# ToxCast Data Analysis Pipeline

## Documentation for package ‘tcpl’ version 1.2.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

blineShift | Shift the baseline to 0
Configure functions | Functions for configuring the tcpl package
flareFunc | Calculate the weighted mean of a square to detect plate flares
Hill model utilites | Functions to solve the Hill model
interlaceFunc | Calculate the weighted mean of a square to detect interlace effect
is.odd | Check for odd numbers
Load assay information | Functions for loading assay information
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
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
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
Method functions | Functions for managing processing methods
Models | Model objective functions
Query functions | Wrappers for sending queries and fetching results
Register/update annotation | Functions for registering & updating annotation information
registerMthd | Add a new analysis method
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
sink.reset | Reset all sinks
tcplAddModel | Draw a tcpl Model onto an exisiting 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
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
tcplDelete | Delete rows from tcpl databases
tcplFit | Fit the data with the constant, hill, and gain-loss models
tcplHillACXX | Functions to solve the Hill model
tcplHillConc | Functions to solve the Hill model
tcplHillVal | Functions to solve the Hill model
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
tcplLoadData | Load tcpl data
tcplLoadUnit | Load response units for assay endpoints
tcplMakeAeidPlts | Create a .pdf with dose-response plots
tcplMthdAssign | Functions for managing processing methods
tcplMthdClear | Functions for managing processing methods
tcplMthdList | Functions for managing processing methods
tcplMthdLoad | Functions for managing processing methods
tcplObjCnst | Model objective functions
tcplObjGnls | Model objective functions
tcplObjHill | Model objective functions
tcplPlotFitc | Plot the fit category tree
tcplPlotFits | Plot summary fits based on fit and dose-response data
tcplPlotM4ID | Plot fit summary plot by m4id
tcplPlotPlate | Plot plate heatmap
tcplPrepOtpt | Map assay/chemcial 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