# Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet

#### Jermiah Joseph

jermiah.joseph@uhn.ca

#### Bartosz Czech

bartosz.w.czech@gmail.com

## Introduction

The `PharmacoGx` package is a popular tool from the Bioconductor project within the field of bioinformatics and computational biology. Whereas the `gDR` package is a valuable tool that provides the framework for the import, processing, analysism and visualization of high-dimensional drug response data, the `PharmacoGx` package provides functionality to containerize processed drug response and genomic data to perform pharmacogenomic analyses. The data structure used by `PharmacoGx` is described as a `PharamcoSet` class, inherited from `CoreGx::CoreSet`. Inspired by the `SummarizedExperiment` class, a new data structure class called the `TreatmentResponseExperiment` was developed to store drug response data within the `PharmacoSet`.

In collaboration with the BHKLab, we have developed functionality to convert between the `gDR`-generated `MultiAssayExperiment (MAE)` object and the `PharmacoSet` object (see the ConvertingPharmacoSetToGDR vignette to convert from a PharmacoSet to gDR object).

# Loading the gDR-generated MAE object

This workflow assumes that you have already generated a `MAE` object using the `gDR` package. We will load in a `MAE` object generated using the data from the KW. Song et al, 2022 study. This `MAE` contains two drugs (`treatments`) and 7 cell lines (`samples`).

    (mae <- qs::qread(
        system.file("extdata", "kyung2022mae", "MAE_E2.qs", package = "gDRimport")
      )
    )
    #> A MultiAssayExperiment object of 2 listed
    #>  experiments with user-defined names and respective classes.
    #>  Containing an ExperimentList class object of length 2:
    #>  [1] matrix: SummarizedExperiment with 1 rows and 7 columns
    #>  [2] single-agent: SummarizedExperiment with 2 rows and 7 columns
    #> Functionality:
    #>  experiments() - obtain the ExperimentList instance
    #>  colData() - the primary/phenotype DataFrame
    #>  sampleMap() - the sample coordination DataFrame
    #>  `$`, `[`, `[[` - extract colData columns, subset, or experiment
    #>  *Format() - convert into a long or wide DataFrame
    #>  assays() - convert ExperimentList to a SimpleList of matrices
    #>  exportClass() - save data to flat files

# Converting the MAE object into a PharmacoSet object

First we will view the experiments and assays within the MultiAssayExperiment object.

    gDRutils::MAEpply(mae, assays)
    #> $matrix
    #> List of length 14
    #> names(14): RawTreated Controls Normalized ... CIScore_50 CIScore_80 Metrics
    #>
    #> $`single-agent`
    #> List of length 5
    #> names(5): RawTreated Controls Normalized Averaged Metrics

We will now convert the `MAE` object into a `PharmacoSet` object. We need to provide a name for the data object, in this example we will use the name of the study.

    pset <- convert_MAE_to_PSet(mae, pset_name="Kyung2022")
    #> 2024-05-01 19:02:29 Building assay index...
    #> 2024-05-01 19:02:29 Joining rowData to assayIndex...
    #> 2024-05-01 19:02:30 Joining colData to assayIndex...
    #> 2024-05-01 19:02:31 Joining assays to assayIndex...
    #> 2024-05-01 19:02:32 Setting assayIndex key...
    #> 2024-05-01 19:02:33 Building LongTable...

We can now view the `PharmacoSet` object.

    pset
    #> <PharmacoSet>
    #> Name: Kyung2022
    #> Date Created: Wed May  1 19:02:33 2024
    #> Number of samples:  7
    #> Molecular profiles: <MultiAssayExperiment>
    #>    ExperimentList class object of length 1:
    #>     [1] emptySE : SummarizedExperiment with 0 rows and 7 columns
    #> Treatment response: <TreatmentResponseExperiment>
    #>    dim:  3 7
    #>    assays(14): RawTreated Controls Normalized Averaged SmoothMatrix BlissExcess
    #>   HSAExcess all_iso_points isobolograms BlissScore HSAScore CIScore_50
    #>   CIScore_80 Metrics
    #>    rownames(3): G02001876_Palbociclib_CDK4|CDK6_168 G02967907_GDC-0077_PI3K-A_168 G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168
    #>    rowData(10): treatmentid Gnumber DrugName ... DrugName_3 drug_moa_3 Duration
    #>    colnames(7): CL129757_MCF-7_Breast_MCF-7_unknown_30 CL130218_BT-474_Breast_BT-474_unknown_70 CL130742_T-47D_Breast_T-47D_unknown_60 ... CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131891_EFM-19_Breast_EFM-19_unknown_64 CL131903_BT-483_Breast_BT-483_unknown_130
    #>    colData(7): sampleid clid CellLineName ... parental_identifier subtype ReferenceDivisionTime
    #>    metadata(0): none

We can view information about the drugs and cell lines in the `PharmacoSet` object using the `treatment` and `sample` slots:

    head(treatmentInfo(pset))
    #>                                                                     treatmentid
    #> 1 G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168
    #> 2                                           G02001876_Palbociclib_CDK4|CDK6_168
    #> 3                                                 G02967907_GDC-0077_PI3K-A_168
    #>     Gnumber    DrugName  drug_moa Gnumber_2  DrugName_2 drug_moa_2 DrugName_3
    #> 1 G02967907    GDC-0077    PI3K-A G02001876 Palbociclib  CDK4|CDK6    vehicle
    #> 2 G02001876 Palbociclib CDK4|CDK6      <NA>        <NA>       <NA>       <NA>
    #> 3 G02967907    GDC-0077    PI3K-A      <NA>        <NA>       <NA>       <NA>
    #>   drug_moa_3 Duration
    #> 1    vehicle      168
    #> 2       <NA>      168
    #> 3       <NA>      168

