toxboot: Bootstrap Methods for 'ToxCast' High Throughput Screening Data

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Provides methods to use bootstrapping to quantify uncertainty in fitting 'ToxCast' concentration response data. Data is stored in memory, written to file, or stored in 'MySQL' or 'MongoDB' databases.

Author
Eric D. Watt [aut, cre]
Date of publication
2016-08-23 20:00:18
Maintainer
Eric D. Watt <eric@ericdwatt.com>
License
MIT + file LICENSE
Version
0.1.1
URLs

View on CRAN

Man pages

dat1000
Bootstrap results for m4id = 9057756 using 1000 replicates
dat10000
Bootstrap results for m4id = 9057756 using 10000 replicates
erl3data
Concentration response data from 200 ER assay curves
erl5data
Fit parameters, model selection, and hit calls from 200 ER...
gnls_curve
Gain Loss Curve.
hill_curve
Hill Curve.
listTonumeric
Convert x to numeric if x is a list.
nullToNA
Replace NULL values with NA.
toxboot
Main function to sample, fit, and write results to mongoDB
toxboot_config_funcs
Functions for configuring the toxboot package
toxbootConnectMongo
Setup connection to toxboot MongoDB
toxbootGetMongoFields
Query mongoDB and get requested fields
toxbootGetMySQLFields
Function to query toxboot results from MySQL
toxbootGetOpts
DEPRECATED
toxbootHitParamCI
Performs Hit Call and Model Winner Selection on Bootstrap...
toxbootmc
Filter and multicore wrapper for 'toxboot'
toxbootMongoCount
Get number of documents that match query.
toxbootMysqlCreateTable
Function to create properly formatted toxboot table in MySQL
toxbootProjectionBuild
Build projection for toxboot MongoDB
toxbootQueryBuild
Build query for toxboot MongoDB
toxbootQueryToxCast
Query ToxCast and format data to pass to 'toxboot'
toxbootReplicates
Generates bootstrap samples of dose response data
toxbootSetOpts
DEPRECATED
toxbootWriteMongo
Write bootstrap results to mongoDB

Files in this package

toxboot
toxboot/inst
toxboot/inst/toxboot.config
toxboot/inst/doc
toxboot/inst/doc/toxboot.Rmd
toxboot/inst/doc/toxboot.R
toxboot/inst/doc/toxboot.html
toxboot/tests
toxboot/tests/testthat.R
toxboot/tests/testthat
toxboot/tests/testthat/test_onload.R
toxboot/tests/testthat/test_utilities.R
toxboot/tests/testthat/test_toxboot.R
toxboot/NAMESPACE
toxboot/NEWS.md
toxboot/data
toxboot/data/datalist
toxboot/data/erl5data.rda
toxboot/data/erl3data.rda
toxboot/data/dat10000.rda
toxboot/data/dat1000.rda
toxboot/R
toxboot/R/onLoad.R
toxboot/R/onAttach.R
toxboot/R/toxbootReplicates.R
toxboot/R/hill_gnls_funcs.R
toxboot/R/toxbootSetOpts.R
toxboot/R/toxbootQueryToxCast.R
toxboot/R/toxbootHitParamCI.R
toxboot/R/toxboot.R
toxboot/R/data.R
toxboot/R/toxbootMongoFuncs.R
toxboot/R/config_funcs.R
toxboot/R/toxbootMySQLFuncs.R
toxboot/R/utility_functions.R
toxboot/R/toxbootMySQLSetup.R
toxboot/R/toxbootmc.R
toxboot/R/non_function_objects.R
toxboot/R/toxbootConf.R
toxboot/R/toxbootGetOpts.R
toxboot/R/toxbootMonitorFuncs.R
toxboot/vignettes
toxboot/vignettes/toxboot.Rmd
toxboot/README.md
toxboot/MD5
toxboot/build
toxboot/build/vignette.rds
toxboot/DESCRIPTION
toxboot/man
toxboot/man/toxbootQueryBuild.Rd
toxboot/man/toxbootMysqlCreateTable.Rd
toxboot/man/dat1000.Rd
toxboot/man/toxbootProjectionBuild.Rd
toxboot/man/hill_curve.Rd
toxboot/man/toxbootConnectMongo.Rd
toxboot/man/toxbootSetOpts.Rd
toxboot/man/toxbootGetMySQLFields.Rd
toxboot/man/erl5data.Rd
toxboot/man/toxbootHitParamCI.Rd
toxboot/man/dat10000.Rd
toxboot/man/erl3data.Rd
toxboot/man/toxboot.Rd
toxboot/man/toxbootGetOpts.Rd
toxboot/man/toxbootMongoCount.Rd
toxboot/man/toxbootWriteMongo.Rd
toxboot/man/toxboot_config_funcs.Rd
toxboot/man/toxbootGetMongoFields.Rd
toxboot/man/listTonumeric.Rd
toxboot/man/toxbootQueryToxCast.Rd
toxboot/man/nullToNA.Rd
toxboot/man/toxbootmc.Rd
toxboot/man/gnls_curve.Rd
toxboot/man/toxbootReplicates.Rd
toxboot/LICENSE