PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

Contains a set of functions to perform large-scale analysis of pharmacogenomic data.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PharmacoGx")
AuthorPetr Smirnov, Zhaleh Safikhani, Mark Freeman, Benjamin Haibe-Kains
Bioconductor views Classification GeneExpression Pharmacogenetics Pharmacogenomics Software
Date of publicationNone
MaintainerBenjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
LicenseArtistic-2.0
Version1.6.0

View on Bioconductor

Man pages

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-set: cellInfo<- Generic

cellNames: cellNames Generic

cellNames-set: cellNames<- Generic

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...

computeAmax: Fits dose-response curves to data given by the user and...

computeAUC: Computes the AUC for a Drug Dose Viability Curve

computeICn: Computes the ICn for any n in 0-100 for a Drug Dose Viability...

computeSlope: Return Slope (normalized slope of the drug response curve)...

connectivityScore: Function computing connectivity scores between two signatures

cosinePerm: Computes the cosine similarity and significance using...

dateCreated: dateCreated Generic

dim-PharmacoSet-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...

drugInfo: drugInfo Generic

drugInfo-set: drugInfo<- Generic

drugNames: drugNames Generic

drugNames-set: drugNames<- Generic

drugPerturbationSig: Creates a signature representing gene expression (or other...

drugSensitivitySig: Creates a signature representing the association between gene...

featureInfo: featureInfo Generic

featureInfo-set: featureInfo<- Generic

filterNoisyCurves: Viability measurements in dose-reponse curves must remain...

fNames: fNames Generic

GDSCsmall: Genomics of Drug Sensitivity in Cancer Example PharmacoSet

gwc: Calculate the gwc score between two vectors, using either a...

HDAC_genes: HDAC Gene Signature

intersectList: Utility to find the intersection between a list of more than...

intersectPSet: Intersects objects of the PharmacoSet class, subsetting them...

LogLogisticRegression: Fits curves of the form E = E_inf + (1 - E_inf)/(1 +...

mcc: Compute a Mathews Correlation Coefficient

mDataNames: mDataNames

molecularProfiles: molecularProfiles Generic

molecularProfiles-set: molecularProfiles<- Generic

pertNumber: pertNumber Generic

pertNumber-set: pertNumber<- Generic

PharmacoSet: PharmacoSet constructor

PharmacoSet-class: A Class to Contain PharmacoGenomic datasets together with...

phenoInfo: phenoInfo Generic

phenoInfo-set: phenoInfo<- Generic

pSetName: pSetName Generic

sensitivityInfo: sensitivityInfo Generic

sensitivityInfo-set: sensitivityInfo<- Generic

sensitivityMeasures: sensitivityMeasures Generic

sensitivityProfiles: sensitivityProfiles Generic

sensitivityProfiles-set: sensitivityProfiles<- Generic

sensNumber: sensNumber Generic

sensNumber-set: sensNumber<- Generic

show-PharmacoSet-method: Show a PharamcoSet

show-PharmacoSig-method: Show PharmacoGx Signatures

showSigAnnot: Show the Annotations of a signature object

sub-PharmacoSet-method: '['

subsetTo: A function to subset a PharmacoSet to data containing only...

summarizeMolecularProfiles: Takes molecular data from a PharmacoSet, and summarises them...

summarizeSensitivityProfiles: Takes the sensitivity data from a PharmacoSet, and summarises...

symSetDiffList: Utility to find the symmetric set difference of a list of two...

unionList: Utility to find the union between a list of more than two...

Functions

amcc Man page
availablePSets Man page
CCLEsmall Man page
cellInfo Man page
cellInfo<- Man page
cellInfo<-,PharmacoSet,data.frame-method Man page
cellInfo,PharmacoSet-method Man page
cellNames Man page
cellNames<- Man page
cellNames<-,PharmacoSet,character-method Man page
cellNames,PharmacoSet-method Man page
checkPSetStructure Man page
CMAPsmall Man page
computeABC Man page
computeAmax Man page
computeAUC Man page
computeIC50 Man page
computeICn Man page
computeSlope Man page
connectivityScore Man page
cosinePerm Man page
dateCreated Man page
dateCreated,PharmacoSet-method Man page
dim,PharmacoSet-method Man page
downloadPertSig Man page
downloadPSet Man page
drugDoseResponseCurve Man page
drugInfo Man page
drugInfo<- Man page
drugInfo<-,PharmacoSet,data.frame-method Man page
drugInfo,PharmacoSet-method Man page
drugNames Man page
drugNames<- Man page
drugNames<-,PharmacoSet,character-method Man page
drugNames,PharmacoSet-method Man page
drugPerturbationSig Man page
drugSensitivitySig Man page
featureInfo Man page
featureInfo<- Man page
featureInfo<-,PharmacoSet,character,data.frame-method Man page
featureInfo,PharmacoSet-method Man page
filterNoisyCurves Man page
fNames Man page
fNames,PharmacoSet-method Man page
GDSCsmall Man page
gwc Man page
HDAC_genes Man page
intersectList Man page
intersectPSet Man page
logLogisticRegression Man page
mcc Man page
mDataNames Man page
molecularProfiles Man page
molecularProfiles<- Man page
molecularProfiles<-,PharmacoSet,character,matrix-method Man page
molecularProfiles,PharmacoSet-method Man page
pertNumber Man page
pertNumber<- Man page
pertNumber<-,PharmacoSet,array-method Man page
pertNumber,PharmacoSet-method Man page
PharmacoSet Man page
.PharmacoSet Man page
PharmacoSet-class Man page
[,PharmacoSet-method Man page
phenoInfo Man page
phenoInfo<- Man page
phenoInfo<-,PharmacoSet,character,data.frame-method Man page
phenoInfo,PharmacoSet-method Man page
pSetName Man page
pSetName,PharmacoSet-method Man page
sensitivityInfo Man page
sensitivityInfo<- Man page
sensitivityInfo<-,PharmacoSet,data.frame-method Man page
sensitivityInfo,PharmacoSet-method Man page
sensitivityMeasures Man page
sensitivityMeasures,PharmacoSet-method Man page
sensitivityProfiles Man page
sensitivityProfiles<- Man page
sensitivityProfiles<-,PharmacoSet,data.frame-method Man page
sensitivityProfiles<-,PharmacoSet,matrix-method Man page
sensitivityProfiles,PharmacoSet-method Man page
sensNumber Man page
sensNumber<- Man page
sensNumber<-,PharmacoSet,matrix-method Man page
sensNumber,PharmacoSet-method Man page
show,PharmacoSet-method Man page
show,PharmacoSig-method Man page
showSigAnnot Man page
subsetTo Man page
summarizeMolecularProfiles Man page
summarizeSensitivityProfiles Man page
symSetDiffList Man page
unionList Man page