    head(sampleInfo(pset))
    #>                                                                              sampleid
    #> CL129757_MCF-7_Breast_MCF-7_unknown_30         CL129757_MCF-7_Breast_MCF-7_unknown_30
    #> CL130218_BT-474_Breast_BT-474_unknown_70     CL130218_BT-474_Breast_BT-474_unknown_70
    #> CL130742_T-47D_Breast_T-47D_unknown_60         CL130742_T-47D_Breast_T-47D_unknown_60
    #> CL131438_CAMA-1_Breast_CAMA-1_unknown_53     CL131438_CAMA-1_Breast_CAMA-1_unknown_53
    #> CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131873_HCC1428_Breast_HCC1428_unknown_74
    #> CL131891_EFM-19_Breast_EFM-19_unknown_64     CL131891_EFM-19_Breast_EFM-19_unknown_64
    #>                                                clid CellLineName Tissue
    #> CL129757_MCF-7_Breast_MCF-7_unknown_30     CL129757        MCF-7 Breast
    #> CL130218_BT-474_Breast_BT-474_unknown_70   CL130218       BT-474 Breast
    #> CL130742_T-47D_Breast_T-47D_unknown_60     CL130742        T-47D Breast
    #> CL131438_CAMA-1_Breast_CAMA-1_unknown_53   CL131438       CAMA-1 Breast
    #> CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131873      HCC1428 Breast
    #> CL131891_EFM-19_Breast_EFM-19_unknown_64   CL131891       EFM-19 Breast
    #>                                            parental_identifier subtype
    #> CL129757_MCF-7_Breast_MCF-7_unknown_30                   MCF-7 unknown
    #> CL130218_BT-474_Breast_BT-474_unknown_70                BT-474 unknown
    #> CL130742_T-47D_Breast_T-47D_unknown_60                   T-47D unknown
    #> CL131438_CAMA-1_Breast_CAMA-1_unknown_53                CAMA-1 unknown
    #> CL131873_HCC1428_Breast_HCC1428_unknown_74             HCC1428 unknown
    #> CL131891_EFM-19_Breast_EFM-19_unknown_64                EFM-19 unknown
    #>                                            ReferenceDivisionTime batchid
    #> CL129757_MCF-7_Breast_MCF-7_unknown_30                        30       1
    #> CL130218_BT-474_Breast_BT-474_unknown_70                      70       1
    #> CL130742_T-47D_Breast_T-47D_unknown_60                        60       1
    #> CL131438_CAMA-1_Breast_CAMA-1_unknown_53                      53       1
    #> CL131873_HCC1428_Breast_HCC1428_unknown_74                    74       1
    #> CL131891_EFM-19_Breast_EFM-19_unknown_64                      64       1

# TreatmentResponseExperiment Object

The `TreatmentResponseExperiment` is a new class that was developed to store drug response data within the `PharmacoSet` object. This vignette will cover some basics about this class, however for more information, please refer to the `PharmacoSet` vignette TreatmentResponseExperiment****.

## Row and Column Names

    tre <- treatmentResponse(pset)
    head(rownames(tre))
    #> [1] "G02001876_Palbociclib_CDK4|CDK6_168"
    #> [2] "G02967907_GDC-0077_PI3K-A_168"
    #> [3] "G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168"
    head(rowData(tre))
    #>                                                                      treatmentid
    #>                                                                           <char>
    #> 1:                                           G02001876_Palbociclib_CDK4|CDK6_168
    #> 2:                                                 G02967907_GDC-0077_PI3K-A_168
    #> 3: G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168
    #>      Gnumber    DrugName  drug_moa Gnumber_2  DrugName_2 drug_moa_2 DrugName_3
    #>       <char>      <char>    <char>    <char>      <char>     <char>     <char>
    #> 1: G02001876 Palbociclib CDK4|CDK6      <NA>        <NA>       <NA>       <NA>
    #> 2: G02967907    GDC-0077    PI3K-A      <NA>        <NA>       <NA>       <NA>
    #> 3: G02967907    GDC-0077    PI3K-A G02001876 Palbociclib  CDK4|CDK6    vehicle
    #>    drug_moa_3 Duration
    #>        <char>    <num>
    #> 1:       <NA>      168
    #> 2:       <NA>      168
    #> 3:    vehicle      168

    head(colnames(tre))
    #> [1] "CL129757_MCF-7_Breast_MCF-7_unknown_30"
    #> [2] "CL130218_BT-474_Breast_BT-474_unknown_70"
    #> [3] "CL130742_T-47D_Breast_T-47D_unknown_60"
    #> [4] "CL131438_CAMA-1_Breast_CAMA-1_unknown_53"
    #> [5] "CL131873_HCC1428_Breast_HCC1428_unknown_74"
    #> [6] "CL131891_EFM-19_Breast_EFM-19_unknown_64"
    head(colData(tre))
    #>                                      sampleid     clid CellLineName Tissue
    #>                                        <char>   <char>       <char> <char>
    #> 1:     CL129757_MCF-7_Breast_MCF-7_unknown_30 CL129757        MCF-7 Breast
    #> 2:   CL130218_BT-474_Breast_BT-474_unknown_70 CL130218       BT-474 Breast
    #> 3:     CL130742_T-47D_Breast_T-47D_unknown_60 CL130742        T-47D Breast
    #> 4:   CL131438_CAMA-1_Breast_CAMA-1_unknown_53 CL131438       CAMA-1 Breast
    #> 5: CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131873      HCC1428 Breast
    #> 6:   CL131891_EFM-19_Breast_EFM-19_unknown_64 CL131891       EFM-19 Breast
    #>    parental_identifier subtype ReferenceDivisionTime
    #>                 <char>  <char>                 <num>
    #> 1:               MCF-7 unknown                    30
    #> 2:              BT-474 unknown                    70
    #> 3:               T-47D unknown                    60
    #> 4:              CAMA-1 unknown                    53
    #> 5:             HCC1428 unknown                    74
    #> 6:              EFM-19 unknown                    64

## `data.table` Subsetting

In addition to regex queries, a `TreatmentResponseExperiment` object supports arbitrarily complex subset queries using the `data.table` API. To access this API, you will need to use the `.` function, which allows you to pass raw R expressions to be evaluated inside the `i` and `j` arguments for `dataTable[i, j]`.

For example if we want to subset to rows where the cell line is “CL131891_EFM-19_Breast_EFM-19_unknown_64” and drug is “G02967907_GDC-0077_PI3K-A_168”.

    tre[
      .(treatmentid=="G02967907_GDC-0077_PI3K-A_168"), # query on row
      .(sampleid=="CL131891_EFM-19_Breast_EFM-19_unknown_64") # query on column
    ]
    #> <TreatmentResponseExperiment>
    #>    dim:  1 1
    #>    assays(14): RawTreated Controls Normalized Averaged SmoothMatrix BlissExcess
    #>   HSAExcess all_iso_points isobolograms BlissScore HSAScore CIScore_50
    #>   CIScore_80 Metrics
    #>    rownames(1): G02967907_GDC-0077_PI3K-A_168
    #>    rowData(10): treatmentid Gnumber DrugName ... DrugName_3 drug_moa_3 Duration
    #>    colnames(1): CL131891_EFM-19_Breast_EFM-19_unknown_64
    #>    colData(7): sampleid clid CellLineName ... parental_identifier subtype ReferenceDivisionTime
    #>    metadata(0): none

