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.


News

tcpl v2.0.1

Updated vignettes to use tempdir and thus not write to install folder.

tcpl v2.0

Major change for tcpl v2.0:

  • Incorporation of tcplLite into the package, a functionality that allows the user to work from local files formatted like invitrodb tables, rather than a MySQL database.
    • Using tcplLite is ideal for handling smaller datasets.
    • The SQLite driver was removed from the package.
    • tcplConf() default is now for tcplLite, which uses .csv files rather than tables in a MySQL database.
    • The MySQL driver is available and recommended for interacting with the entire dataset as a database.
    • The package vignettes run using tcplLite. Additional updates for tcpl v2.0
  • tcplLvlCount: function added to count the samples at each level of processing for each aeid.
  • Addition of mc4 methods: the baseline median absolute deviation can now be calculated based on the lowest two concentrations or on the neutral control wells. An mc4 method must now be assigned for analysis.
  • tcplGetAeid: function added to find assays based on matching a character string within any assay endpoint name.
  • tcplMakeAeidMultiPlts: 3x2 grid of plots on each page of a PDF, for a single aeid.
  • tcplMakeChidMultiPlts: 3x2 grid of plots on each page of a PDF, for a single chemical id (chid).
  • Vignettes are now posted as html from RMarkdown files for Introduction and appendices, data retrieval, and data processing.
  • Various bug fixes and additions to the methods tables.

tcpl v1.4.0

Changes from v1.2.2

  • .plotFit (not exported) was updated to work with the new behavior of nchar for R>3.3 (PR#10/#26)

  • tcplPlotPlate now works with single-conc data. Previously it only worked with the multi-conc data. (PR#14)

  • Deleted out the 'nddr' level 6 methods. They were specific to one dataset and are no longer used. (PR#16)

  • Removed all instances of "with = FALSE" in data.table calls. (PR#25)

  • The package no longer writes to the installation directory. The vignette is now built in TMPDIR and the location of the configuration file must be specified by the user. This is to comply CRAN policies. The benefit to users that share an installation, is they can now each have their own config file. (PR#28)

  • The specific method imports were removed for the RSQLite and RMySQL packages. This change reflects the new behavior of the RSQLite package. The RMySQL imports were removed to simplify the package, as they were found unnecessary. (PR#29)

tcpl v1.2.3

Changes from v1.2.2

  • .plotFit (not exported) was updated to work with the new behavior of nchar for R>3.3 (PR#10/#26)

  • tcplPlotPlate now works with single-conc data. Previously it only worked with the multi-conc data. (PR#14)

  • Deleted out the 'nddr' level 6 methods. They were specific to one dataset and are no longer used. (PR#16)

  • Removed all instances of "with = FALSE" in data.table calls. (PR#25)

  • The package no longer writes to the installation directory. The vignette is now built in TMPDIR and the location of the configuration file must be specified by the user. This is to comply CRAN policies. The benefit to users that share an installation, is they can now each have their own config file. (PR#28)

  • The specific method imports were removed for the RSQLite and RMySQL packages. This change reflects the new behavior of the RSQLite package. The RMySQL imports were removed to simplify the package, as they were found unnecessary. (PR#29)

tcpl v1.2.2

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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install.packages("tcpl")

2.0.1 by Richard S Judson, 4 months ago


https://github.com/USEPA/CompTox-ToxCast-tcpl


Browse source code at https://github.com/cran/tcpl


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


Documentation:   PDF Manual  


GPL-2 license


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

Depends on data.table

Suggests roxygen2, knitr, prettydoc, rmarkdown, htmlTable


See at CRAN