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.
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.
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
- 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
- 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
- '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
- 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.