Analysis of Large-Scale Toxico-Genomic Data

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Documentation for package ‘ToxicoGx’ version 1.4.0

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

Help Pages

.ToxicoSet	Class to contain Toxico-genomic Data
annotation	annotation Slot Getter
annotation-method	Class to contain Toxico-genomic Data
annotation<-	annotation<- Slot Setter
annotation<--method	Class to contain Toxico-genomic Data
availableTSets	Return a table of ToxicoSets available for download
cellInfo-method	Class to contain Toxico-genomic Data
cellInfo<--method	Class to contain Toxico-genomic Data
cellNames-method	Class to contain Toxico-genomic Data
cellNames<--method	Class to contain Toxico-genomic Data
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	curation Slot Getter
curation-method	Class to contain Toxico-genomic Data
curation<-	curation<- Slot Setter
curation<--method	Class to contain Toxico-genomic Data
datasetType	datasetType Generic
datasetType-method	Class to contain Toxico-genomic Data
datasetType<-	datasetType<- Replacement Generic
datasetType<--method	Class to contain Toxico-genomic Data
dateCreated-method	Class to contain Toxico-genomic Data
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	drugInfo Getter
drugInfo-method	Class to contain Toxico-genomic Data
drugInfo<-	drugInfo<- Setter method
drugInfo<--method	Class to contain Toxico-genomic Data
drugNames	drugNames Generic
drugNames-method	Class to contain Toxico-genomic Data
drugNames<-	drugNames<- Generic
drugNames<--method	Class to contain Toxico-genomic Data
drugPerturbationSig	Drug perturbation analysis
drugTimeResponseCurve	Compares viabilities at a given dose over different experimental durations
featureInfo-method	Class to contain Toxico-genomic Data
featureInfo<--method	Class to contain Toxico-genomic Data
fNames-method	Class to contain Toxico-genomic Data
fNames<--method	Class to contain Toxico-genomic Data
HCC_sig	HCC_sig dataset
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.
mDataNames-method	mDataNames
molecularProfiles-method	Class to contain Toxico-genomic Data
molecularProfiles<--method	Class to contain Toxico-genomic Data
molecularProfilesSlot-method	Class to contain Toxico-genomic Data
molecularProfilesSlot<--method	Class to contain Toxico-genomic Data
name-method	name Getter method
pertNumber-method	Class to contain Toxico-genomic Data
pertNumber<--method	Class to contain Toxico-genomic Data
phenoInfo-method	Class to contain Toxico-genomic Data
phenoInfo<--method	Class to contain Toxico-genomic Data
sensitivityInfo-method	Class to contain Toxico-genomic Data
sensitivityInfo<--method	Class to contain Toxico-genomic Data
sensitivityMeasures-method	Class to contain Toxico-genomic Data
sensitivityProfiles-method	Class to contain Toxico-genomic Data
sensitivityProfiles<--method	Class to contain Toxico-genomic Data
sensitivityRaw	sensitivityRaw Generic
sensitivityRaw-method	Class to contain Toxico-genomic Data
sensitivityRaw<-	sensitivityRaw<- Replacement Generic
sensitivityRaw<--method	Class to contain Toxico-genomic Data
sensitivitySlot	sensitivitySlot Generic
sensitivitySlot-method	Class to contain Toxico-genomic Data
sensitivitySlot<-	sensitivitySlot<- Replacement Generic
sensitivitySlot<--method	Class to contain Toxico-genomic Data
sensNumber-method	Class to contain Toxico-genomic Data
sensNumber<--method	Class to contain Toxico-genomic Data
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
TGGATESsmall	TGGATESsmall dataset
ToxicoSet	ToxicoSet constructor
ToxicoSet-class	Class to contain Toxico-genomic Data
[-method	'['