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  "Title": "Analysis of Large-Scale Pharmacogenomic Data",
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  "Date": "2025-05-22",
  "Authors@R": "c(\nperson(given=\"Petr\", family=\"Smirnov\", email=\"petr.smirnov@uhnresearch.ca\",\nrole=c(\"aut\")),\nperson(given=\"Christopher\", family=\"Eeles\",\nemail=\"christopher.eeles@uhnresearch.ca\", role=c(\"aut\")),\nperson(given=\"Jermiah\", family=\"Joseph\",\nemail=\"jermiah.joseph@uhn.ca\", role=c(\"aut\")),\nperson(given=\"Zhaleh\", family=\"Safikhani\", role=c(\"aut\")),\nperson(given=\"Mark\", family=\"Freeman\", role=c(\"aut\")),\nperson(given=\"Feifei\", family=\"Li\", email=\"ff.li@mail.utoronto.ca\", role=c(\"aut\")),\nperson(\"Benjamin\", \"Haibe-Kains\", email=\"benjamin.haibe.kains@utoronto.ca\", role=c(\"aut\", \"cre\"))\n)",
  "Description": "Contains a set of functions to perform large-scale\nanalysis of pharmaco-genomic data. These include the\nPharmacoSet object for storing the results of pharmacogenomic\nexperiments, as well as a number of functions for computing\ncommon summaries of drug-dose response and correlating them\nwith the molecular features in a cancer cell-line.",
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  "biocViews": "GeneExpression, Pharmacogenetics, Pharmacogenomics,\nSoftware, Classification",
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    "drugPerturbationSig",
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    "featureInfo",
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    "fitTwowayZIP",
    "fNames",
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    "logLogisticRegression",
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    "name",
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    "PharmacoSet",
    "PharmacoSet2",
    "PharmacoSig",
    "phenoInfo",
    "phenoInfo<-",
    "sampleInfo",
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    "sampleNames",
    "sampleNames<-",
    "sensitivityInfo",
    "sensitivityInfo<-",
    "sensitivityMeasures",
    "sensitivityProfiles",
    "sensitivityProfiles<-",
    "sensitivityRaw",
    "sensitivityRaw<-",
    "sensNumber",
    "sensNumber<-",
    "show",
    "showSigAnnot",
    "subsetByFeature",
    "subsetBySample",
    "subsetByTreatment",
    "subsetTo",
    "summarizeMolecularProfiles",
    "summarizeSensitivityProfiles",
    "treatmentInfo",
    "treatmentInfo<-",
    "treatmentNames",
    "treatmentNames<-",
    "treatmentResponse",
    "treatmentResponse<-",
    "updateObject"
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      "name": "CCLEsmall",
      "title": "Cancer Cell Line Encyclopedia (CCLE) Example PharmacoSet",
      "object": "CCLEsmall",
      "file": "CCLEsmall.rda",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
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      "title": "Connectivity Map Example PharmacoSet",
      "object": "CMAPsmall",
      "file": "CMAPsmall.rda",
      "class": [
        "PharmacoSet"
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      "fields": [],
      "table": false,
      "tojson": false
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      "name": "GDSCsmall",
      "title": "Genomics of Drug Sensitivity in Cancer Example PharmacoSet",
      "object": "GDSCsmall",
      "file": "GDSCsmall.rda",
      "class": [
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      "table": false,
      "tojson": false
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      "name": "HDAC_genes",
      "title": "HDAC Gene Signature",
      "object": "HDAC_genes",
      "file": "HDAC_genes.rda",
      "class": [
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        "direction"
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      "table": true,
      "tojson": true
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      "page": "sub-PharmacoSet-ANY-ANY-ANY-method",
      "title": "'['",
      "topics": [
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      ]
    },
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      "page": "amcc",
      "title": "Adaptive Matthews Correlation Coefficient",
      "topics": [
        "amcc"
      ]
    },
    {
      "page": "availablePSets",
      "title": "Return a table of PharmacoSets available for download",
      "topics": [
        "availablePSets"
      ]
    },
    {
      "page": "callingWaterfall",
      "title": "Drug sensitivity calling using waterfall plots",
      "topics": [
        "callingWaterfall"
      ]
    },
    {
      "page": "CCLEsmall",
      "title": "Cancer Cell Line Encyclopedia (CCLE) Example PharmacoSet",
      "topics": [
        "CCLEsmall"
      ]
    },
    {
      "page": "checkPsetStructure",
      "title": "A function to verify the structure of a PharmacoSet",
      "topics": [
        "checkPsetStructure"
      ]
    },
    {
      "page": "CMAPsmall",
      "title": "Connectivity Map Example PharmacoSet",
      "topics": [
        "CMAPsmall"
      ]
    },
    {
      "page": "computeABC",
      "title": "Fits dose-response curves to data given by the user and returns the ABC of the fitted curves.",
      "topics": [
        "computeABC"
      ]
    },
    {
      "page": "computeAmax",
      "title": "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)",
      "topics": [
        "computeAmax"
      ]
    },
    {
      "page": "computeAUC",
      "title": "Computes the AUC for a Drug Dose Viability Curve",
      "topics": [
        "computeAUC"
      ]
    },
    {
      "page": "computeBliss",
      "title": "Compute Bliss Null References",
      "topics": [
        "computeBliss"
      ]
    },
    {
      "page": "computeHSA",
      "title": "Compute HSA Null References",
      "topics": [
        "computeHSA"
      ]
    },
    {
      "page": "computeICn",
      "title": "Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve",
      "topics": [
        "computeIC50",
        "computeICn"
      ]
    },
    {
      "page": "computeLoewe",
      "title": "Computes Loewe Null References",
      "topics": [
