# Analysis of Large-Scale Pharmacogenomic Data

## Documentation for package ‘PharmacoGx’ version 1.12.0

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

## Help Pages

.PharmacoSet | A Class to Contain PharmacoGenomic datasets together with their curations
amcc | Calculate an Adaptive Matthews Correlation Coefficient
availablePSets | Return a table of PharmacoSets available for download
CCLEsmall | Cancer Cell Line Encyclopedia (CCLE) Example PharmacoSet
cellInfo | cellInfo Generic
cellInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations
cellInfo<- | cellInfo<- Generic
cellInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations
cellNames | cellNames Generic
cellNames-method | A Class to Contain PharmacoGenomic datasets together with their curations
cellNames<- | cellNames<- Generic
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 | Computes the cosine similarity and significance using permutation test
dateCreated | dateCreated Generic
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 | featureInfo Generic
featureInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations
featureInfo<- | featureInfo<- Generic
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 | fNames Generic
fNames-method | A Class to Contain PharmacoGenomic datasets together with their curations
GDSCsmall | Genomics of Drug Sensitivity in Cancer Example PharmacoSet
gwc | Calculate the gwc score between two vectors, using either a weighted spearman or pearson correlation
HDAC_genes | HDAC Gene Signature
intersectList | Utility to find the intersection between a list of more than two vectors or lists
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 | mDataNames
molecularProfiles | molecularProfiles Generic
molecularProfiles-method | A Class to Contain PharmacoGenomic datasets together with their curations
molecularProfiles<- | molecularProfiles<- Generic
molecularProfiles<--method | A Class to Contain PharmacoGenomic datasets together with their curations
pertNumber | pertNumber Generic
pertNumber-method | A Class to Contain PharmacoGenomic datasets together with their curations
pertNumber<- | pertNumber<- Generic
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 | phenoInfo Generic
phenoInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations
phenoInfo<- | phenoInfo<- Generic
phenoInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations
pSetName | pSetName Generic
pSetName-method | A Class to Contain PharmacoGenomic datasets together with their curations
sensitivityInfo | sensitivityInfo Generic
sensitivityInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations
sensitivityInfo<- | sensitivityInfo<- Generic
sensitivityInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations
sensitivityMeasures | sensitivityMeasures Generic
sensitivityMeasures-method | A Class to Contain PharmacoGenomic datasets together with their curations
sensitivityProfiles | sensitivityProfiles Generic
sensitivityProfiles-method | A Class to Contain PharmacoGenomic datasets together with their curations
sensitivityProfiles<- | sensitivityProfiles<- Generic
sensitivityProfiles<--method | A Class to Contain PharmacoGenomic datasets together with their curations
sensNumber | sensNumber Generic
sensNumber-method | A Class to Contain PharmacoGenomic datasets together with their curations
sensNumber<- | sensNumber<- Generic
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
symSetDiffList | Utility to find the symmetric set difference of a list of two or more vectors or lists
unionList | Utility to find the union between a list of more than two vectors or lists
[-method | '['