PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

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

AuthorPetr Smirnov, Zhaleh Safikhani, Mark Freeman, Benjamin Haibe-Kains
Date of publicationNone
MaintainerBenjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
LicenseArtistic-2.0
Version1.4.3

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

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