We can also invert matches or subset on other columns in `rowData` or `colData`:

    tre[
      .(treatmentid!="G02967907_GDC-0077_PI3K-A_168"), # query on row
      .(sampleid!="CL131891_EFM-19_Breast_EFM-19_unknown_64") # query on column
    ]
    #> <TreatmentResponseExperiment>
    #>    dim:  2 6
    #>    assays(14): RawTreated Controls Normalized Averaged SmoothMatrix BlissExcess
    #>   HSAExcess all_iso_points isobolograms BlissScore HSAScore CIScore_50
    #>   CIScore_80 Metrics
    #>    rownames(2): G02001876_Palbociclib_CDK4|CDK6_168 G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168
    #>    rowData(10): treatmentid Gnumber DrugName ... DrugName_3 drug_moa_3 Duration
    #>    colnames(6): CL129757_MCF-7_Breast_MCF-7_unknown_30 CL130218_BT-474_Breast_BT-474_unknown_70 CL130742_T-47D_Breast_T-47D_unknown_60 CL131438_CAMA-1_Breast_CAMA-1_unknown_53 CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131903_BT-483_Breast_BT-483_unknown_130
    #>    colData(7): sampleid clid CellLineName ... parental_identifier subtype ReferenceDivisionTime
    #>    metadata(0): none

## assays

The assays can be viewed through the `assays` function. Each assay has a column “data_type” which references which `SummarizedExperiment` from the `MAE` the data corresponds with.

