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ToxicoGx

A statistical analysis package for use exploring the relationship between toxicity and gene expression in specific cell types. The package includes a specialized object, the ToxicoSet, which allows unified storage of all data related to a specific toxico-genomic study. Methods accepting this object are inlcuded for summarize results and annotaiton, conduct various analyses as well as to visualize the results thereof.

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Version

Install

install.packages('ToxicoGx')

Monthly Downloads

8

Version

0.1.1

License

MIT + file LICENSE

Maintainer

Benjamin HaibeKains

Last Published

January 20th, 2020

Functions in ToxicoGx (0.1.1)

drugTimeResponseCurve

Compares viabilities at a given dose over different experimental durations
.saveTSetAsGroundTruth

Generate data to test a tSet object and class accessor methods
downloadTSet

Download a ToxicoSet object
drugInfo

drugInfo Generic
msg_verbose

Message if verbose
drugNames<-

drugNames<- Generic
names,ToxicoSet-method

tSet Name
rankGeneDrugPerturbation

Rank genes based on drug effect
pharmacoSettoToxicoSet

Coerce pSet to tSet
geneDrugPerturbation

Compute gene-drug associations
ToxicoSet

ToxicoSet constructor
drugPerturbationSig

Drug perturbation analysis
drugNames

drugNames Generic
summarizeSensitivityProfiles

Takes the sensitivity data from a ToxicoSet, and summarises them into a drug vs cell line table
show,ToxicoSig-method

Show ToxicoGx Signatures
show,ToxicoSet-method

Show a ToxicoSet
summarizeMolecularProfiles

Takes molecular data from a ToxicoSet, and summarises them into one entry per drug and experimental condition.
mDataNames,ToxicoSet-method

mDataNames
logLogisticRegression

Fits curves of the form E = E_inf + (1 - E_inf)/(1 + (c/EC50)^HS) to dose-response data points (c, E) given by the user and returns a vector containing estimates for HS, E_inf, and EC50.
subsetTo

A function to subset a ToxicoSet to data containing only specified drugs, cells and genes
updateCellId

A function to update cell ids
[,ToxicoSet,ANY,ANY,ANY-method

`[`
drugInfo<-

drugInfo<- Generic
drugGeneResponseCurve

Compares gene expression for a specificed set of features over specific drug dosages vs time
showSigAnnot

Show the Annotations of a signature object
updateDrugId

A function to update drug ids
warn_verbose

Warning if verbose
computeAUC

Computes the AUC for a Drug Dose Viability Curve
checkTSetStructure

A function to verify the structure of a ToxicoSet
dim,ToxicoSet-method

Get the dimensions of a ToxicoSet
TGGATESsmall

TGGATESsmall dataset
computeIC50

Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve
HCC_sig

HCC_sig dataset
ToxicoSet-class

Class to contain Toxico-genomic Data
availableTSets

Return a table of ToxicoSets available for download
ToxicoSig

ToxicoSig Constructor