        "computeLoewe"
      ]
    },
    {
      "page": "computeSlope",
      "title": "Return Slope (normalized slope of the drug response curve) for an experiment of a pSet by taking its concentration and viability as input.",
      "topics": [
        "computeSlope"
      ]
    },
    {
      "page": "computeZIP",
      "title": "Computes ZIP Null References",
      "topics": [
        "computeZIP"
      ]
    },
    {
      "page": "computeZIPdelta",
      "title": "Generic to compute ZIP delta scores from an S4 object",
      "topics": [
        "computeZIPdelta"
      ]
    },
    {
      "page": "computeZIPdelta-TreatmentResponseExperiment-method",
      "title": "Compute ZIP delta score",
      "topics": [
        "computeZIPdelta,TreatmentResponseExperiment-method"
      ]
    },
    {
      "page": "connectivityScore",
      "title": "Function computing connectivity scores between two signatures",
      "topics": [
        "connectivityScore"
      ]
    },
    {
      "page": "cosinePerm",
      "title": "Cosine Permuations",
      "topics": [
        "cosinePerm"
      ]
    },
    {
      "page": "dim-PharmacoSet-method",
      "title": "Get the dimensions of a PharmacoSet",
      "topics": [
        "dim,PharmacoSet-method"
      ]
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    {
      "page": "downloadPertSig",
      "title": "Download Drug Perturbation Signatures",
      "topics": [
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      "page": "downloadPSet",
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    {
      "page": "drugDoseResponseCurve",
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    },
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      "page": "drugPerturbationSig",
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      "page": "drugSensitivitySig-PharmacoSet-method",
      "title": "Creates a signature representing the association between gene expression (or other molecular profile) and drug dose response, for use in drug sensitivity analysis.",
      "topics": [
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    {
      "page": "effectToDose",
      "title": "Inverse function of Hill equation",
      "topics": [
        "effectToDose"
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    {
      "page": "estimateProjParams",
      "title": "Estimate the projected Hill coefficient, efficacy, and potency",
      "topics": [
        "estimateProjParams"
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    },
    {
      "page": "filterNoisyCurves",
      "title": "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.",
      "topics": [
        "filterNoisyCurves"
      ]
    },
    {
      "page": "fitTwowayZIP",
      "title": "Two-way fitting for projected dose-response curve.",
      "topics": [
        "fitTwowayZIP"
      ]
    },
    {
      "page": "GDSCsmall",
      "title": "Genomics of Drug Sensitivity in Cancer Example PharmacoSet",
      "topics": [
        "GDSCsmall"
      ]
    },
    {
      "page": "geneDrugSensitivity",
      "title": "Calcualte The Gene Drug Sensitivity",
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    },
    {
      "page": "geneDrugSensitivityPBCorr",
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        "geneDrugSensitivityPBCorr"
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    },
    {
      "page": "geneDrugSensitivityPCorr",
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        "geneDrugSensitivityPCorr"
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    },
    {
      "page": "gwc",
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        "gwc"
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    },
    {
      "page": "HDAC_genes",
      "title": "HDAC Gene Signature",
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        "HDAC_genes"
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    },
    {
      "page": "hillCurve",
      "title": "4-Parameter Hill Equation for Stimuli-Response Curves",
      "topics": [
        "hillCurve"
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    {
      "page": "intersectPSet",
      "title": "Intersects objects of the PharmacoSet class, subsetting them to the common drugs and/or cell lines as selected by the user.",
      "topics": [
        "intersectPSet"
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    },
    {
      "page": "loeweCI",
      "title": "Loewe Additive Combination Index (CI)",
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        "loeweCI"
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    },
    {
      "page": "logLogisticRegression",
      "title": "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.",
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    },
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      "page": "mcc",
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        "mcc"
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      "page": "partialCorQUICKSTOP",
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        "partialCorQUICKSTOP"
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      "page": "PharmacoSet",
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        "PharmacoSet"
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      "page": "PharmacoSet-accessors",
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      "title": "A Class to Contain PharmacoGenomic datasets together with their curations",
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      "page": "PharmacoSet2",
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      "page": "PharmacoSig",
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      "page": "show-PharmacoSet-method",
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      "page": "show-PharmacoSig-method",
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      "page": "showSigAnnot-PharmacoSig-method",
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      "page": "updateObject-PharmacoSet-method",
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