Files

.Rinstignore
DESCRIPTION
NAMESPACE
R
R/AdaptiveMatthewCor.R R/ComputeGR.R R/GR.R R/GWC.R R/LogLogisticRegression.R R/MatthewCor.R R/PharmacoSetClass.R R/SanityCheck.R R/callingWaterfall.R R/combineTest.R R/computeABC.R R/computeAUC.R R/computeAUC_old.R R/computeAmax.R R/computeDSS.R R/computeDrugSensitivity.R R/computeIC50.R R/computeICn.R R/computeSlope.R R/connectivityScore.R R/corWeighted.R R/cosinePerm.R R/datasets.R R/distancePointLine.R R/distancePointSegment.R R/dmedncauchys.R R/dmednnormals.R R/downloadPSet.R R/downloadSignatures.R R/drugDoseResponseCurve.R R/drugPerturbationSig.R R/drugSensitivitySig.R R/filterNoisyCurves.R R/geneDrugPerturbation.R R/geneDrugSensitivity.R R/getRawSensitivityMatrix.R R/intersectList.R R/intersectPSets.R R/rankGeneDrugPerturbation.R R/rankGeneDrugSensitivity.R R/rescale.R R/signatureClass.R R/stripWhiteSpace.R R/summarizeMolecularProfiles.R R/summarizeSensitivityProfiles.R R/symSetDiffList.R R/unionList.R
README
build
build/vignette.rds
data
data/CCLEsmall.rda
data/CMAPsmall.rda
data/GDSCsmall.rda
data/HDAC_genes.rda
data/datalist
inst
inst/CITATION
inst/doc
inst/doc/CreatingPharmacoSet.R
inst/doc/CreatingPharmacoSet.Rnw
inst/doc/CreatingPharmacoSet.pdf
inst/doc/PharmacoGx.R
inst/doc/PharmacoGx.Rnw
inst/doc/PharmacoGx.pdf
man
man/CCLEsmall.Rd man/CMAPsmall.Rd man/GDSCsmall.Rd man/HDAC_genes.Rd man/LogLogisticRegression.Rd man/PharmacoSet-class.Rd man/PharmacoSet.Rd man/amcc.Rd man/availablePSets.Rd man/cellInfo-set.Rd man/cellInfo.Rd man/cellNames-set.Rd man/cellNames.Rd man/checkPSetStructure.Rd man/computeABC.Rd man/computeAUC.Rd man/computeAmax.Rd man/computeICn.Rd man/computeSlope.Rd man/connectivityScore.Rd man/cosinePerm.Rd man/dateCreated.Rd man/dim-PharmacoSet-method.Rd man/downloadPSet.Rd man/downloadPertSig.Rd man/drugDoseResponseCurve.Rd man/drugInfo-set.Rd man/drugInfo.Rd man/drugNames-set.Rd man/drugNames.Rd man/drugPerturbationSig.Rd man/drugSensitivitySig.Rd man/fNames.Rd man/featureInfo-set.Rd man/featureInfo.Rd man/filterNoisyCurves.Rd man/gwc.Rd man/intersectList.Rd man/intersectPSet.Rd man/mDataNames.Rd man/mcc.Rd man/molecularProfiles-set.Rd man/molecularProfiles.Rd man/pSetName.Rd man/pertNumber-set.Rd man/pertNumber.Rd man/phenoInfo-set.Rd man/phenoInfo.Rd man/sensNumber-set.Rd man/sensNumber.Rd man/sensitivityInfo-set.Rd man/sensitivityInfo.Rd man/sensitivityMeasures.Rd man/sensitivityProfiles-set.Rd man/sensitivityProfiles.Rd man/show-PharmacoSet-method.Rd man/show-PharmacoSig-method.Rd man/showSigAnnot.Rd man/sub-PharmacoSet-method.Rd man/subsetTo.Rd man/summarizeMolecularProfiles.Rd man/summarizeSensitivityProfiles.Rd man/symSetDiffList.Rd man/unionList.Rd
vignettes
vignettes/CreatingPharmacoSet.Rnw
vignettes/PharmacoGx.Rnw
vignettes/biblio.bib
vignettes/pharmacogx.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.