# Analysis of Large-Scale Pharmacogenomic Data

## Documentation for package ‘PharmacoGx’ version 3.2.0

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

## Help Pages

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

## -- A --

amcc | Adaptive Matthews Correlation Coefficient
annotation | Accessing and modifying information in a 'PharmacoSet'
annotation-method | Accessing and modifying information in a 'PharmacoSet'
annotation<- | Accessing and modifying information in a 'PharmacoSet'
annotation<--method | Accessing and modifying information in a 'PharmacoSet'
availablePSets | Return a table of PharmacoSets available for download

## -- C --

callingWaterfall | Drug sensitivity calling using waterfall plots
CCLEsmall | Cancer Cell Line Encyclopedia (CCLE) Example PharmacoSet
cellInfo | Accessing and modifying information in a 'PharmacoSet'
cellInfo-method | Accessing and modifying information in a 'PharmacoSet'
cellInfo<- | Accessing and modifying information in a 'PharmacoSet'
cellInfo<--method | Accessing and modifying information in a 'PharmacoSet'
cellName-method | Accessing and modifying information in a 'PharmacoSet'
cellNames | Accessing and modifying information in a 'PharmacoSet'
cellNames<- | Accessing and modifying information in a 'PharmacoSet'
cellNames<--method | Accessing and modifying information in a 'PharmacoSet'
checkPsetStructure | A function to verify the structure of a PharmacoSet
CMAPsmall | Connectivity Map Example PharmacoSet
computeABC | Fits dose-response curves to data given by the user and returns the ABC of the fitted curves.
computeAmax | Fits dose-response curves to data given by the user and returns the Amax of the fitted curve. Amax: 100 - viability at maximum concentarion (in fitted curve)
computeAUC | Computes the AUC for a Drug Dose Viability Curve
computeBliss | Compute Bliss Null References
computeHSA | Compute HSA Null References
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
computeLoewe | Computes Loewe Null References
computeSlope | Return Slope (normalized slope of the drug response curve) for an experiment of a pSet by taking its concentration and viability as input.
computeZIP | Computes ZIP Null References
computeZIPdelta | Generic to compute ZIP delta scores from an S4 object
computeZIPdelta-method | Compute ZIP delta score
connectivityScore | Function computing connectivity scores between two signatures
cosinePerm | Cosine Permuations
curation | Accessing and modifying information in a 'PharmacoSet'
curation-method | Accessing and modifying information in a 'PharmacoSet'
curation<- | Accessing and modifying information in a 'PharmacoSet'
curation<--method | Accessing and modifying information in a 'PharmacoSet'

## -- D --

datasetType | Accessing and modifying information in a 'PharmacoSet'
datasetType-method | Accessing and modifying information in a 'PharmacoSet'
datasetType<- | Accessing and modifying information in a 'PharmacoSet'
datasetType<--method | Accessing and modifying information in a 'PharmacoSet'
dateCreated | Accessing and modifying information in a 'PharmacoSet'
dateCreated-method | Accessing and modifying information in a 'PharmacoSet'
dateCreated<- | Accessing and modifying information in a 'PharmacoSet'
dateCreated<--method | Accessing and modifying information in a 'PharmacoSet'
dim-method | Get the dimensions of a PharmacoSet
downloadPertSig | Download Drug Perturbation Signatures
downloadPSet | Download a PharmacoSet object
drugDoseResponseCurve | Plot drug response curve of a given drug and a given cell for a list of pSets (objects of the PharmacoSet class).
drugInfo | Accessing and modifying information in a 'PharmacoSet'
drugInfo<- | Accessing and modifying information in a 'PharmacoSet'
drugNames | Accessing and modifying information in a 'PharmacoSet'
drugNames<- | Accessing and modifying information in a 'PharmacoSet'
drugPerturbationSig | Creates a signature representing gene expression (or other molecular profile) change induced by administrating a drug, for use in drug effect analysis.
drugSensitivitySig-method | Creates a signature representing the association between gene expression (or other molecular profile) and drug dose response, for use in drug sensitivity analysis.

