Package: PharmacoGx 3.11.0
Benjamin Haibe-Kains
PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data
Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.
Authors:
PharmacoGx_3.11.0.tar.gz
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PharmacoGx.pdf |PharmacoGx.html✨
PharmacoGx/json (API)
NEWS
| # Install 'PharmacoGx' in R: |
| install.packages('PharmacoGx', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bhklab/pharmacogx/issues
- CCLEsmall - Cancer Cell Line Encyclopedia (CCLE) Example PharmacoSet
- CMAPsmall - Connectivity Map Example PharmacoSet
- GDSCsmall - Genomics of Drug Sensitivity in Cancer Example PharmacoSet
- HDAC_genes - HDAC Gene Signature
On BioConductor:PharmacoGx-3.11.0(bioc 3.21)PharmacoGx-3.10.0(bioc 3.20)
geneexpressionpharmacogeneticspharmacogenomicssoftwareclassificationdatasetspharmacogenomicpharmacogx
Last updated 17 days agofrom:18017f6cf6. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 14 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 14 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 14 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 14 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 14 2024 |
| R-4.4-mac-aarch64 | WARNING | Nov 14 2024 |
| R-4.3-win-x86_64 | WARNING | Nov 14 2024 |
| R-4.3-mac-x86_64 | WARNING | Nov 14 2024 |
| R-4.3-mac-aarch64 | WARNING | Nov 14 2024 |
Exports:.computeAUCUnderFittedCurve.computeZIPdelta.deltaScore.logcosh.parseToRoxygen.plotProjHillamccannotationannotation<-availablePSetscheckPsetStructurecomputeABCcomputeAmaxcomputeAUCcomputeBlisscomputeHSAcomputeIC50computeICncomputeLoewecomputeSlopecomputeZIPcomputeZIPdeltaconnectivityScorecosinePermcurationcuration<-datasetTypedatasetType<-dateCreateddateCreated<-downloadPertSigdownloadPSetdrugDoseResponseCurvedrugInfodrugInfo<-drugNamesdrugNames<-drugPerturbationSigdrugSensitivitySigeffectToDoseestimateProjParamsfeatureInfofeatureInfo<-filterNoisyCurvesfitTwowayZIPfNamesfNames<-gwchillCurveintersectPSetloeweCIlogLogisticRegressionmccmDataNamesmDataNames<-molecularProfilesmolecularProfiles<-molecularProfilesSlotmolecularProfilesSlot<-namename<-pertNumberpertNumber<-PharmacoSetPharmacoSet2PharmacoSigphenoInfophenoInfo<-sampleInfosampleInfo<-sampleNamessampleNames<-sensitivityInfosensitivityInfo<-sensitivityMeasuressensitivityProfilessensitivityProfiles<-sensitivityRawsensitivityRaw<-sensNumbersensNumber<-showshowSigAnnotsubsetByFeaturesubsetBySamplesubsetByTreatmentsubsetTosummarizeMolecularProfilessummarizeSensitivityProfilestreatmentInfotreatmentInfo<-treatmentNamestreatmentNames<-treatmentResponsetreatmentResponse<-updateObject
Dependencies:abindaskpassbackportsbase64encbenchBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbitopsbootbslibBumpyMatrixcachemcaToolscelestialcheckmatecliclustercodetoolscolorspacecommonmarkcoopCoreGxcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydigestdownloaderdplyrDTevaluatefansifarverfastmapfastmatchfgseafontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalsamagicaxismagrittrmapprojmapsmarrayMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMultiAssayExperimentmunsellNISTunitsnlmeopensslpianopillarpkgconfigplotrixplyrpracmaprofmempromisespurrrR6RANNrappdirsRColorBrewerRcpprelationsreshape2rlangrmarkdownS4ArraysS4VectorssassscalessetsshinyshinydashboardshinyjsslamsmsnowSnowballCsourcetoolsSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitevisNetworkwithrxfunxtableXVectoryamlzlibbioc
PharmacoGx: An R Package for Analysis of Large Pharmacogenomic Datasets
Rendered fromCreatingPharmacoSet.Rmdusingknitr::rmarkdownon Nov 14 2024.Last update: 2024-04-08
Started: 2020-04-26
Detecting Drug Synergy and Antagonism with PharmacoGx 3.0+
Rendered fromDetectingDrugSynergyAndAntagonism.Rmdusingknitr::rmarkdownon Nov 14 2024.Last update: 2023-04-21
Started: 2022-12-07
PharmacoGx: An R Package for Analysis of Large Pharmacogenomic Datasets
Rendered fromPharmacoGx.Rmdusingknitr::rmarkdownon Nov 14 2024.Last update: 2023-04-21
