Analysis of Large-Scale Toxico-Genomic Data

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Documentation for package ‘ToxicoGx’ version 2.4.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

A C D F H L M N P S T U misc

-- A --

annotation	Accessing and modifying information in a 'CoreSet'
annotation-method	Accessing and modifying information in a 'CoreSet'
annotation<-	Accessing and modifying information in a 'CoreSet'
annotation<--method	Accessing and modifying information in a 'CoreSet'
availableTSets	Return a table of ToxicoSets available for download

-- C --

cellInfo	Accessing and modifying information in a 'CoreSet'
cellInfo-method	Accessing and modifying information in a 'CoreSet'
cellInfo<-	Accessing and modifying information in a 'CoreSet'
cellInfo<--method	Accessing and modifying information in a 'CoreSet'
cellName-method	Accessing and modifying information in a 'CoreSet'
cellNames	Accessing and modifying information in a 'CoreSet'
cellNames<-	Accessing and modifying information in a 'CoreSet'
cellNames<--method	Accessing and modifying information in a 'CoreSet'
checkTSetStructure	A function to verify the structure of a ToxicoSet
computeAUC	Computes the AUC for a Drug Dose Viability Curve
computeIC50	Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve
computeICn	Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve
computeLimmaDiffExpr	Generic method for performing differential expression analysis on an S4 object using the limma package
computeLimmaDiffExpr-method	Conduct differential expression analysis using the limma R pacakge
curation	Accessing and modifying information in a 'CoreSet'
curation-method	Accessing and modifying information in a 'CoreSet'
curation<-	Accessing and modifying information in a 'CoreSet'
curation<--method	Accessing and modifying information in a 'CoreSet'

-- D --

datasetType	Accessing and modifying information in a 'CoreSet'
datasetType-method	Accessing and modifying information in a 'CoreSet'
datasetType<-	Accessing and modifying information in a 'CoreSet'
datasetType<--method	Accessing and modifying information in a 'CoreSet'
dateCreated	Accessing and modifying information in a 'CoreSet'
dateCreated-method	Accessing and modifying information in a 'CoreSet'
dateCreated<-	Accessing and modifying information in a 'CoreSet'
dateCreated<--method	Accessing and modifying information in a 'CoreSet'
dim-method	Get the dimensions of a ToxicoSet
downloadTSet	Download a ToxicoSet object
drugGeneResponseCurve	Compares gene expression for a specificed set of features over specific drug dosages vs time
drugInfo	Accessing and modifying information in a 'CoreSet'
drugInfo<-	Accessing and modifying information in a 'CoreSet'
drugNames	Accessing and modifying information in a 'CoreSet'
drugNames<-	Accessing and modifying information in a 'CoreSet'
drugPerturbationSig	Drug perturbation analysis
drugTimeResponseCurve	Compares viabilities at a given dose over different experimental durations

-- F --

featureInfo	Accessing and modifying information in a 'CoreSet'
featureInfo-method	Accessing and modifying information in a 'CoreSet'
featureInfo<-	Accessing and modifying information in a 'CoreSet'
featureInfo<--method	Accessing and modifying information in a 'CoreSet'
fNames	Accessing and modifying information in a 'CoreSet'
fNames-method	Accessing and modifying information in a 'CoreSet'
fNames<-	Accessing and modifying information in a 'CoreSet'
fNames<--method	Accessing and modifying information in a 'CoreSet'

-- H --

HCC_sig

HCC_sig dataset

-- L --

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.

-- M --

mDataNames	Accessing and modifying information in a 'CoreSet'
mDataNames-method	Accessing and modifying information in a 'CoreSet'
mDataNames<-	Accessing and modifying information in a 'CoreSet'
mDataNames<--method	Accessing and modifying information in a 'CoreSet'
molecularProfiles	Accessing and modifying information in a 'CoreSet'
molecularProfiles-method	Accessing and modifying information in a 'CoreSet'
molecularProfiles<-	Accessing and modifying information in a 'CoreSet'
molecularProfiles<--method	Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot	Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot-method	Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot<-	Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot<--method	Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot<-ToxicoSet-method	Accessing and modifying information in a 'CoreSet'
moleculerProfilesSlot-method	Accessing and modifying information in a 'CoreSet'

-- N --

name	Accessing and modifying information in a 'CoreSet'
name-method	Accessing and modifying information in a 'CoreSet'
name<-	Accessing and modifying information in a 'CoreSet'
name<--method	Accessing and modifying information in a 'CoreSet'

