tcpl: 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.

AuthorDayne L Filer [aut, cre], Parth Kothiya [ctb], Woodrow R Setzer [ctb], Richard S Judson [ths], Matthew T Martin [ctb, ths]
Date of publication2016-05-18 06:53:36
MaintainerDayne L Filer <dayne.filer@gmail.com>
LicenseGPL-2
Version1.2.2
http://www.epa.gov/ncct/toxcast/

View on CRAN

Man pages

assay_funcs: Functions for loading assay information

blineShift: Shift the baseline to 0

config_funcs: Functions for configuring the tcpl package

flareFunc: Calculate the weighted mean of a square to detect plate...

hill_utils: Functions to solve the Hill model

interlaceFunc: Calculate the weighted mean of a square to detect interlace...

is.odd: Check for odd numbers

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

mc3: Perform level 3 multiple-concentration processing

MC3_Methods: 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

mc6: Perform level 6 multiple-concentration processing

MC6_Methods: Load list of level 6 multiple-concentration flag methods

Models: Model objective functions

mthd_funcs: Functions for managing processing methods

query_funcs: Wrappers for sending queries and fetching results

registerMthd: Add a new analysis method

rgstr_funcs: Functions for registering & updating annotation information

sc1: Perform level 1 single-concentration processing

SC1_Methods: 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

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

tcplCytoPt: Calculate the cytotoxicity point based on the "burst"...

