ToxCast Data Analysis Pipeline

A set of tools for processing and modeling high-throughput and high-content chemical screening data. The package was developed for the the chemical screening data generated by the US EPA ToxCast program, but can be used for diverse chemical screening efforts.


tcpl v1.2.1

Changes from v1.2

  • A try-statement was added to the underlying function that draws the plot for tcplPlotHeat, so that the function does not return a figure margin error when running the checks for the package.

tcpl v1.2

Changes from beta versions:

  • The tcpl4 function now checks the new 'fit_all' field in the assay_component_endpoint table, and will attempt to fit every curve when 'fit_all' is 1.
  • The TCPL_CHEM and TCPL_INT settings have been deprecated and are no longer needed. To facilitate easier use and understanding, chemical tables included in the tcpl database are restructured.
  • The TCPL_LOG setting has been deprecated.
  • tcplUpdate is renamed to tcplSendQuery.
  • Single concentration screening is now implemented.
  • Added tcplRegister and tcplUpdate to make populating the database with new data easier.
  • Changed the underlying database structure. The old database will not work with beta versions of the package.
  • tcplPlotL4ID is now tcplPlotM4ID to match the new database structure.
  • The tcpl1, tcpl2, etc. functions have been renamed and are no longer exported. All processing is intended to occur through the tcplRun function.
  • tcplRunPipe is now tcplRun, and no longer defaults to writing a log file. A log file can still be written using the 'outfile' setting, as previously.
  • Level 5 multiple-concentration processing has changed -- there is no longer a minimum cutoff. All cutoff values must be specified with the new level 5 methods.
  • Level 6 multiple-concentration processing has changed -- some of the flag methodologies were updated.
  • tcplSetOpts renamed to tcplConf.
  • tcplSetOpts (now called tcplConf) can now be given only one or a subset of settings to change.
  • tcplListOpts renamed to tcplConfList.
  • tcplConfLoad, tcplConfSave, tcplConfDefault, and tcplConfReset added to make working with the package settings easier for the user.
  • Due a change in the underlying code for rapply the package now must use R version 3.2.0 or higher.
  • Added processing methods.
  • tcplWriteLvl0 now excludes loading data for acsn values that are not registered, but will load data for acsn values that are registered without returning an error.
  • tcpl now imports RMySQL.
  • tcplACVal and tcplACXX renamed tcplHillConc and tcplHillACXX, respectively.
  • tcplHillVal added.
  • Bug in tcplPlotPlate that caused incorrect coloring when the input data.table contained multiple assays is fixed.
  • 'fname' paramter is added to tcplMakeAeidPlts, and the default filename is changed.
  • 'quant' parameter is added to tcplPlotPlate.
  • tcplLoadAsid deprecated, and is no longer exported.
  • tcplLoadUnit deprecated, and is no longer exported.
  • The call to 'browser' in tcplPlotFits is changed to skip the other lines in the loop to make scanning through plots a little easier.
  • Extensive updates to documentation and the vignette, now called "tcpl_Overview."
  • tcplAssignMthd, tcplLoadMthd, tcplListMthd, and tcplClearMthd functions are renamed as tcplMthd- (e.g. tcplMthdLoad instead of tcplLoadMthd).
  • tcplMthdClear no longer returns TRUE, matching the behavior of tcplMthdAssign.
  • Added tcplCytoPt function to calculate the cytotoxicity points for chemical (this functionality used to be delivered by tcplVarMat, but is now separate).
  • 'argx' and 'srgx' parameters are removed from tcplPrepOtpt.
  • 'srgx' paramter is removed from tcplMakeAeidPlts.
  • tcplLoadAsidInfo & tcplLoadAeidInfo deprecated, and are no longer exported.
  • tcplPrepOtpt longer contains the 'clib' parameter.

Reference manual

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1.2.2 by Dayne L Filer, 2 years ago

Browse source code at

Authors: Dayne L Filer [aut, cre], Parth Kothiya [ctb], Woodrow R Setzer [ctb], Richard S Judson [ths], Matthew T Martin [ctb, ths]

Documentation:   PDF Manual  

GPL-2 license

Imports DBI, RMySQL, RSQLite, numDeriv, RColorBrewer, utils, stats, methods, graphics, grDevices

Depends on data.table

Suggests roxygen2

Imported by toxboot, toxplot.

See at CRAN