    lapply(assays(tre), head)
    #> $RawTreated
    #> Key: <treatmentid, sampleid>
    #>    treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
    #>         <char>   <char>   <char>     <char>     <char>    <num>  <char>
    #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #>    Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
    #>       <char>   <char>     <char>     <char>       <char>                 <num>
    #> 1:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 2:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 3:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 4:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 5:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 6:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #>    Tissue   clid parental_identifier subtype    data_type Concentration
    #>    <char> <char>              <char>  <char>       <char>         <num>
    #> 1:   <NA>   <NA>                <NA>    <NA> single-agent   0.001524158
    #> 2:   <NA>   <NA>                <NA>    <NA> single-agent   0.001524158
    #> 3:   <NA>   <NA>                <NA>    <NA> single-agent   0.001524158
    #> 4:   <NA>   <NA>                <NA>    <NA> single-agent   0.001524158
    #> 5:   <NA>   <NA>                <NA>    <NA> single-agent   0.004572471
    #> 6:   <NA>   <NA>                <NA>    <NA> single-agent   0.004572471
    #>    Concentration_2   Barcode ReadoutValue BackgroundValue
    #>              <num>    <char>        <num>           <num>
    #> 1:              NA 30190103p       921614             483
    #> 2:              NA 30190103p       999312             483
    #> 3:              NA 30190103p      1104556             483
    #> 4:              NA 30190103p      1122112             483
    #> 5:              NA 30190103p       874807             483
    #> 6:              NA 30190103p       994797             483
    #>                                Template WellRow WellColumn record_id masked
    #>                                  <char>  <char>     <char>     <int> <lgcl>
    #> 1: Template_0077_Palbo_7daytreated.xlsx       D         20      2832  FALSE
    #> 2: Template_0077_Palbo_7daytreated.xlsx       C         20      2831  FALSE
    #> 3: Template_0077_Palbo_7daytreated.xlsx       D         19      2830  FALSE
    #> 4: Template_0077_Palbo_7daytreated.xlsx       C         19      2829  FALSE
    #> 5: Template_0077_Palbo_7daytreated.xlsx       C         18      2835  FALSE
    #> 6: Template_0077_Palbo_7daytreated.xlsx       D         18      2836  FALSE
    #>    CorrectedReadout swap_sa i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2
    #>               <num>  <lgcl>    <char>      <char>     <char>      <char>
    #> 1:           921131      NA G02001876 Palbociclib  CDK4|CDK6        <NA>
    #> 2:           998829      NA G02001876 Palbociclib  CDK4|CDK6        <NA>
    #> 3:          1104073      NA G02001876 Palbociclib  CDK4|CDK6        <NA>
    #> 4:          1121629      NA G02001876 Palbociclib  CDK4|CDK6        <NA>
    #> 5:           874324      NA G02001876 Palbociclib  CDK4|CDK6        <NA>
    #> 6:           994314      NA G02001876 Palbociclib  CDK4|CDK6        <NA>
    #>    i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid
    #>          <char>       <char>       <char>       <char>      <num>   <char>
    #> 1:         <NA>         <NA>         <NA>         <NA>        168 CL129757
    #> 2:         <NA>         <NA>         <NA>         <NA>        168 CL129757
    #> 3:         <NA>         <NA>         <NA>         <NA>        168 CL129757
    #> 4:         <NA>         <NA>         <NA>         <NA>        168 CL129757
    #> 5:         <NA>         <NA>         <NA>         <NA>        168 CL129757
    #> 6:         <NA>         <NA>         <NA>         <NA>        168 CL129757
    #>    i.CellLineName i.Tissue i.parental_identifier i.subtype
    #>            <char>   <char>                <char>    <char>
    #> 1:          MCF-7   Breast                 MCF-7   unknown
    #> 2:          MCF-7   Breast                 MCF-7   unknown
    #> 3:          MCF-7   Breast                 MCF-7   unknown
    #> 4:          MCF-7   Breast                 MCF-7   unknown
    #> 5:          MCF-7   Breast                 MCF-7   unknown
    #> 6:          MCF-7   Breast                 MCF-7   unknown
    #>    i.ReferenceDivisionTime
    #>                      <num>
    #> 1:                      30
    #> 2:                      30
    #> 3:                      30
    #> 4:                      30
    #> 5:                      30
    #> 6:                      30
    #>
    #> $Controls
    #> Key: <treatmentid, sampleid>
    #>    treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
    #>         <char>   <char>   <char>     <char>     <char>    <num>  <char>
    #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #>    Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
    #>       <char>   <char>     <char>     <char>       <char>                 <num>
    #> 1:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 2:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 3:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 4:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 5:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 6:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #>    Tissue   clid parental_identifier subtype    data_type control_type
    #>    <char> <char>              <char>  <char>       <char>       <char>
    #> 1:   <NA>   <NA>                <NA>    <NA> single-agent  Day0Readout
    #> 2:   <NA>   <NA>                <NA>    <NA> single-agent  Day0Readout
    #> 3:   <NA>   <NA>                <NA>    <NA> single-agent  Day0Readout
    #> 4:   <NA>   <NA>                <NA>    <NA> single-agent  Day0Readout
    #> 5:   <NA>   <NA>                <NA>    <NA> single-agent  Day0Readout
    #> 6:   <NA>   <NA>                <NA>    <NA> single-agent  Day0Readout
    #>    CorrectedReadout record_id   Barcode isDay0 i.Gnumber  i.DrugName i.drug_moa
    #>               <num>     <int>    <char> <lgcl>    <char>      <char>     <char>
    #> 1:            97219      2401 20190103p   TRUE G02001876 Palbociclib  CDK4|CDK6
    #> 2:            97219      2402 20190103p   TRUE G02001876 Palbociclib  CDK4|CDK6
    #> 3:            97219      2403 20190103p   TRUE G02001876 Palbociclib  CDK4|CDK6
    #> 4:            97219      2404 20190103p   TRUE G02001876 Palbociclib  CDK4|CDK6
    #> 5:            97219      2405 20190103p   TRUE G02001876 Palbociclib  CDK4|CDK6
    #> 6:            97219      2406 20190103p   TRUE G02001876 Palbociclib  CDK4|CDK6
    #>    i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration
    #>         <char>       <char>       <char>       <char>       <char>      <num>
    #> 1:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 2:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 3:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 4:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 5:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 6:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #>      i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
    #>      <char>         <char>   <char>                <char>    <char>
    #> 1: CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 2: CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 3: CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 4: CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 5: CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 6: CL129757          MCF-7   Breast                 MCF-7   unknown
    #>    i.ReferenceDivisionTime
    #>                      <num>
    #> 1:                      30
    #> 2:                      30
    #> 3:                      30
    #> 4:                      30
    #> 5:                      30
    #> 6:                      30
    #>
    #> $Normalized
    #> Key: <treatmentid, sampleid>
    #>    treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
    #>         <char>   <char>   <char>     <char>     <char>    <num>  <char>
    #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #>    Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
    #>       <char>   <char>     <char>     <char>       <char>                 <num>
    #> 1:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 2:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 3:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 4:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 5:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 6:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #>    Tissue   clid parental_identifier subtype    data_type Concentration
    #>    <char> <char>              <char>  <char>       <char>         <num>
    #> 1:   <NA>   <NA>                <NA>    <NA> single-agent   0.001524158
    #> 2:   <NA>   <NA>                <NA>    <NA> single-agent   0.001524158
    #> 3:   <NA>   <NA>                <NA>    <NA> single-agent   0.001524158
    #> 4:   <NA>   <NA>                <NA>    <NA> single-agent   0.001524158
    #> 5:   <NA>   <NA>                <NA>    <NA> single-agent   0.004572471
    #> 6:   <NA>   <NA>                <NA>    <NA> single-agent   0.004572471
    #>    Concentration_2 masked normalization_type      x i.Gnumber  i.DrugName
    #>              <num> <lgcl>             <fctr>  <num>    <char>      <char>
    #> 1:              NA  FALSE                 RV 0.8253 G02001876 Palbociclib
    #> 2:              NA  FALSE                 RV 0.8949 G02001876 Palbociclib
    #> 3:              NA  FALSE                 RV 0.9892 G02001876 Palbociclib
    #> 4:              NA  FALSE                 RV 1.0049 G02001876 Palbociclib
    #> 5:              NA  FALSE                 RV 0.7833 G02001876 Palbociclib
    #> 6:              NA  FALSE                 RV 0.8908 G02001876 Palbociclib
    #>    i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3
    #>        <char>      <char>       <char>       <char>       <char>       <char>
    #> 1:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 2:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 3:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 4:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 5:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 6:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #>    i.Duration   i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
    #>         <num>   <char>         <char>   <char>                <char>    <char>
    #> 1:        168 CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 2:        168 CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 3:        168 CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 4:        168 CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 5:        168 CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 6:        168 CL129757          MCF-7   Breast                 MCF-7   unknown
    #>    i.ReferenceDivisionTime
    #>                      <num>
    #> 1:                      30
    #> 2:                      30
    #> 3:                      30
    #> 4:                      30
    #> 5:                      30
    #> 6:                      30
    #>
    #> $Averaged
    #> Key: <treatmentid, sampleid>
    #>    treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
    #>         <char>   <char>   <char>     <char>     <char>    <num>  <char>
    #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #>    Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
    #>       <char>   <char>     <char>     <char>       <char>                 <num>