## -- E --

effectToDose | Inverse function of Hill equation
estimateProjParams | Estimate the projected Hill coefficient, efficacy, and potency

## -- F --

featureInfo | Accessing and modifying information in a 'PharmacoSet'
featureInfo-method | Accessing and modifying information in a 'PharmacoSet'
featureInfo<- | Accessing and modifying information in a 'PharmacoSet'
featureInfo<--method | Accessing and modifying information in a 'PharmacoSet'
filterNoisyCurves | Viability measurements in dose-reponse curves must remain stable or decrease monotonically reflecting response to the drug being tested. filterNoisyCurves flags dose-response curves that strongly violate these assumptions.
fitTwowayZIP | Two-way fitting for projected dose-response curve.
fNames | Accessing and modifying information in a 'PharmacoSet'
fNames-method | Accessing and modifying information in a 'PharmacoSet'
fNames<- | Accessing and modifying information in a 'PharmacoSet'
fNames<--method | Accessing and modifying information in a 'PharmacoSet'

## -- G --

GDSCsmall | Genomics of Drug Sensitivity in Cancer Example PharmacoSet
geneDrugSensitivity | Calcualte The Gene Drug Sensitivity
geneDrugSensitivityPBCorr | Calculate The Gene Drug Sensitivity
geneDrugSensitivityPCorr | Calculate The Gene Drug Sensitivity
gwc | GWC Score

## -- H --

HDAC_genes | HDAC Gene Signature
hillCurve | 4-Parameter Hill Equation for Stimuli-Response Curves

## -- I --

intersectPSet | Intersects objects of the PharmacoSet class, subsetting them to the common drugs and/or cell lines as selected by the user.

## -- L --

loeweCI | Loewe Additive Combination Index (CI)
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 --

mcc | Compute a Mathews Correlation Coefficient
mDataNames | Accessing and modifying information in a 'PharmacoSet'
mDataNames-method | Accessing and modifying information in a 'PharmacoSet'
mDataNames<- | Accessing and modifying information in a 'PharmacoSet'
mDataNames<--method | Accessing and modifying information in a 'PharmacoSet'
molecularProfiles | Accessing and modifying information in a 'PharmacoSet'
molecularProfiles-method | Accessing and modifying information in a 'PharmacoSet'
molecularProfiles<- | Accessing and modifying information in a 'PharmacoSet'
molecularProfiles<--method | Accessing and modifying information in a 'PharmacoSet'
molecularProfilesSlot | Accessing and modifying information in a 'PharmacoSet'
molecularProfilesSlot-method | Accessing and modifying information in a 'PharmacoSet'
molecularProfilesSlot<- | Accessing and modifying information in a 'PharmacoSet'
molecularProfilesSlot<--method | Accessing and modifying information in a 'PharmacoSet'
molecularProfilesSlot<-PharmacoSet-method | Accessing and modifying information in a 'PharmacoSet'
moleculerProfilesSlot-method | Accessing and modifying information in a 'PharmacoSet'

## -- N --

name | Accessing and modifying information in a 'PharmacoSet'
name-method | Accessing and modifying information in a 'PharmacoSet'
name<- | Accessing and modifying information in a 'PharmacoSet'
name<--method | Accessing and modifying information in a 'PharmacoSet'

## -- P --

partialCorQUICKSTOP | QUICKSTOP significance testing for partial correlation
pertNumber | Accessing and modifying information in a 'PharmacoSet'
pertNumber-method | Accessing and modifying information in a 'PharmacoSet'
pertNumber<- | Accessing and modifying information in a 'PharmacoSet'
pertNumber<--method | Accessing and modifying information in a 'PharmacoSet'
PharmacoSet | PharmacoSet constructor
PharmacoSet-accessors | Accessing and modifying information in a 'PharmacoSet'
PharmacoSet-class | A Class to Contain PharmacoGenomic datasets together with their curations
PharmacoSet-utils | Utility methods for a 'PharmacoSet' object.
PharmacoSet2 | Make a CoreSet with the updated class structure
PharmacoSig | Contructor for the PharmacoSig S4 class
phenoInfo | Accessing and modifying information in a 'PharmacoSet'
phenoInfo-method | Accessing and modifying information in a 'PharmacoSet'
phenoInfo<- | Accessing and modifying information in a 'PharmacoSet'
phenoInfo<--method | Accessing and modifying information in a 'PharmacoSet'
plot.PharmacoSig | Plots a PharmacoSig object into a Volcano Plot

