Package: tcpl 3.1.0

Jason Brown

tcpl: ToxCast Data Analysis Pipeline

The ToxCast Data Analysis Pipeline (tcpl) is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, invitrodb. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but tcpl can be used to support diverse chemical screening efforts.

Authors:Richard S Judson [ctb, ths], Dayne L Filer [aut], Jason Brown [cre], Sarah E Davidson-Fritz [ctb], Madison Feshuk [ctb], Carter Thunes [ctb], Ashley Ko [ctb], Kelly Carstens [ctb], Todd Zurlinden [ctb], Lori Kolaczkowski [ctb], Kurt Dunham [ctb], Parth Kothiya [ctb], Woodrow R Setzer [ctb], Matthew T Martin [ctb, ths], Katie Paul Friedman [ctb]

tcpl_3.1.0.tar.gz
tcpl_3.1.0.zip(r-4.5)tcpl_3.1.0.zip(r-4.4)tcpl_3.1.0.zip(r-4.3)
tcpl_3.1.0.tgz(r-4.4-any)tcpl_3.1.0.tgz(r-4.3-any)
tcpl_3.1.0.tar.gz(r-4.5-noble)tcpl_3.1.0.tar.gz(r-4.4-noble)
tcpl_3.1.0.tgz(r-4.4-emscripten)tcpl_3.1.0.tgz(r-4.3-emscripten)
tcpl.pdf |tcpl.html✨
tcpl/json (API)
NEWS

# Install 'tcpl' in R:
install.packages('tcpl', repos = c('https://usepa.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/usepa/comptox-toxcast-tcpl/issues

Datasets:
  • invitrodb_dd - Short descriptions of fields for different tables are stored in a data dictionary.
  • load_data_columns - Lists of column names returned from tcplLoadData invitrodb v4.1 (same as CCTE Bioactivity API version).
  • mc_test - List of lists containing queries sent to tcplQuery associated with each test case. Each list also contains the associated ids with each case. Only meant to be used with automated testing with mocking for mc data.
  • mc_vignette - List with multi-concentration data for the vignette
  • mcdat - A subset of ToxCast data showing changes in the activity of the intracellular estrogen receptor.
  • sc_test - List of lists containing queries sent to tcplQuery associated with each test case. Each list also contains the associated ids with each case. Only meant to be used with automated testing with mocking for sc data.
  • sc_vignette - List with single-concentration data for the vignette
  • scdat - A subset of ToxCast data showing changes in transcription factor activity for multiple targets.
  • test_api - List containing ids used for different automated tests of tcpl integration with the CTX APIs, randomly selected from what is available via API.

On CRAN:

cctecomptoxord

56 exports 28 stars 3.85 score 90 dependencies 3 mentions 83 scripts 1.5k downloads

Last updated 9 days agofrom:3c92de418c. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILSep 10 2024
R-4.5-winWARNINGSep 10 2024
R-4.5-linuxWARNINGSep 10 2024
R-4.4-winWARNINGSep 10 2024
R-4.4-macWARNINGSep 10 2024
R-4.3-winWARNINGSep 10 2024
R-4.3-macWARNINGSep 10 2024

Exports:lulwsink.resettcplAddModeltcplAICProbtcplCode2CASNtcplConftcplConfDefaulttcplConfListtcplConfLoadtcplConfResettcplConfSavetcplCytoPttcpldbStatstcplDefinetcplFittcplGetAeidtcplHillACXXtcplHillConctcplHillValtcplListFldstcplLoadAcidtcplLoadAeidtcplLoadAidtcplLoadAsidtcplLoadChemtcplLoadChemListtcplLoadDatatcplLvlCounttcplMakeAeidMultiPltstcplMakeAeidPltstcplMakeChidMultiPltstcplMthdAssigntcplMthdCleartcplMthdListtcplMthdLoadtcplMultiplottcplObjCnsttcplObjGnlstcplObjHilltcplPlottcplPlotFitctcplPlotFitstcplPlotLoadDatatcplPlotM4IDtcplPlotPlatetcplPrepOtpttcplQuerytcplQueryAPItcplRegistertcplRuntcplSendQuerytcplSubsetChidtcplUpdatetcplVarMattcplWriteLvl0

