tcpl3.3.0 package

Functions for loading assay information

Shift the baseline to 0

Function that checks if the most recent v3 table schema is used in the...

Functions for configuring the tcpl package

Generate query for assay information

Function to support queries by chemical

Function to support queries by chemical

Convert assay names to their abbreviations

Load data for tcpl6

Plot plate heatmap

Paste appropriate table name to field name

dynamic_table_trunc Dynamically truncate lengths of column values of t...

Calculate the weighted mean of a square to detect plate flares

get_plot_caption Generate plot caption given number of flags and lengt...

get_plot_title Generate plot title given number of rows and length of ...

get_verbose_tables Generates 'gt' package tables containing annotation...

Functions to solve the Hill model

Calculate the weighted mean of a square to detect interlace effect

Check for odd numbers

Abbreviation for length(unique(x))

Abbreviation for length(which(x))

Perform level 1 multiple-concentration processing

List of level 2 multiple-concentration correction functions

Perform level 2 multiple-concentration processing

List of level 3 multiple-concentration normalization methods

Perform level 3 multiple-concentration processing

List of level 4 multiple-concentration methods for calculating bmad

Perform level 4 multiple-concentration processing

Load list of level 5 multiple-concentration cutoff methods

Perform level 5 multiple-concentration processing

Load list of level 6 multiple-concentration flag methods

Perform level 6 multiple-concentration processing

Model objective functions

MORELETTERS Extends LETTERS recursively to any number of letters

Functions for managing processing methods

Wrappers for sending queries and fetching results

Add a new analysis method

Functions for registering & updating annotation information

round_n General function to round/shorten values for plotting tables

List of level 1 single-concentration normalization functions

Perform level 1 single-concentration processing

List of level 2 single-concentration hit-call functions

Perform level 2 single-concentration processing

Reset all sinks

Draw a tcpl Model onto an existing plot

Calculate the AIC probabilities

Append rows to a table

Do a cascading delete on tcpl screening data

Convert chemical code to CAS Registry Number

Calculate the cytotoxicity point based on the "burst" endpoints

Get summary statistics for the database

Load data dictionary descriptions

Delete rows from tcpl databases

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

tcplfit2_fun Returns tcplfit2 function for drawing models given input

Nest dataframe into a list that is readable by tcplfit2

Unnest tcplfit2 parameters into a dataframe

tcpl Wrapper for tcplfit2_core including additional calculations to fi...

get Aeid for endpoint name

tcplggplot2

Hitcalling with tcplfit2

tcplLegacyPlot

Load the field names for a table

Load sample/chemical information

Load chemical list information

Load concentration units for assay endpoints

Load tcpl data

Load response units for assay endpoints

Load tcpl level counts

Create a .pdf with all dose-response plots for a given aeid, 6 per pag...

Create a .pdf with dose-response plots

Create a .pdf with all dose-response plots for a given chid, 6 per pag...

Plot summary fits based on fit and dose-response data

Generic Plotting Function for tcpl

tcplPlotCalcAspectRatio

Plot the fit category tree

Plot summary fits based on fit and dose-response data

Utility function to load data for tcplPlot

tcplPlotLoadWllt Replaces NA dtxsid and chnm with a string description...

tcplPlotlyPlot

Plot fit summary plot by m4id

Plot plate heatmap

tcplPlotSetYRange

tcplPlotValidate

Map assay/chemical ID values to annotation information

Perform data processing

Subset level 5 data to a single sample per chemical

Create chemical by assay matrices

Write screening data into the tcpl databases

Write level 0 screening data into the tcpl databases

Write level 4 with updated schema