    #> 1:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 2:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 3:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 4:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 5:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 6:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #>    Tissue   clid parental_identifier subtype    data_type normalization_type
    #>    <char> <char>              <char>  <char>       <char>             <fctr>
    #> 1:   <NA>   <NA>                <NA>    <NA> single-agent                 RV
    #> 2:   <NA>   <NA>                <NA>    <NA> single-agent                 GR
    #> 3:   <NA>   <NA>                <NA>    <NA> single-agent                 RV
    #> 4:   <NA>   <NA>                <NA>    <NA> single-agent                 GR
    #> 5:   <NA>   <NA>                <NA>    <NA> single-agent                 RV
    #> 6:   <NA>   <NA>                <NA>    <NA> single-agent                 GR
    #>    Concentration Concentration_2        x      x_std i.Gnumber  i.DrugName
    #>            <num>           <num>    <num>      <num>    <char>      <char>
    #> 1:   0.001524158              NA 0.928575 0.08426274 G02001876 Palbociclib
    #> 2:   0.001524158              NA 0.952225 0.05675581 G02001876 Palbociclib
    #> 3:   0.004572471              NA 0.885050 0.07091133 G02001876 Palbociclib
    #> 4:   0.004572471              NA 0.923000 0.04998000 G02001876 Palbociclib
    #> 5:   0.013717406              NA 0.843800 0.05585201 G02001876 Palbociclib
    #> 6:   0.013717406              NA 0.894475 0.04037973 G02001876 Palbociclib
    #>    i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3
    #>        <char>      <char>       <char>       <char>       <char>       <char>
    #> 1:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 2:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 3:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 4:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 5:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 6:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #>    i.Duration   i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
    #>         <num>   <char>         <char>   <char>                <char>    <char>
    #> 1:        168 CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 2:        168 CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 3:        168 CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 4:        168 CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 5:        168 CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 6:        168 CL129757          MCF-7   Breast                 MCF-7   unknown
    #>    i.ReferenceDivisionTime
    #>                      <num>
    #> 1:                      30
    #> 2:                      30
    #> 3:                      30
    #> 4:                      30
    #> 5:                      30
    #> 6:                      30
    #>
    #> $SmoothMatrix
    #> Key: <treatmentid, sampleid>
    #>    treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
    #>         <char>   <char>   <char>     <char>     <char>    <num>  <char>
    #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #>    Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
    #>       <char>   <char>     <char>     <char>       <char>                 <num>
    #> 1:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 2:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 3:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 4:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 5:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 6:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #>    Tissue   clid parental_identifier subtype    data_type Concentration
    #>    <char> <char>              <char>  <char>       <char>         <num>
    #> 1:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 2:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 3:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 4:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 5:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 6:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #>    Concentration_2     x normalization_type i.Gnumber  i.DrugName i.drug_moa
    #>              <num> <num>             <char>    <char>      <char>     <char>
    #> 1:              NA    NA               <NA> G02001876 Palbociclib  CDK4|CDK6
    #> 2:              NA    NA               <NA> G02001876 Palbociclib  CDK4|CDK6
    #> 3:              NA    NA               <NA> G02001876 Palbociclib  CDK4|CDK6
    #> 4:              NA    NA               <NA> G02001876 Palbociclib  CDK4|CDK6
    #> 5:              NA    NA               <NA> G02967907    GDC-0077     PI3K-A
    #> 6:              NA    NA               <NA> G02967907    GDC-0077     PI3K-A
    #>    i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration
    #>         <char>       <char>       <char>       <char>       <char>      <num>
    #> 1:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 2:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 3:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 4:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 5:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 6:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #>      i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
    #>      <char>         <char>   <char>                <char>    <char>
    #> 1: CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 2: CL130742          T-47D   Breast                 T-47D   unknown
    #> 3: CL131873        HCC1428   Breast               HCC1428   unknown
    #> 4: CL131903         BT-483   Breast                BT-483   unknown
    #> 5: CL130218         BT-474   Breast                BT-474   unknown
    #> 6: CL131438         CAMA-1   Breast                CAMA-1   unknown
    #>    i.ReferenceDivisionTime
    #>                      <num>
    #> 1:                      30
    #> 2:                      60
    #> 3:                      74
    #> 4:                     130
    #> 5:                      70
    #> 6:                      53
    #>
    #> $BlissExcess
    #> Key: <treatmentid, sampleid>
    #>    treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
    #>         <char>   <char>   <char>     <char>     <char>    <num>  <char>
    #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #>    Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
    #>       <char>   <char>     <char>     <char>       <char>                 <num>
    #> 1:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 2:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 3:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 4:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 5:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 6:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #>    Tissue   clid parental_identifier subtype    data_type Concentration
    #>    <char> <char>              <char>  <char>       <char>         <num>
    #> 1:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 2:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 3:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 4:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 5:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 6:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #>    Concentration_2     x normalization_type i.Gnumber  i.DrugName i.drug_moa
    #>              <num> <num>             <char>    <char>      <char>     <char>
    #> 1:              NA    NA               <NA> G02001876 Palbociclib  CDK4|CDK6
    #> 2:              NA    NA               <NA> G02001876 Palbociclib  CDK4|CDK6
    #> 3:              NA    NA               <NA> G02001876 Palbociclib  CDK4|CDK6
    #> 4:              NA    NA               <NA> G02001876 Palbociclib  CDK4|CDK6
    #> 5:              NA    NA               <NA> G02967907    GDC-0077     PI3K-A
    #> 6:              NA    NA               <NA> G02967907    GDC-0077     PI3K-A
    #>    i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration
    #>         <char>       <char>       <char>       <char>       <char>      <num>
    #> 1:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 2:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 3:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 4:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 5:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 6:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #>      i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
    #>      <char>         <char>   <char>                <char>    <char>
    #> 1: CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 2: CL130742          T-47D   Breast                 T-47D   unknown
    #> 3: CL131873        HCC1428   Breast               HCC1428   unknown
    #> 4: CL131903         BT-483   Breast                BT-483   unknown
    #> 5: CL130218         BT-474   Breast                BT-474   unknown
    #> 6: CL131438         CAMA-1   Breast                CAMA-1   unknown
    #>    i.ReferenceDivisionTime
    #>                      <num>
    #> 1:                      30
    #> 2:                      60
    #> 3:                      74
    #> 4:                     130
    #> 5:                      70
    #> 6:                      53
    #>
    #> $HSAExcess
    #> Key: <treatmentid, sampleid>
    #>    treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
    #>         <char>   <char>   <char>     <char>     <char>    <num>  <char>
    #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #>    Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
    #>       <char>   <char>     <char>     <char>       <char>                 <num>
    #> 1:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 2:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 3:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 4:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 5:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 6:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #>    Tissue   clid parental_identifier subtype    data_type Concentration
    #>    <char> <char>              <char>  <char>       <char>         <num>
    #> 1:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 2:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 3:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 4:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 5:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #> 6:   <NA>   <NA>                <NA>    <NA> single-agent            NA
    #>    Concentration_2     x normalization_type i.Gnumber  i.DrugName i.drug_moa
    #>              <num> <num>             <char>    <char>      <char>     <char>
    #> 1:              NA    NA               <NA> G02001876 Palbociclib  CDK4|CDK6
    #> 2:              NA    NA               <NA> G02001876 Palbociclib  CDK4|CDK6
    #> 3:              NA    NA               <NA> G02001876 Palbociclib  CDK4|CDK6
    #> 4:              NA    NA               <NA> G02001876 Palbociclib  CDK4|CDK6
    #> 5:              NA    NA               <NA> G02967907    GDC-0077     PI3K-A
    #> 6:              NA    NA               <NA> G02967907    GDC-0077     PI3K-A
    #>    i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration
    #>         <char>       <char>       <char>       <char>       <char>      <num>
    #> 1:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 2:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 3:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 4:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 5:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #> 6:        <NA>         <NA>         <NA>         <NA>         <NA>        168
    #>      i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
