit | Fit the data with the constant, hill, and gain-loss models |
| tcplFit2 | tcpl Wrapper for tcplfit2_core including additional... |
| tcplFit2_nest | Nest dataframe into a list that is readable by tcplfit2 |
| tcplFit2_unnest | Unnest tcplfit2 parameters into a dataframe |
| tcplGetAeid | get Aeid for endpoint name |
| tcplggplot | tcplggplot |
| tcplggplotCompare | tcplggplotCompare |
| tcplHit2 | Hitcalling with tcplfit2 |
| tcplLegacyPlot | tcplLegacyPlot |
| tcplListFlds | Load the field names for a table |
| tcplLoadChem | Load sample/chemical information |
| tcplLoadChemList | Load chemical list information |
| tcplLoadConcUnit | Load concentration units for assay endpoints |
| tcplLoadData | Load tcpl data |
| tcplLoadUnit | Load response units for assay endpoints |
| tcplLvlCount | Load tcpl level counts |
| tcplMakeAeidMultiPlts | Create a .pdf with all dose-response plots for a given aeid,... |
| tcplMakeAeidPlts | Create a .pdf with dose-response plots |
| tcplMakeChidMultiPlts | Create a .pdf with all dose-response plots for a given chid,... |
| tcplMultiplot | Plot summary fits based on fit and dose-response data |
| tcplPlot | #—————— Generic Plotting Function for tcpl |
| tcplPlotFitc | Plot the fit category tree |
| tcplPlotFits | Plot summary fits based on fit and dose-response data |
| tcplPlotLoadData | Utility function to load data for tcplPlot |
| tcplPlotlyPlot | tcplPlotlyPlot |
| tcplPlotM4ID | Plot fit summary plot by m4id |
| tcplPlotPlate | Plot plate heatmap |
| tcplPlotSetYRange | tcplPlotSetYRange |
| tcplPlotValidate | tcplPlotValidate |
| tcplPrepOtpt | Map assay/chemical ID values to annotation information |
| tcplRun | Perform data processing |
| tcplSubsetChid | Subset level 5 data to a single sample per chemical |
| tcplVarMat | Create chemical by assay matrices |
| tcplWriteData | Write screening data into the tcpl databases |
| tcplWriteLvl0 | Write level 0 screening data into the tcpl databases |
| test_api | List containing ids used for different automated tests of... |
| write_lvl_4 | Write level 4 with updated schema |