Started: 2020-04-26
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| '[' | [,PharmacoSet,ANY,ANY,ANY-method |
| Adaptive Matthews Correlation Coefficient | amcc |
| Return a table of PharmacoSets available for download | availablePSets |
| Drug sensitivity calling using waterfall plots | callingWaterfall |
| Cancer Cell Line Encyclopedia (CCLE) Example PharmacoSet | CCLEsmall |
| A function to verify the structure of a PharmacoSet | checkPsetStructure |
| Connectivity Map Example PharmacoSet | CMAPsmall |
| Fits dose-response curves to data given by the user and returns the ABC of the fitted curves. | computeABC |
| 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) | computeAmax |
| Computes the AUC for a Drug Dose Viability Curve | computeAUC |
| Compute Bliss Null References | computeBliss |
| Compute HSA Null References | computeHSA |
| Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve | computeIC50 computeICn |
| Computes Loewe Null References | computeLoewe |
| Return Slope (normalized slope of the drug response curve) for an experiment of a pSet by taking its concentration and viability as input. | computeSlope |
| Computes ZIP Null References | computeZIP |
| Generic to compute ZIP delta scores from an S4 object | computeZIPdelta |
| Compute ZIP delta score | computeZIPdelta,TreatmentResponseExperiment-method |
| Function computing connectivity scores between two signatures | connectivityScore |
| Cosine Permuations | cosinePerm |
| Get the dimensions of a PharmacoSet | dim,PharmacoSet-method |
| Download Drug Perturbation Signatures | downloadPertSig |
| Download a PharmacoSet object | downloadPSet |
| Plot drug response curve of a given drug and a given cell for a list of pSets (objects of the PharmacoSet class). | drugDoseResponseCurve |
| Creates a signature representing gene expression (or other molecular profile) change induced by administrating a drug, for use in drug effect analysis. | drugPerturbationSig |
| Creates a signature representing the association between gene expression (or other molecular profile) and drug dose response, for use in drug sensitivity analysis. | drugSensitivitySig,PharmacoSet-method |
| Inverse function of Hill equation | effectToDose |
| Estimate the projected Hill coefficient, efficacy, and potency | estimateProjParams |
| 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. | filterNoisyCurves |
| Two-way fitting for projected dose-response curve. | fitTwowayZIP |
| Genomics of Drug Sensitivity in Cancer Example PharmacoSet | GDSCsmall |
| Calcualte The Gene Drug Sensitivity | geneDrugSensitivity |
| Calculate The Gene Drug Sensitivity | geneDrugSensitivityPBCorr |
| Calculate The Gene Drug Sensitivity | geneDrugSensitivityPCorr |
| GWC Score | gwc |
| HDAC Gene Signature | HDAC_genes |
| 4-Parameter Hill Equation for Stimuli-Response Curves | hillCurve |
| Intersects objects of the PharmacoSet class, subsetting them to the common drugs and/or cell lines as selected by the user. | intersectPSet |
| Loewe Additive Combination Index (CI) | loeweCI |
| 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. | logLogisticRegression |
| Compute a Mathews Correlation Coefficient | mcc |
| QUICKSTOP significance testing for partial correlation | partialCorQUICKSTOP |
| PharmacoSet constructor | PharmacoSet |
| Accessing and modifying information in a 'PharmacoSet' | annotation annotation,PharmacoSet-method annotation<- annotation<-,PharmacoSet,list-method cellInfo cellInfo,PharmacoSet-method cellInfo<- cellInfo<-,PharmacoSet,data.frame-method cellName,PharmacoSet-method cellNames cellNames<- cellNames<-,PharmacoSet,list-method curation curation,PharmacoSet-method curation<- curation<-,PharmacoSet,list-method datasetType datasetType,PharmacoSet-method datasetType<- datasetType<-,PharmacoSet,character-method dateCreated dateCreated,PharmacoSet-method dateCreated<- dateCreated<-,PharmacoSet,character-method