    #>      <char>         <char>   <char>                <char>    <char>
    #> 1: CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 2: CL130742          T-47D   Breast                 T-47D   unknown
    #> 3: CL131873        HCC1428   Breast               HCC1428   unknown
    #> 4: CL131903         BT-483   Breast                BT-483   unknown
    #> 5: CL130218         BT-474   Breast                BT-474   unknown
    #> 6: CL131438         CAMA-1   Breast                CAMA-1   unknown
    #>    i.ReferenceDivisionTime
    #>                      <num>
    #> 1:                      30
    #> 2:                      60
    #> 3:                      74
    #> 4:                     130
    #> 5:                      70
    #> 6:                      53
    #>
    #> $all_iso_points
    #> Key: <treatmentid, sampleid>
    #>    treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
    #>         <char>   <char>   <char>     <char>     <char>    <num>  <char>
    #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #>    Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
    #>       <char>   <char>     <char>     <char>       <char>                 <num>
    #> 1:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 2:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 3:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 4:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 5:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 6:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #>    Tissue   clid parental_identifier subtype    data_type normalization_type
    #>    <char> <char>              <char>  <char>       <char>             <char>
    #> 1:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 2:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 3:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 4:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 5:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 6:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #>    i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2
    #>       <char>      <char>     <char>      <char>       <char>       <char>
    #> 1: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 2: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 3: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 4: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 5: G02967907    GDC-0077     PI3K-A        <NA>         <NA>         <NA>
    #> 6: G02967907    GDC-0077     PI3K-A        <NA>         <NA>         <NA>
    #>    i.DrugName_3 i.drug_moa_3 i.Duration   i.clid i.CellLineName i.Tissue
    #>          <char>       <char>      <num>   <char>         <char>   <char>
    #> 1:         <NA>         <NA>        168 CL129757          MCF-7   Breast
    #> 2:         <NA>         <NA>        168 CL130742          T-47D   Breast
    #> 3:         <NA>         <NA>        168 CL131873        HCC1428   Breast
    #> 4:         <NA>         <NA>        168 CL131903         BT-483   Breast
    #> 5:         <NA>         <NA>        168 CL130218         BT-474   Breast
    #> 6:         <NA>         <NA>        168 CL131438         CAMA-1   Breast
    #>    i.parental_identifier i.subtype i.ReferenceDivisionTime      x
    #>                   <char>    <char>                   <num> <lgcl>
    #> 1:                 MCF-7   unknown                      30     NA
    #> 2:                 T-47D   unknown                      60     NA
    #> 3:               HCC1428   unknown                      74     NA
    #> 4:                BT-483   unknown                     130     NA
    #> 5:                BT-474   unknown                      70     NA
    #> 6:                CAMA-1   unknown                      53     NA
    #>
    #> $isobolograms
    #> Key: <treatmentid, sampleid>
    #>    treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
    #>         <char>   <char>   <char>     <char>     <char>    <num>  <char>
    #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #>    Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
    #>       <char>   <char>     <char>     <char>       <char>                 <num>
    #> 1:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 2:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 3:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 4:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 5:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 6:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #>    Tissue   clid parental_identifier subtype    data_type normalization_type
    #>    <char> <char>              <char>  <char>       <char>             <char>
    #> 1:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 2:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 3:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 4:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 5:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 6:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #>    i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2
    #>       <char>      <char>     <char>      <char>       <char>       <char>
    #> 1: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 2: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 3: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 4: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 5: G02967907    GDC-0077     PI3K-A        <NA>         <NA>         <NA>
    #> 6: G02967907    GDC-0077     PI3K-A        <NA>         <NA>         <NA>
    #>    i.DrugName_3 i.drug_moa_3 i.Duration   i.clid i.CellLineName i.Tissue
    #>          <char>       <char>      <num>   <char>         <char>   <char>
    #> 1:         <NA>         <NA>        168 CL129757          MCF-7   Breast
    #> 2:         <NA>         <NA>        168 CL130742          T-47D   Breast
    #> 3:         <NA>         <NA>        168 CL131873        HCC1428   Breast
    #> 4:         <NA>         <NA>        168 CL131903         BT-483   Breast
    #> 5:         <NA>         <NA>        168 CL130218         BT-474   Breast
    #> 6:         <NA>         <NA>        168 CL131438         CAMA-1   Breast
    #>    i.parental_identifier i.subtype i.ReferenceDivisionTime      x
    #>                   <char>    <char>                   <num> <lgcl>
    #> 1:                 MCF-7   unknown                      30     NA
    #> 2:                 T-47D   unknown                      60     NA
    #> 3:               HCC1428   unknown                      74     NA
    #> 4:                BT-483   unknown                     130     NA
    #> 5:                BT-474   unknown                      70     NA
    #> 6:                CAMA-1   unknown                      53     NA
    #>
    #> $BlissScore
    #> Key: <treatmentid, sampleid>
    #>    treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
    #>         <char>   <char>   <char>     <char>     <char>    <num>  <char>
    #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #>    Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
    #>       <char>   <char>     <char>     <char>       <char>                 <num>
    #> 1:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 2:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 3:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 4:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 5:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 6:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #>    Tissue   clid parental_identifier subtype    data_type normalization_type
    #>    <char> <char>              <char>  <char>       <char>             <char>
    #> 1:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 2:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 3:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 4:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 5:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 6:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #>        x i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2
    #>    <num>    <char>      <char>     <char>      <char>       <char>       <char>
    #> 1:    NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 2:    NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 3:    NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 4:    NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 5:    NA G02967907    GDC-0077     PI3K-A        <NA>         <NA>         <NA>
    #> 6:    NA G02967907    GDC-0077     PI3K-A        <NA>         <NA>         <NA>
    #>    i.DrugName_3 i.drug_moa_3 i.Duration   i.clid i.CellLineName i.Tissue
    #>          <char>       <char>      <num>   <char>         <char>   <char>
    #> 1:         <NA>         <NA>        168 CL129757          MCF-7   Breast
    #> 2:         <NA>         <NA>        168 CL130742          T-47D   Breast
    #> 3:         <NA>         <NA>        168 CL131873        HCC1428   Breast
    #> 4:         <NA>         <NA>        168 CL131903         BT-483   Breast
    #> 5:         <NA>         <NA>        168 CL130218         BT-474   Breast
    #> 6:         <NA>         <NA>        168 CL131438         CAMA-1   Breast
    #>    i.parental_identifier i.subtype i.ReferenceDivisionTime
    #>                   <char>    <char>                   <num>
    #> 1:                 MCF-7   unknown                      30
    #> 2:                 T-47D   unknown                      60
    #> 3:               HCC1428   unknown                      74
    #> 4:                BT-483   unknown                     130
    #> 5:                BT-474   unknown                      70
    #> 6:                CAMA-1   unknown                      53
    #>
    #> $HSAScore
    #> Key: <treatmentid, sampleid>
    #>    treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
    #>         <char>   <char>   <char>     <char>     <char>    <num>  <char>
    #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #>    Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
    #>       <char>   <char>     <char>     <char>       <char>                 <num>
    #> 1:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 2:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 3:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 4:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 5:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 6:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #>    Tissue   clid parental_identifier subtype    data_type normalization_type
    #>    <char> <char>              <char>  <char>       <char>             <char>
    #> 1:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 2:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 3:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 4:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 5:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 6:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #>        x i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2
    #>    <num>    <char>      <char>     <char>      <char>       <char>       <char>
    #> 1:    NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 2:    NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 3:    NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 4:    NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>
    #> 5:    NA G02967907    GDC-0077     PI3K-A        <NA>         <NA>         <NA>
    #> 6:    NA G02967907    GDC-0077     PI3K-A        <NA>         <NA>         <NA>
    #>    i.DrugName_3 i.drug_moa_3 i.Duration   i.clid i.CellLineName i.Tissue
    #>          <char>       <char>      <num>   <char>         <char>   <char>
    #> 1:         <NA>         <NA>        168 CL129757          MCF-7   Breast
    #> 2:         <NA>         <NA>        168 CL130742          T-47D   Breast
