# Analysis of Large-Scale Pharmacogenomic Data

## Documentation for package ‘PharmacoGx’ version 2.0.0

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

## Help Pages

.PharmacoSet | A Class to Contain PharmacoGenomic datasets together with their curations
amcc | Adaptive Matthews Correlation Coefficient
availablePSets | Return a table of PharmacoSets available for download
callingWaterfall | Drug sensitivity calling using waterfall plots
CCLEsmall | Cancer Cell Line Encyclopedia (CCLE) Example PharmacoSet
cellInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations
cellInfo<--method | cellInfo<- Generic
cellNames-method | A Class to Contain PharmacoGenomic datasets together with their curations
cellNames<--method | A Class to Contain PharmacoGenomic datasets together with their curations
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
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
computeSlope | Return Slope (normalized slope of the drug response curve) for an experiment of a pSet by taking its concentration and viability as input.
connectivityScore | Function computing connectivity scores between two signatures
cosinePerm | Cosine Permuations
dateCreated-method | A Class to Contain PharmacoGenomic datasets together with their curations
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 | drugInfo Generic
drugInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations
drugInfo<- | drugInfo<- Generic
drugInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations
drugNames | drugNames Generic
drugNames-method | A Class to Contain PharmacoGenomic datasets together with their curations
drugNames<- | drugNames<- Generic
drugNames<--method | A Class to Contain PharmacoGenomic datasets together with their curations
drugPerturbationSig | Creates a signature representing gene expression (or other molecular profile) change induced by administrating a drug, for use in drug effect analysis.
drugSensitivitySig | Creates a signature representing the association between gene expression (or other molecular profile) and drug dose response, for use in drug sensitivity analysis.
featureInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations
featureInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations
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.
fNames-method | A Class to Contain PharmacoGenomic datasets together with their curations
fNames<--method | fNames<-
GDSCsmall | Genomics of Drug Sensitivity in Cancer Example PharmacoSet
geneDrugSensitivity | Calcualte The Gene Drug Sensitivity
gwc | GWC Score
HDAC_genes | HDAC Gene Signature
intersectPSet | Intersects objects of the PharmacoSet class, subsetting them to the common drugs and/or cell lines as selected by the user.
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.
mcc | Compute a Mathews Correlation Coefficient
mDataNames-method | mDataNames
molecularProfiles-method | A Class to Contain PharmacoGenomic datasets together with their curations
molecularProfiles<--method | A Class to Contain PharmacoGenomic datasets together with their curations
name-method | A Class to Contain PharmacoGenomic datasets together with their curations
pertNumber-method | A Class to Contain PharmacoGenomic datasets together with their curations
pertNumber<--method | A Class to Contain PharmacoGenomic datasets together with their curations
PharmacoSet | PharmacoSet constructor
PharmacoSet-class | A Class to Contain PharmacoGenomic datasets together with their curations
phenoInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations
phenoInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations
plot.PharmacoSig | Plots a PharmacoSig object into a Volcano Plot
sensitivityInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations
sensitivityInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations
sensitivityMeasures-method | A Class to Contain PharmacoGenomic datasets together with their curations
sensitivityProfiles-method | A Class to Contain PharmacoGenomic datasets together with their curations
sensitivityProfiles<--method | A Class to Contain PharmacoGenomic datasets together with their curations
sensNumber-method | A Class to Contain PharmacoGenomic datasets together with their curations
sensNumber<--method | A Class to Contain PharmacoGenomic datasets together with their curations
show-method | Show a PharamcoSet
show-method | Show PharmacoGx Signatures
showSigAnnot | Show the Annotations of a signature object
subsetTo | A function to subset a PharmacoSet to data containing only specified drugs, cells and genes
summarizeMolecularProfiles | Takes molecular data from a PharmacoSet, and summarises them into one entry per drug
summarizeSensitivityProfiles | Takes the sensitivity data from a PharmacoSet, and summarises them into a drug vs cell line table
[-method | '['