Analysis of Large-Scale Pharmacogenomic Data


[Up] [Top]

Documentation for package ‘PharmacoGx’ version 1.13.0

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 '['