    #> 3:         <NA>         <NA>        168 CL131873        HCC1428   Breast
    #> 4:         <NA>         <NA>        168 CL131903         BT-483   Breast
    #> 5:         <NA>         <NA>        168 CL130218         BT-474   Breast
    #> 6:         <NA>         <NA>        168 CL131438         CAMA-1   Breast
    #>    i.parental_identifier i.subtype i.ReferenceDivisionTime
    #>                   <char>    <char>                   <num>
    #> 1:                 MCF-7   unknown                      30
    #> 2:                 T-47D   unknown                      60
    #> 3:               HCC1428   unknown                      74
    #> 4:                BT-483   unknown                     130
    #> 5:                BT-474   unknown                      70
    #> 6:                CAMA-1   unknown                      53
    #>
    #> $CIScore_50
    #> Key: <treatmentid, sampleid>
    #>    treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
    #>         <char>   <char>   <char>     <char>     <char>    <num>  <char>
    #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #>    Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
    #>       <char>   <char>     <char>     <char>       <char>                 <num>
    #> 1:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 2:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 3:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 4:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 5:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 6:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #>    Tissue   clid parental_identifier subtype    data_type normalization_type
    #>    <char> <char>              <char>  <char>       <char>             <char>
    #> 1:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 2:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 3:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 4:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 5:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 6:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #>         x i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2
    #>    <lgcl>    <char>      <char>     <char>      <char>       <char>
    #> 1:     NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>
    #> 2:     NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>
    #> 3:     NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>
    #> 4:     NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>
    #> 5:     NA G02967907    GDC-0077     PI3K-A        <NA>         <NA>
    #> 6:     NA G02967907    GDC-0077     PI3K-A        <NA>         <NA>
    #>    i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid i.CellLineName
    #>          <char>       <char>       <char>      <num>   <char>         <char>
    #> 1:         <NA>         <NA>         <NA>        168 CL129757          MCF-7
    #> 2:         <NA>         <NA>         <NA>        168 CL130742          T-47D
    #> 3:         <NA>         <NA>         <NA>        168 CL131873        HCC1428
    #> 4:         <NA>         <NA>         <NA>        168 CL131903         BT-483
    #> 5:         <NA>         <NA>         <NA>        168 CL130218         BT-474
    #> 6:         <NA>         <NA>         <NA>        168 CL131438         CAMA-1
    #>    i.Tissue i.parental_identifier i.subtype i.ReferenceDivisionTime
    #>      <char>                <char>    <char>                   <num>
    #> 1:   Breast                 MCF-7   unknown                      30
    #> 2:   Breast                 T-47D   unknown                      60
    #> 3:   Breast               HCC1428   unknown                      74
    #> 4:   Breast                BT-483   unknown                     130
    #> 5:   Breast                BT-474   unknown                      70
    #> 6:   Breast                CAMA-1   unknown                      53
    #>
    #> $CIScore_80
    #> Key: <treatmentid, sampleid>
    #>    treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
    #>         <char>   <char>   <char>     <char>     <char>    <num>  <char>
    #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #>    Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
    #>       <char>   <char>     <char>     <char>       <char>                 <num>
    #> 1:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 2:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 3:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 4:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 5:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 6:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #>    Tissue   clid parental_identifier subtype    data_type normalization_type
    #>    <char> <char>              <char>  <char>       <char>             <char>
    #> 1:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 2:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 3:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 4:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 5:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #> 6:   <NA>   <NA>                <NA>    <NA> single-agent               <NA>
    #>         x i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2
    #>    <lgcl>    <char>      <char>     <char>      <char>       <char>
    #> 1:     NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>
    #> 2:     NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>
    #> 3:     NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>
    #> 4:     NA G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>
    #> 5:     NA G02967907    GDC-0077     PI3K-A        <NA>         <NA>
    #> 6:     NA G02967907    GDC-0077     PI3K-A        <NA>         <NA>
    #>    i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid i.CellLineName
    #>          <char>       <char>       <char>      <num>   <char>         <char>
    #> 1:         <NA>         <NA>         <NA>        168 CL129757          MCF-7
    #> 2:         <NA>         <NA>         <NA>        168 CL130742          T-47D
    #> 3:         <NA>         <NA>         <NA>        168 CL131873        HCC1428
    #> 4:         <NA>         <NA>         <NA>        168 CL131903         BT-483
    #> 5:         <NA>         <NA>         <NA>        168 CL130218         BT-474
    #> 6:         <NA>         <NA>         <NA>        168 CL131438         CAMA-1
    #>    i.Tissue i.parental_identifier i.subtype i.ReferenceDivisionTime
    #>      <char>                <char>    <char>                   <num>
    #> 1:   Breast                 MCF-7   unknown                      30
    #> 2:   Breast                 T-47D   unknown                      60
    #> 3:   Breast               HCC1428   unknown                      74
    #> 4:   Breast                BT-483   unknown                     130
    #> 5:   Breast                BT-474   unknown                      70
    #> 6:   Breast                CAMA-1   unknown                      53
    #>
    #> $Metrics
    #> Key: <treatmentid, sampleid>
    #>    treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
    #>         <char>   <char>   <char>     <char>     <char>    <num>  <char>
    #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>       NA    <NA>
    #>    Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
    #>       <char>   <char>     <char>     <char>       <char>                 <num>
    #> 1:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 2:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 3:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 4:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 5:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #> 6:      <NA>     <NA>       <NA>       <NA>         <NA>                    NA
    #>    Tissue   clid parental_identifier subtype    data_type    x_mean     x_AOC
    #>    <char> <char>              <char>  <char>       <char>     <num>     <num>
    #> 1:   <NA>   <NA>                <NA>    <NA> single-agent 0.4766169 0.5233831
    #> 2:   <NA>   <NA>                <NA>    <NA> single-agent 0.6438030 0.3561970
    #> 3:   <NA>   <NA>                <NA>    <NA> single-agent 0.5797408 0.4202592
    #> 4:   <NA>   <NA>                <NA>    <NA> single-agent 0.4888085 0.5111915
    #> 5:   <NA>   <NA>                <NA>    <NA> single-agent 0.6458536 0.3541464
    #> 6:   <NA>   <NA>                <NA>    <NA> single-agent 0.4821213 0.5178787
    #>    x_AOC_range       xc50    x_max       ec50      x_inf   x_0         h
    #>          <num>      <num>    <num>      <num>      <num> <num>     <num>
    #> 1:   0.5685724 0.07649828 0.107050 0.06354470 0.08684205     1 1.0283168
    #> 2:   0.3828886 0.26119890 0.281750 0.09897928 0.32080324     1 1.0574543
    #> 3:   0.4560827 0.10802210 0.207125 0.08784832 0.21933259     1 2.7932767
    #> 4:   0.5620006 0.06629065 0.111625 0.05911087 0.12311310     1 2.4657832
    #> 5:   0.3770687 0.26781723 0.228300 0.13626047 0.27577126     1 1.1867664
    #> 6:   0.5639825 0.06294109 0.148225 0.04029515 0.16592442     1 0.9041923
    #>           r2   x_sd_avg               fit_type maxlog10Concentration N_conc
    #>        <num>      <num>                 <char>                 <num>  <int>
    #> 1: 0.9853800 0.05272629 DRC3pHillFitModelFixS0                     1     10
    #> 2: 0.9465590 0.07259453 DRC3pHillFitModelFixS0                     1     10
    #> 3: 0.9787945 0.06655135 DRC3pHillFitModelFixS0                     1     10
    #> 4: 0.9946671 0.07915584 DRC3pHillFitModelFixS0                     1     10
    #> 5: 0.9616801 0.06463053 DRC3pHillFitModelFixS0                     1     10
    #> 6: 0.9740112 0.05594059 DRC3pHillFitModelFixS0                     1     10
    #>    normalization_type fit_source cotrt_value source i.Gnumber  i.DrugName
    #>                <char>     <char>       <num> <char>    <char>      <char>
    #> 1:                 RV        gDR          NA   <NA> G02001876 Palbociclib
    #> 2:                 RV        gDR          NA   <NA> G02001876 Palbociclib
    #> 3:                 RV        gDR          NA   <NA> G02001876 Palbociclib
    #> 4:                 RV        gDR          NA   <NA> G02001876 Palbociclib
    #> 5:                 RV        gDR          NA   <NA> G02001876 Palbociclib
    #> 6:                 RV        gDR          NA   <NA> G02001876 Palbociclib
    #>    i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3
    #>        <char>      <char>       <char>       <char>       <char>       <char>
    #> 1:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 2:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 3:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 4:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 5:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 6:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #>    i.Duration   i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
    #>         <num>   <char>         <char>   <char>                <char>    <char>
    #> 1:        168 CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 2:        168 CL130218         BT-474   Breast                BT-474   unknown
    #> 3:        168 CL130742          T-47D   Breast                 T-47D   unknown
    #> 4:        168 CL131438         CAMA-1   Breast                CAMA-1   unknown
    #> 5:        168 CL131873        HCC1428   Breast               HCC1428   unknown
    #> 6:        168 CL131891         EFM-19   Breast                EFM-19   unknown
    #>    i.ReferenceDivisionTime
    #>                      <num>
    #> 1:                      30
    #> 2:                      70
    #> 3:                      60
    #> 4:                      53
    #> 5:                      74
    #> 6:                      64

