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.

Install the latest version of this package by entering the following in R:
install.packages("tcpl")
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

Functions

blineShift Man page
Configure functions Man page
flareFunc Man page
Hill model utilites Man page
interlaceFunc Man page
is.odd Man page
Load assay information Man page
lu Man page
lw Man page
mc1 Man page
mc2 Man page
MC2_Methods Man page
mc2_mthds Man page
mc3 Man page
MC3_Methods Man page
mc3_mthds Man page
mc4 Man page
mc5 Man page
MC5_Methods Man page
mc5_mthds Man page
mc6 Man page
MC6_Methods Man page
mc6_mthds Man page
Method functions Man page
Models Man page
Query functions Man page
registerMthd Man page
Register/update annotation Man page
sc1 Man page
SC1_Methods Man page
sc1_mthds Man page
sc2 Man page
SC2_Methods Man page
sc2_mthds Man page
sink.reset Man page
tcplAddModel Man page
tcplAICProb Man page
tcplAppend Man page
tcplCascade Man page
tcplCode2CASN Man page
tcplConf Man page
tcplConfDefault Man page
tcplConfList Man page
tcplConfLoad Man page
tcplConfReset Man page
tcplConfSave Man page
tcplCytoPt Man page
tcplDelete Man page
tcplFit Man page
tcplHillACXX Man page
tcplHillConc Man page
tcplHillVal Man page
tcplListFlds Man page
tcplLoadAcid Man page
tcplLoadAeid Man page
tcplLoadAid Man page
tcplLoadAsid Man page
tcplLoadChem Man page
tcplLoadClib Man page
tcplLoadData Man page
tcplLoadUnit Man page
tcplMakeAeidPlts Man page
tcplMthdAssign Man page
tcplMthdClear Man page
tcplMthdList Man page
tcplMthdLoad Man page
tcplObjCnst Man page
tcplObjGnls Man page
tcplObjHill Man page
tcplPlotFitc Man page
tcplPlotFits Man page
tcplPlotM4ID Man page
tcplPlotPlate Man page
tcplPrepOtpt Man page
tcplQuery Man page
tcplRegister Man page
tcplRun Man page
tcplSendQuery Man page
tcplSubsetChid Man page
tcplUpdate Man page
tcplVarMat Man page
tcplWriteData Man page
tcplWriteLvl0 Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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