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tcpl (version 1.2.2)

ToxCast Data Analysis Pipeline

Description

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.

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Version

Install

install.packages('tcpl')

Monthly Downloads

849

Version

1.2.2

License

GPL-2

Maintainer

Dayne L Filer

Last Published

May 18th, 2016

Functions in tcpl (1.2.2)

MC6_Methods

Load list of level 6 multiple-concentration flag methods
Method functions

Functions for managing processing methods
MC2_Methods

List of level 2 multiple-concentration correction functions
interlaceFunc

Calculate the weighted mean of a square to detect interlace effect
Register/update annotation

Functions for registering & updating annotation information
SC2_Methods

List of level 2 single-concentration hit-call functions
Hill model utilites

Functions to solve the Hill model
Models

Model objective functions
mc6

Perform level 6 multiple-concentration processing
mc1

Perform level 1 multiple-concentration processing
Configure functions

Functions for configuring the tcpl package
mc3

Perform level 3 multiple-concentration processing
mc2

Perform level 2 multiple-concentration processing
sc2

Perform level 2 single-concentration processing
Query functions

Wrappers for sending queries and fetching results
tcplListFlds

Load the field names for a table
tcplPlotFits

Plot summary fits based on fit and dose-response data
tcplAppend

Append rows to a table
tcplPrepOtpt

Map assay/chemcial ID values to annotation information
is.odd

Check for odd numbers
tcplLoadUnit

Load response units for assay endpoints
tcplMakeAeidPlts

Create a .pdf with dose-response plots
tcplCode2CASN

Convert chemical code to CAS Registry Number
tcplSubsetChid

Subset level 5 data to a single sample per chemical
blineShift

Shift the baseline to 0
tcplPlotFitc

Plot the fit category tree
tcplLoadClib

Load chemical library information
tcplPlotM4ID

Plot fit summary plot by m4id
tcplDelete

Delete rows from tcpl databases
tcplRun

Perform data processing
mc4

Perform level 4 multiple-concentration processing
tcplLoadData

Load tcpl data
lw

Abbreviation for length(which(x))
MC3_Methods

List of level 3 multiple-concentration normalization methods
tcplCytoPt

Calculate the cytotoxicity point based on the "burst" endpoints
tcplPlotPlate

Plot plate heatmap
tcplWriteLvl0

Write level 0 screening data into the tcpl databases
tcplWriteData

Write screening data into the tcpl databases
tcplVarMat

Create chemical by assay matrices
tcplLoadChem

Load sample/chemical information
Load assay information

Functions for loading assay information
tcplCascade

Do a cascading delete on tcpl screening data
mc5

Perform level 5 multiple-concentration processing
sc1

Perform level 1 single-concentration processing
registerMthd

Add a new analysis method
tcplFit

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

Calculate the weighted mean of a square to detect plate flares
MC5_Methods

Load list of level 5 multiple-concentration cutoff methods
lu

Abbreviation for length(unique(x))
tcplAddModel

Draw a tcpl Model onto an exisiting plot
tcplAICProb

Calculate the AIC probabilities
SC1_Methods

List of level 1 single-concentration normalization functions
sink.reset

Reset all sinks