tcpl: ToxCast Data Analysis Pipeline

Share:

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.

Author
Dayne L Filer [aut, cre], Parth Kothiya [ctb], Woodrow R Setzer [ctb], Richard S Judson [ths], Matthew T Martin [ctb, ths]
Date of publication
2016-05-18 06:53:36
Maintainer
Dayne L Filer <dayne.filer@gmail.com>
License
GPL-2
Version
1.2.2
URLs

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