dateCreated<-,PharmacoSet-method drugInfo drugInfo<- drugNames drugNames<- featureInfo featureInfo,PharmacoSet-method featureInfo<- featureInfo<-,PharmacoSet,character,data.frame-method featureInfo<-,PharmacoSet,character,DataFrame-method fNames fNames,PharmacoSet,character-method fNames<- fNames<-,PharmacoSet,character,character-method mDataNames mDataNames,PharmacoSet-method mDataNames<- mDataNames<-,PharmacoSet,ANY-method mDataNames<-,PharmacoSet-method molecularProfiles molecularProfiles,PharmacoSet-method molecularProfiles<- molecularProfiles<-,PharmacoSet,character,character,matrix-method molecularProfiles<-,PharmacoSet,character,missing,matrix-method molecularProfiles<-,PharmacoSet,missing,missing,list-method molecularProfiles<-,PharmacoSet,missing,missing,MutliAssayExperiment-method molecularProfilesSlot molecularProfilesSlot,PharmacoSet-method molecularProfilesSlot<- molecularProfilesSlot<-,PharmacoSet,list-method molecularProfilesSlot<-,PharmacoSet,list_OR_MAE-method molecularProfilesSlot<-PharmacoSet,MultiAssayExperiment-method moleculerProfilesSlot,PharmacoSet-method name name,PharmacoSet-method name<- name<-,PharmacoSet,character-method name<-,PharmacoSet-method pertNumber pertNumber,PharmacoSet-method pertNumber<- pertNumber<-,PharmacoSet,array-method PharmacoSet-accessors phenoInfo phenoInfo,PharmacoSet,character-method phenoInfo<- phenoInfo<-,PharmacoSet,character,data.frame-method phenoInfo<-,PharmacoSet,character,DataFrame-method sampleInfo sampleInfo,PharmacoSet-method sampleInfo<- sampleInfo<-,PharmacoSet,data.frame-method sampleName,PharmacoSet-method sampleNames sampleNames,PharmacoSet-method sampleNames<- sampleNames<-,PharmacoSet,character-method sampleNames<-,PharmacoSet,list-method sensitivityInfo,PharmacoSet,character-method sensitivityInfo,PharmacoSet,missing-method sensitivityInfo,PharmacoSet-method sensitivityInfo<-,PharmacoSet,data.frame-method sensitivityInfo<-,PharmacoSet,missing,data.frame-method sensitivityMeasures,PharmacoSet-method sensitivityMeasures<-,PharmacoSet,character-method sensitivityProfiles,PharmacoSet-method sensitivityProfiles<-,PharmacoSet,data.frame-method sensitivityRaw,PharmacoSet-method sensitivityRaw<-,PharmacoSet,array-method sensitivitySlot sensitivitySlot<- sensitvityInfo<-,PharmacoSet,character,data.frame-method sensNumber sensNumber,PharmacoSet-method sensNumber<- sensNumber<-,PharmacoSet,matrix-method treamentResponse<-,PharmacoSet,list-method treatmentInfo treatmentInfo,PharmacoSet-method treatmentInfo<- treatmentInfo<-,PharmacoSet,data.frame-method treatmentNames treatmentNames,PharmacoSet-method treatmentNames<- treatmentNames<-,PharmacoSet,character-method treatmentResponse treatmentResponse,PharmacoSet-method treatmentResponse<- treatmentResponse<-,PharmacoSet,list_OR_LongTable-method treatmentResponse<-,PharmacoSet,LongTable-method |
| A Class to Contain PharmacoGenomic datasets together with their curations | .PharmacoSet PharmacoSet-class |
| Utility methods for a 'PharmacoSet' object. | PharmacoSet-utils subsetByFeature subsetByFeature,PharmacoSet-method subsetBySample subsetBySample,CoreSet-method subsetBySample,PharmacoSet-method subsetByTreatment subsetByTreatment,PharmacoSet-method |
| Make a CoreSet with the updated class structure | PharmacoSet2 |
| Contructor for the PharmacoSig S4 class | PharmacoSig |
| Plots a PharmacoSig object into a Volcano Plot | plot.PharmacoSig |
| Show a PharamcoSet | show,PharmacoSet-method |
| Show PharmacoGx Signatures | show,PharmacoSig-method |
| Show the Annotations of a signature object | showSigAnnot,PharmacoSig-method |
| A function to subset a PharmacoSet to data containing only specified drugs, cells and genes | subsetTo,PharmacoSet-method |
| Takes the sensitivity data from a PharmacoSet, and summarises them into a drug vs cell line table | summarizeSensitivityProfiles,PharmacoSet-method |
| Update the PharmacoSet class after changes in it struture or API | updateObject,PharmacoSet-method |
