# ToxCast Data Analysis Pipeline

## Documentation for package ‘tcpl’ version 3.3.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

B C D F G H I L M Q R S T W misc

## -- B --

blineShift | Shift the baseline to 0

## -- C --

check_tcpl_db_schema | Function that checks if the most recent v3 table schema is used in the database schema
Configure functions | Functions for configuring the tcpl package

## -- D --

dynamic_table_trunc | dynamic_table_trunc Dynamically truncate lengths of column values of they are longer than a calculated width. Strings contained in verbose table output can be very long, and this function ensures that the 128 character row limit is kept while growing/shrinking default columns widths that may or may not need the space.

## -- F --

flareFunc | Calculate the weighted mean of a square to detect plate flares

## -- G --

get_plot_caption | get_plot_caption Generate plot caption given number of flags and length of unique elements
get_plot_title | get_plot_title Generate plot title given number of rows and length of unique elements
get_verbose_tables | get_verbose_tables Generates 'gt' package tables containing annotations and level 5 metrics

## -- H --

Hill model utilites | Functions to solve the Hill model

## -- I --

interlaceFunc | Calculate the weighted mean of a square to detect interlace effect
invitrodb_dd | Short descriptions of fields for different tables are stored in a data dictionary.
is.odd | Check for odd numbers

## -- L --

Load assay information | Functions for loading assay information
load_data_columns | Lists of column names returned from tcplLoadData invitrodb v4.1 (same as CCTE Bioactivity API version).
lu | Abbreviation for 'length(unique(x))'
lw | Abbreviation for 'length(which(x))'

## -- M --

mc1 | Perform level 1 multiple-concentration processing
mc2 | Perform level 2 multiple-concentration processing
MC2_Methods | List of level 2 multiple-concentration correction functions
mc2_mthds | 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
mc3_mthds | List of level 3 multiple-concentration normalization methods
mc4 | Perform level 4 multiple-concentration processing
MC4_Methods | List of level 4 multiple-concentration methods for calculating bmad
mc4_mthds | List of level 4 multiple-concentration methods for calculating bmad
mc5 | Perform level 5 multiple-concentration processing
MC5_Methods | Load list of level 5 multiple-concentration cutoff methods
mc5_mthds | 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
mc6_mthds | Load list of level 6 multiple-concentration flag methods
mcdat | A subset of ToxCast data showing changes in the activity of the intracellular estrogen receptor.
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
Method functions | Functions for managing processing methods
Models | Model objective functions
MORELETTERS | MORELETTERS Extends LETTERS recursively to any number of letters
mthd_list_defaults | Lists of data frames returned from tcplMthdList invitrodb v4.2

## -- Q --

Query functions | Wrappers for sending queries and fetching results

## -- R --

Register/update annotation | Functions for registering & updating annotation information
registerMthd | Add a new analysis method
round_n | round_n General function to round/shorten values for plotting tables

## -- S --

sc1 | Perform level 1 single-concentration processing
SC1_Methods | List of level 1 single-concentration normalization functions
sc1_mthds | 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
sc2_mthds | List of level 2 single-concentration hit-call functions
scdat | A subset of ToxCast data showing changes in transcription factor activity for multiple targets.
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
sink.reset | Reset all sinks

## -- T --

tcplAddModel | Draw a tcpl Model onto an existing 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
tcplConf | Functions for configuring the tcpl package
tcplConfDefault | Functions for configuring the tcpl package
tcplConfList | Functions for configuring the tcpl package
tcplConfLoad | Functions for configuring the tcpl package
tcplConfReset | Functions for configuring the tcpl package
tcplConfSave | Functions for configuring the tcpl package
tcplCytoPt | Calculate the cytotoxicity point based on the "burst" endpoints
tcpldbStats | Get summary statistics for the database
tcplDefine | Load data dictionary descriptions
tcplDelete | Delete rows from tcpl databases
tcplFit | Fit the data with the constant, hill, and gain-loss models
tcplFit2 | tcpl Wrapper for tcplfit2_core including additional calculations to fit into new schema
tcplfit2_fun | tcplfit2_fun Returns tcplfit2 function for drawing models given input
tcplFit2_nest | Nest dataframe into a list that is readable by tcplfit2
tcplFit2_unnest | Unnest tcplfit2 parameters into a dataframe
tcplGetAeid | get Aeid for endpoint name
tcplggplot2 | tcplggplot2
tcplHillACXX | Functions to solve the Hill model
tcplHillConc | Functions to solve the Hill model
tcplHillVal | Functions to solve the Hill model
tcplHit2 | Hitcalling with tcplfit2
tcplLegacyPlot | tcplLegacyPlot
tcplListFlds | Load the field names for a table
tcplLoadAcid | Functions for loading assay information
tcplLoadAeid | Functions for loading assay information
tcplLoadAid | Functions for loading assay information
tcplLoadAsid | Functions for loading assay information
tcplLoadChem | Load sample/chemical information
tcplLoadChemList | Load chemical list information
tcplLoadConcUnit | Load concentration units for assay endpoints
tcplLoadData | Load tcpl data
tcplLoadUnit | Load response units for assay endpoints
tcplLvlCount | Load tcpl level counts
tcplMakeAeidMultiPlts | Create a .pdf with all dose-response plots for a given aeid, 6 per page
tcplMakeAeidPlts | Create a .pdf with dose-response plots
tcplMakeChidMultiPlts | Create a .pdf with all dose-response plots for a given chid, 6 per page
tcplMthdAssign | Functions for managing processing methods
tcplMthdClear | Functions for managing processing methods
tcplMthdList | Functions for managing processing methods
tcplMthdLoad | Functions for managing processing methods
tcplMultiplot | Plot summary fits based on fit and dose-response data
tcplObjCnst | Model objective functions
tcplObjGnls | Model objective functions
tcplObjHill | Model objective functions
tcplPlot | Generic Plotting Function for tcpl
tcplPlotCalcAspectRatio | tcplPlotCalcAspectRatio
tcplPlotFitc | Plot the fit category tree
tcplPlotFits | Plot summary fits based on fit and dose-response data
tcplPlotLoadData | Utility function to load data for tcplPlot
tcplPlotLoadWllt | tcplPlotLoadWllt Replaces NA dtxsid and chnm with a string description of the sample's well type(s)
tcplPlotlyPlot | tcplPlotlyPlot
tcplPlotM4ID | Plot fit summary plot by m4id
tcplPlotPlate | Plot plate heatmap
tcplPlotSetYRange | tcplPlotSetYRange
tcplPlotValidate | tcplPlotValidate
tcplPrepOtpt | Map assay/chemical ID values to annotation information
tcplQuery | Wrappers for sending queries and fetching results
tcplQueryAPI | Wrappers for sending queries and fetching results
tcplRegister | Functions for registering & updating annotation information
tcplRun | Perform data processing
tcplSendQuery | Wrappers for sending queries and fetching results
tcplSubsetChid | Subset level 5 data to a single sample per chemical
tcplUpdate | Functions for registering & updating annotation information
tcplVarMat | Create chemical by assay matrices
tcplWriteData | Write screening data into the tcpl databases
tcplWriteLvl0 | Write level 0 screening data into the tcpl databases
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.

## -- W --

write_lvl_4 | Write level 4 with updated schema

## -- misc --

.buildAssayQ | Generate query for assay information
.ChemListQ | Function to support queries by chemical
.ChemQ | Function to support queries by chemical
.convertNames | Convert assay names to their abbreviations
.load6DR | Load data for tcpl6
.plateHeat | Plot plate heatmap
.prepField | Paste appropriate table name to field name