Dependencies:askpassbase64encbitbit64blobbslibcachemchronclicolorspacecpp11crosstalkctxRcurldata.tableDBIdigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegridExtragsubfngtablehighrhmshtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimemunsellnlmenumDerivopensslpillarpkgconfigplogrplotlypromisesprotopurrrR6rappdirsRColorBrewerRcpprlangRMariaDBrmarkdownRSQLitesassscalessqldfstringistringrsystcplfit2tibbletidyrtidyselecttimechangetinytextriebeardurltoolsutf8vctrsviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Generate query for assay information.buildAssayQ
Convert assay names to their abbreviations.convertNames
Load data for tcpl6.load6DR
Plot plate heatmap.plateHeat
Paste appropriate table name to field name.prepField
Shift the baseline to 0blineShift
Function that checks if the most recent v3 table schema is used in the database schemacheck_tcpl_db_schema
Functions for configuring the tcpl packageConfigure functions tcplConf tcplConfDefault tcplConfList tcplConfLoad tcplConfReset tcplConfSave
Calculate the weighted mean of a square to detect plate flaresflareFunc
Functions to solve the Hill modelHill model utilites tcplHillACXX tcplHillConc tcplHillVal
Calculate the weighted mean of a square to detect interlace effectinterlaceFunc
Short descriptions of fields for different tables are stored in a data dictionary.invitrodb_dd
Check for odd numbersis.odd
Functions for loading assay informationLoad assay information tcplLoadAcid tcplLoadAeid tcplLoadAid tcplLoadAsid
Lists of column names returned from tcplLoadData invitrodb v4.1 (same as CCTE Bioactivity API version).load_data_columns
Abbreviation for 'length(unique(x))'lu
Abbreviation for 'length(which(x))'lw
List of lists containing queries sent to tcplQuery associated with each test case. Each list also contains the associated ids with each case. Only meant to be used with automated testing with mocking for mc data.mc_test
List with multi-concentration data for the vignettemc_vignette
Perform level 1 multiple-concentration processingmc1
Perform level 2 multiple-concentration processingmc2
List of level 2 multiple-concentration correction functionsMC2_Methods mc2_mthds
Perform level 3 multiple-concentration processingmc3
List of level 3 multiple-concentration normalization methodsMC3_Methods mc3_mthds
Perform level 4 multiple-concentration processingmc4
List of level 4 multiple-concentration methods for calculating bmadMC4_Methods mc4_mthds
Perform level 5 multiple-concentration processingmc5
Load list of level 5 multiple-concentration cutoff methodsMC5_Methods mc5_mthds
Perform level 6 multiple-concentration processingmc6
Load list of level 6 multiple-concentration flag methodsMC6_Methods mc6_mthds
A subset of ToxCast data showing changes in the activity of the intracellular estrogen receptor.mcdat
Functions for managing processing methodsMethod functions tcplMthdAssign tcplMthdClear tcplMthdList tcplMthdLoad
Model objective functionsModels tcplObjCnst tcplObjGnls tcplObjHill
Wrappers for sending queries and fetching resultsQuery functions tcplQuery tcplQueryAPI tcplSendQuery
Functions for registering & updating annotation informationRegister/update annotation tcplRegister tcplUpdate
Add a new analysis methodregisterMthd
List of lists containing queries sent to tcplQuery associated with each test case. Each list also contains the associated ids with each case. Only meant to be used with automated testing with mocking for sc data.sc_test
List with single-concentration data for the vignettesc_vignette
Perform level 1 single-concentration processingsc1
List of level 1 single-concentration normalization functionsSC1_Methods sc1_mthds
Perform level 2 single-concentration processingsc2
List of level 2 single-concentration hit-call functionsSC2_Methods sc2_mthds
A subset of ToxCast data showing changes in transcription factor activity for multiple targets.scdat
Reset all sinkssink.reset
Draw a tcpl Model onto an existing plottcplAddModel
Calculate the AIC probabilitiestcplAICProb
Append rows to a tabletcplAppend
Do a cascading delete on tcpl screening datatcplCascade
Convert chemical code to CAS Registry NumbertcplCode2CASN
Calculate the cytotoxicity point based on the "burst" endpointstcplCytoPt
Get summary statistics for the databasetcpldbStats
Load data dictionary descriptionstcplDefine
Delete rows from tcpl databasestcplDelete
Fit the data with the constant, hill, and gain-loss modelstcplFit
tcpl Wrapper for tcplfit2_core including additional calculations to fit into new schematcplFit2
Nest dataframe into a list that is readable by tcplfit2tcplFit2_nest
Unnest tcplfit2 parameters into a dataframetcplFit2_unnest
get Aeid for endpoint nametcplGetAeid
tcplggplottcplggplot
tcplggplotComparetcplggplotCompare
Hitcalling with tcplfit2tcplHit2
Load the field names for a tabletcplListFlds
Load sample/chemical informationtcplLoadChem
Load chemical list informationtcplLoadChemList
Load concentration units for assay endpointstcplLoadConcUnit
Load tcpl datatcplLoadData
Load response units for assay endpointstcplLoadUnit
Load tcpl level countstcplLvlCount
Create a .pdf with all dose-response plots for a given aeid, 6 per pagetcplMakeAeidMultiPlts
Create a .pdf with dose-response plotstcplMakeAeidPlts
Create a .pdf with all dose-response plots for a given chid, 6 per pagetcplMakeChidMultiPlts
Plot summary fits based on fit and dose-response datatcplMultiplot
#--------------------------- Generic Plotting Function for tcpltcplPlot
Plot the fit category treetcplPlotFitc
Plot summary fits based on fit and dose-response datatcplPlotFits
Utility function to load data for tcplPlottcplPlotLoadData
tcplPlotlyPlottcplPlotlyPlot
Plot fit summary plot by m4idtcplPlotM4ID
Plot plate heatmaptcplPlotPlate
Map assay/chemical ID values to annotation informationtcplPrepOtpt
Perform data processingtcplRun
Subset level 5 data to a single sample per chemicaltcplSubsetChid
Create chemical by assay matricestcplVarMat
Write screening data into the tcpl databasestcplWriteData
Write level 0 screening data into the tcpl databasestcplWriteLvl0
List containing ids used for different automated tests of tcpl integration with the CTX APIs, randomly selected from what is available via API.test_api
Write level 4 with updated schemawrite_lvl_4