-- P --

pertNumber	Accessing and modifying information in a 'CoreSet'
pertNumber-method	Accessing and modifying information in a 'CoreSet'
pertNumber<-	Accessing and modifying information in a 'CoreSet'
pertNumber<--method	Accessing and modifying information in a 'CoreSet'
phenoInfo	Accessing and modifying information in a 'CoreSet'
phenoInfo-method	Accessing and modifying information in a 'CoreSet'
phenoInfo<-	Accessing and modifying information in a 'CoreSet'
phenoInfo<--method	Accessing and modifying information in a 'CoreSet'

-- S --

sampleInfo	Accessing and modifying information in a 'CoreSet'
sampleInfo-method	Accessing and modifying information in a 'CoreSet'
sampleInfo<-	Accessing and modifying information in a 'CoreSet'
sampleInfo<--method	Accessing and modifying information in a 'CoreSet'
sampleName-method	Accessing and modifying information in a 'CoreSet'
sampleNames	Accessing and modifying information in a 'CoreSet'
sampleNames-method	Accessing and modifying information in a 'CoreSet'
sampleNames<-	Accessing and modifying information in a 'CoreSet'
sampleNames<--method	Accessing and modifying information in a 'CoreSet'
sensitivityInfo-method	Accessing and modifying information in a 'CoreSet'
sensitivityInfo<--method	Accessing and modifying information in a 'CoreSet'
sensitivityMeasures-method	Accessing and modifying information in a 'CoreSet'
sensitivityMeasures<--method	Accessing and modifying information in a 'CoreSet'
sensitivityProfiles-method	Accessing and modifying information in a 'CoreSet'
sensitivityProfiles<--method	Accessing and modifying information in a 'CoreSet'
sensitivityRaw-method	Accessing and modifying information in a 'CoreSet'
sensitivityRaw<--method	Accessing and modifying information in a 'CoreSet'
sensitivitySlot	Accessing and modifying information in a 'CoreSet'
sensitivitySlot<-	Accessing and modifying information in a 'CoreSet'
sensitvityInfo<--method	Accessing and modifying information in a 'CoreSet'
sensNumber	Accessing and modifying information in a 'CoreSet'
sensNumber-method	Accessing and modifying information in a 'CoreSet'
sensNumber<-	Accessing and modifying information in a 'CoreSet'
sensNumber<--method	Accessing and modifying information in a 'CoreSet'
show-method	Show a ToxicoSet
show-method	Show ToxicoGx Signatures
showSigAnnot	Show the Annotations of a signature object
subsetTo	A function to subset a ToxicoSet to data containing only specified drugs, cells and genes
summarizeMolecularProfiles	Takes molecular data from a ToxicoSet, and summarises them into one entry per drug and experimental condition.
summarizeSensitivityProfiles	Takes the sensitivity data from a ToxicoSet, and summarises them into a drug vs cell line table

-- T --

TGGATESsmall	TGGATESsmall dataset
ToxicoSet	ToxicoSet constructor
ToxicoSet-accessors	Accessing and modifying information in a 'CoreSet'
ToxicoSet-class	Class to contain Toxico-genomic Data
treamentResponse<--method	Accessing and modifying information in a 'CoreSet'
treatmentInfo	Accessing and modifying information in a 'CoreSet'
treatmentInfo-method	Accessing and modifying information in a 'CoreSet'
treatmentInfo<-	Accessing and modifying information in a 'CoreSet'
treatmentInfo<--method	Accessing and modifying information in a 'CoreSet'
treatmentNames	Accessing and modifying information in a 'CoreSet'
treatmentNames-method	Accessing and modifying information in a 'CoreSet'
treatmentNames<-	Accessing and modifying information in a 'CoreSet'
treatmentNames<--method	Accessing and modifying information in a 'CoreSet'
treatmentResponse	Accessing and modifying information in a 'CoreSet'
treatmentResponse-method	Accessing and modifying information in a 'CoreSet'
treatmentResponse<-	Accessing and modifying information in a 'CoreSet'
treatmentResponse<--method	Accessing and modifying information in a 'CoreSet'

-- U --

updateObject-method

Update the ToxicoSet class after changes in it struture or API

-- misc --

.ToxicoSet	Class to contain Toxico-genomic Data
[-method	'['