Analysis of Large-Scale Pharmacogenomic Data

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Documentation for package ‘PharmacoGx’ version 3.13.2

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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 '['