PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

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

Author
Petr Smirnov, Zhaleh Safikhani, Mark Freeman, Benjamin Haibe-Kains
Date of publication
None
Maintainer
Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
License
Artistic-2.0
Version
1.4.0

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

Files in this package

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