## -- S --

sampleInfo | Accessing and modifying information in a 'PharmacoSet'
sampleInfo-method | Accessing and modifying information in a 'PharmacoSet'
sampleInfo<- | Accessing and modifying information in a 'PharmacoSet'
sampleInfo<--method | Accessing and modifying information in a 'PharmacoSet'
sampleName-method | Accessing and modifying information in a 'PharmacoSet'
sampleNames | Accessing and modifying information in a 'PharmacoSet'
sampleNames-method | Accessing and modifying information in a 'PharmacoSet'
sampleNames<- | Accessing and modifying information in a 'PharmacoSet'
sampleNames<--method | Accessing and modifying information in a 'PharmacoSet'
sensitivityInfo-method | Accessing and modifying information in a 'PharmacoSet'
sensitivityInfo<--method | Accessing and modifying information in a 'PharmacoSet'
sensitivityMeasures-method | Accessing and modifying information in a 'PharmacoSet'
sensitivityMeasures<--method | Accessing and modifying information in a 'PharmacoSet'
sensitivityProfiles-method | Accessing and modifying information in a 'PharmacoSet'
sensitivityProfiles<--method | Accessing and modifying information in a 'PharmacoSet'
sensitivityRaw-method | Accessing and modifying information in a 'PharmacoSet'
sensitivityRaw<--method | Accessing and modifying information in a 'PharmacoSet'
sensitivitySlot | Accessing and modifying information in a 'PharmacoSet'
sensitivitySlot<- | Accessing and modifying information in a 'PharmacoSet'
sensitvityInfo<--method | Accessing and modifying information in a 'PharmacoSet'
sensNumber | Accessing and modifying information in a 'PharmacoSet'
sensNumber-method | Accessing and modifying information in a 'PharmacoSet'
sensNumber<- | Accessing and modifying information in a 'PharmacoSet'
sensNumber<--method | Accessing and modifying information in a 'PharmacoSet'
show-method | Show a PharamcoSet
show-method | Show PharmacoGx Signatures
showSigAnnot-method | Show the Annotations of a signature object
subsetByFeature | Utility methods for a 'PharmacoSet' object.
subsetByFeature-method | Utility methods for a 'PharmacoSet' object.
subsetBySample | Utility methods for a 'PharmacoSet' object.
subsetBySample-method | Utility methods for a 'PharmacoSet' object.
subsetByTreatment | Utility methods for a 'PharmacoSet' object.
subsetByTreatment-method | Utility methods for a 'PharmacoSet' object.
subsetTo-method | A function to subset a PharmacoSet to data containing only specified drugs, cells and genes
summarizeSensitivityProfiles-method | Takes the sensitivity data from a PharmacoSet, and summarises them into a drug vs cell line table

## -- T --

treamentResponse<--method | Accessing and modifying information in a 'PharmacoSet'
treatmentInfo | Accessing and modifying information in a 'PharmacoSet'
treatmentInfo-method | Accessing and modifying information in a 'PharmacoSet'
treatmentInfo<- | Accessing and modifying information in a 'PharmacoSet'
treatmentInfo<--method | Accessing and modifying information in a 'PharmacoSet'
treatmentNames | Accessing and modifying information in a 'PharmacoSet'
treatmentNames-method | Accessing and modifying information in a 'PharmacoSet'
treatmentNames<- | Accessing and modifying information in a 'PharmacoSet'
treatmentNames<--method | Accessing and modifying information in a 'PharmacoSet'
treatmentResponse | Accessing and modifying information in a 'PharmacoSet'
treatmentResponse-method | Accessing and modifying information in a 'PharmacoSet'
treatmentResponse<- | Accessing and modifying information in a 'PharmacoSet'
treatmentResponse<--method | Accessing and modifying information in a 'PharmacoSet'

## -- U --

updateObject-method | Update the PharmacoSet class after changes in it struture or API

## -- misc --

.PharmacoSet | A Class to Contain PharmacoGenomic datasets together with their curations
[-method | '['