ToxCast Data Analysis Pipeline
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Documentation for package ‘tcpl’ version 3.1.0
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-- B --
| blineShift | Shift the baseline to 0 |
-- C --
| chdat | Chemical library of tested chemicals in the example datasets with the corresponding sample IDs. |
| check_tcpl_db_schema | Function that checks if the most recent v3 table schema is used in the database schema |
| Configure functions | Functions for configuring the tcpl package |
-- F --
| flareFunc | Calculate the weighted mean of a square to detect plate flares |
-- H --
| Hill model utilites | Functions to solve the Hill model |
-- I --
| interlaceFunc | Calculate the weighted mean of a square to detect interlace effect |
| invitrodb_dd | Short descriptions of fields for different tables are stored in a data dictionary. |
| is.odd | Check for odd numbers |
-- L --
| Load assay information | Functions for loading assay information |
| lu | Abbreviation for 'length(unique(x))' |
| lw | Abbreviation for 'length(which(x))' |
-- M --
| mc1 | Perform level 1 multiple-concentration processing |
| mc2 | Perform level 2 multiple-concentration processing |
| MC2_Methods | List of level 2 multiple-concentration correction functions |
| mc2_mthds | 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 |
| mc3_mthds | 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 calculating bmad |
| mc4_mthds | List of level 4 multiple-concentration methods for calculating bmad |
| mc5 | Perform level 5 multiple-concentration processing |
| MC5_Methods | Load list of level 5 multiple-concentration cutoff methods |
| mc5_mthds | 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 |
| mc6_mthds | Load list of level 6 multiple-concentration flag methods |
| mcdat | A subset of ToxCast data showing changes in the activity of the intracellular estrogen receptor. |
| mc_vignette | List with multi-concentration data for the vignette |
| Method functions | Functions for managing processing methods |
| Models | Model objective functions |
-- Q --
| Query functions | Wrappers for sending queries and fetching results |
-- R --
| Register/update annotation | Functions for registering & updating annotation information |
| registerMthd | Add a new analysis method |
-- S --
| sc1 | Perform level 1 single-concentration processing |
| SC1_Methods | List of level 1 single-concentration normalization functions |
| sc1_mthds | 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 |
| sc2_mthds | List of level 2 single-concentration hit-call functions |
| scdat | A subset of ToxCast data showing changes in transcription factor activity for multiple targets. |
| sc_vignette | List with single-concentration data for the vignette |
| sink.reset | Reset all sinks |
-- T --
| 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 |
| tcplConf | Functions for configuring the tcpl package |
| tcplConfDefault | Functions for configuring the tcpl package |
| tcplConfExample | Functions for configuring the tcpl package |
| tcplConfList | Functions for configuring the tcpl package |
| tcplConfLoad | Functions for configuring the tcpl package |
| tcplConfReset | Functions for configuring the tcpl package |
| tcplConfSave | Functions for configuring the tcpl package |
| tcplCytoPt | Calculate the cytotoxicity point based on the "burst" endpoints |
| 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 calculations to fit into new schema |
| 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 |
| tcplHillACXX | Functions to solve the Hill model |
| tcplHillConc | Functions to solve the Hill model |
| tcplHillVal | Functions to solve the Hill model |
| tcplHit2 | Hitcalling with tcplfit2 |
| tcplListFlds | Load the field names for a table |
| tcplLoadAcid | Functions for loading assay information |
| tcplLoadAeid | Functions for loading assay information |
| tcplLoadAid | Functions for loading assay information |
| tcplLoadAsid | Functions for loading assay information |
| tcplLoadChem | Load sample/chemical information |
| tcplLoadClib | Load chemical library 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, 6 per page |
| tcplMakeAeidPlts | Create a .pdf with dose-response plots |
| tcplMakeChidMultiPlts | Create a .pdf with all dose-response plots for a given chid, 6 per page |
| tcplMthdAssign | Functions for managing processing methods |
| tcplMthdClear | Functions for managing processing methods |
| tcplMthdList | Functions for managing processing methods |
| tcplMthdLoad | Functions for managing processing methods |
| tcplMultiplot | Plot summary fits based on fit and dose-response data |
| tcplObjCnst | Model objective functions |
| tcplObjGnls | Model objective functions |
| tcplObjHill | Model objective functions |
| tcplPlot | #--- Generic Plotting Function for tcpl |
| tcplPlotFitc | Plot the fit category tree |
| tcplPlotFits | Plot summary fits based on fit and dose-response data |
| tcplPlotlyPlot | tcplPlotlyPlot |
| tcplPlotM4ID | Plot fit summary plot by m4id |
| tcplPlotPlate | Plot plate heatmap |
| tcplPrepOtpt | Map assay/chemical ID values to annotation information |
| tcplQuery | Wrappers for sending queries and fetching results |
| tcplRegister | Functions for registering & updating annotation information |
| tcplRun | Perform data processing |
| tcplSendQuery | Wrappers for sending queries and fetching results |
| tcplSubsetChid | Subset level 5 data to a single sample per chemical |
| tcplUpdate | Functions for registering & updating annotation information |
| tcplVarMat | Create chemical by assay matrices |
| tcplWriteData | Write screening data into the tcpl databases |
| tcplWriteLvl0 | Write level 0 screening data into the tcpl databases |
-- W --
| write_lvl_4 | Write level 4 with updated schema |
-- misc --
| .buildAssayQ | Generate query for assay information |
| .convertNames | Convert assay names to their abbreviations |
| .load6DR | Load data for tcpl6 |
| .plateHeat | Plot plate heatmap |
| .prepField | Paste appropriate table name to field name |