tcplDelete: Delete rows from tcpl databases

tcplFit: Fit the data with the constant, hill, and gain-loss models

tcplListFlds: Load the field names for a table

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

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

tcplRun: Perform data processing

tcplSubsetChid: Subset level 5 data to a single sample per chemical

tcplVarMat: Create chemical by assay matrices

tcplWriteData: Write screening data into the tcpl databases

tcplWriteLvl0: Write level 0 screening data into the tcpl databases

Files in this package

tcpl
tcpl/inst
tcpl/inst/sql
tcpl/inst/sql/mcdat.csv
tcpl/inst/sql/chdat.csv
tcpl/inst/sql/tcpldb_schema.sql
tcpl/inst/sql/scdat.csv
tcpl/inst/sql/tcpldb.sqlite
tcpl/inst/TCPL.config
tcpl/inst/doc
tcpl/inst/doc/tcpl_Overview.Rnw
tcpl/inst/doc/tcpl_Overview.pdf
tcpl/inst/doc/tcpl_Overview.R
tcpl/NAMESPACE
tcpl/NEWS
tcpl/R
tcpl/R/tcplQuery.R tcpl/R/mc4.R tcpl/R/mc2_mthds.R tcpl/R/tcplConfLoad.R tcpl/R/hill_utils.R tcpl/R/mc1.R tcpl/R/interlaceFunc.R tcpl/R/sc2.R tcpl/R/mc5_mthds.R tcpl/R/assay_funcs.R tcpl/R/tcplMthdLoad.R tcpl/R/tcplSendQuery.R tcpl/R/query_funcs.R tcpl/R/tcplConfList.R tcpl/R/chemQueries.R tcpl/R/onLoad.R tcpl/R/tcplCascade.R tcpl/R/mthd_funcs.R tcpl/R/onAttach.R tcpl/R/tcplLoadAeid.R tcpl/R/tcplLoadChem.R tcpl/R/tcplSubsetChid.R tcpl/R/tcplLoadData.R tcpl/R/tcplRun.R tcpl/R/tcplPrepOtpt.R tcpl/R/sc1.R tcpl/R/tcplLoadClib.R tcpl/R/registerMthd.R tcpl/R/sc1_mthds.R tcpl/R/attachFormals.R tcpl/R/tcplPlotFits.R tcpl/R/plotFit.R tcpl/R/tcplConf.R tcpl/R/tcplConfSave.R tcpl/R/prepField.R tcpl/R/tcplConfDefault.R tcpl/R/mc5.R tcpl/R/tcplPlotPlate.R tcpl/R/lu.R tcpl/R/config_funcs.R tcpl/R/tcplCode2CASN.R tcpl/R/tcplLoadUnit.R tcpl/R/sc2_mthds.R tcpl/R/multProc.R tcpl/R/tcplRegister.R tcpl/R/drawCircles.R tcpl/R/mc3.R tcpl/R/tcplMthdList.R tcpl/R/tcplAppend.R tcpl/R/rgstr_funcs.R tcpl/R/lw.R tcpl/R/tcplVarMat.R tcpl/R/tcplMthdAssign.R tcpl/R/sink.reset.R tcpl/R/tcplObjGnls.R tcpl/R/blineShift.R tcpl/R/plateHeat.R tcpl/R/tcplFit.R tcpl/R/tcplHillACXX.R tcpl/R/tcplAddModel.R tcpl/R/tcplCytoPt.R tcpl/R/buildAssayQ.R tcpl/R/tcplUpdate.R tcpl/R/mc6_mthds.R tcpl/R/tcplPlotM4ID.R tcpl/R/flareFunc.R tcpl/R/tcplMakeAeidPlts.R tcpl/R/mc3_mthds.R tcpl/R/mc6.R tcpl/R/convertNames.R tcpl/R/tcplWriteLvl0.R tcpl/R/tcplConfReset.R tcpl/R/tcplLoadAsid.R tcpl/R/tcplObjCnst.R tcpl/R/tcplLoadAcid.R tcpl/R/mc2.R tcpl/R/tcplHillVal.R tcpl/R/tcplLoadAid.R tcpl/R/tcplListFlds.R tcpl/R/tcplObjHill.R tcpl/R/tcplHillConc.R tcpl/R/tcplWriteData.R tcpl/R/tcplMthdClear.R tcpl/R/is.odd.R tcpl/R/tcplDelete.R tcpl/R/tcplPlotFitc.R tcpl/R/tcplAICProb.R tcpl/R/Models.R tcpl/R/load6DR.R
tcpl/vignettes
tcpl/vignettes/tcpl_Overview.Rnw
tcpl/MD5
tcpl/build
tcpl/build/vignette.rds
tcpl/DESCRIPTION
tcpl/man
tcpl/man/tcplWriteLvl0.Rd tcpl/man/tcplCascade.Rd tcpl/man/tcplFit.Rd tcpl/man/tcplAICProb.Rd tcpl/man/mthd_funcs.Rd tcpl/man/query_funcs.Rd tcpl/man/tcplPlotM4ID.Rd tcpl/man/sc2.Rd tcpl/man/MC5_Methods.Rd tcpl/man/tcplVarMat.Rd tcpl/man/mc6.Rd tcpl/man/SC2_Methods.Rd tcpl/man/config_funcs.Rd tcpl/man/is.odd.Rd tcpl/man/registerMthd.Rd tcpl/man/mc5.Rd tcpl/man/blineShift.Rd tcpl/man/tcplCytoPt.Rd tcpl/man/tcplLoadClib.Rd tcpl/man/tcplLoadChem.Rd tcpl/man/sc1.Rd tcpl/man/tcplWriteData.Rd tcpl/man/mc1.Rd tcpl/man/hill_utils.Rd tcpl/man/mc4.Rd tcpl/man/interlaceFunc.Rd tcpl/man/rgstr_funcs.Rd tcpl/man/tcplPlotFits.Rd tcpl/man/SC1_Methods.Rd tcpl/man/mc2.Rd tcpl/man/sink.reset.Rd tcpl/man/tcplPlotFitc.Rd tcpl/man/tcplRun.Rd tcpl/man/tcplLoadUnit.Rd tcpl/man/tcplSubsetChid.Rd tcpl/man/lu.Rd tcpl/man/tcplLoadData.Rd tcpl/man/tcplPrepOtpt.Rd tcpl/man/tcplAppend.Rd tcpl/man/tcplCode2CASN.Rd tcpl/man/MC3_Methods.Rd tcpl/man/tcplListFlds.Rd tcpl/man/tcplMakeAeidPlts.Rd tcpl/man/Models.Rd tcpl/man/lw.Rd tcpl/man/tcplAddModel.Rd tcpl/man/flareFunc.Rd tcpl/man/tcplPlotPlate.Rd tcpl/man/tcplDelete.Rd tcpl/man/MC2_Methods.Rd tcpl/man/MC6_Methods.Rd tcpl/man/assay_funcs.Rd tcpl/man/mc3.Rd

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