    assayNames(tre)
    #>  [1] "RawTreated"     "Controls"       "Normalized"     "Averaged"
    #>  [5] "SmoothMatrix"   "BlissExcess"    "HSAExcess"      "all_iso_points"
    #>  [9] "isobolograms"   "BlissScore"     "HSAScore"       "CIScore_50"
    #> [13] "CIScore_80"     "Metrics"

    head(assay(tre, "Metrics"),3)
    #> Key: <treatmentid, sampleid>
    #>                            treatmentid                                 sampleid
    #>                                 <char>                                   <char>
    #> 1: G02001876_Palbociclib_CDK4|CDK6_168   CL129757_MCF-7_Breast_MCF-7_unknown_30
    #> 2: G02001876_Palbociclib_CDK4|CDK6_168 CL130218_BT-474_Breast_BT-474_unknown_70
    #> 3: G02001876_Palbociclib_CDK4|CDK6_168   CL130742_T-47D_Breast_T-47D_unknown_60
    #>       DrugName DrugName_2 DrugName_3 Duration   Gnumber Gnumber_2  drug_moa
    #>         <char>     <char>     <char>    <num>    <char>    <char>    <char>
    #> 1: Palbociclib       <NA>       <NA>      168 G02001876      <NA> CDK4|CDK6
    #> 2: Palbociclib       <NA>       <NA>      168 G02001876      <NA> CDK4|CDK6
    #> 3: Palbociclib       <NA>       <NA>      168 G02001876      <NA> CDK4|CDK6
    #>    drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime Tissue     clid
    #>        <char>     <char>       <char>                 <num> <char>   <char>
    #> 1:       <NA>       <NA>        MCF-7                    30 Breast CL129757
    #> 2:       <NA>       <NA>       BT-474                    70 Breast CL130218
    #> 3:       <NA>       <NA>        T-47D                    60 Breast CL130742
    #>    parental_identifier subtype    data_type    x_mean     x_AOC x_AOC_range
    #>                 <char>  <char>       <char>     <num>     <num>       <num>
    #> 1:               MCF-7 unknown single-agent 0.4774514 0.5225486   0.5592516
    #> 2:              BT-474 unknown single-agent 0.5916887 0.4083113   0.4338082
    #> 3:               T-47D unknown single-agent 0.5478704 0.4521296   0.4876840
    #>         xc50     x_max      ec50       x_inf   x_0         h        r2
    #>        <num>     <num>     <num>       <num> <num>     <num>     <num>
    #> 1: 0.1100133 -0.017025 0.1161741 -0.03117468     1 1.1100114 0.9880388
    #> 2: 0.2091202  0.114275 0.1360264  0.16571556     1 0.9361851 0.9555750
    #> 3: 0.1164343  0.111425 0.1033672  0.13053185     1 2.5415386 0.9815621
    #>      x_sd_avg               fit_type maxlog10Concentration N_conc
    #>         <num>                 <char>                 <num>  <int>
    #> 1: 0.05887778 DRC3pHillFitModelFixS0                     1     10
    #> 2: 0.08197778 DRC3pHillFitModelFixS0                     1     10
    #> 3: 0.06581980 DRC3pHillFitModelFixS0                     1     10
    #>    normalization_type fit_source cotrt_value source i.Gnumber  i.DrugName
    #>                <char>     <char>       <num> <char>    <char>      <char>
    #> 1:                 GR        gDR          NA   <NA> G02001876 Palbociclib
    #> 2:                 GR        gDR          NA   <NA> G02001876 Palbociclib
    #> 3:                 GR        gDR          NA   <NA> G02001876 Palbociclib
    #>    i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3
    #>        <char>      <char>       <char>       <char>       <char>       <char>
    #> 1:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 2:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #> 3:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA>
    #>    i.Duration   i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
    #>         <num>   <char>         <char>   <char>                <char>    <char>
    #> 1:        168 CL129757          MCF-7   Breast                 MCF-7   unknown
    #> 2:        168 CL130218         BT-474   Breast                BT-474   unknown
    #> 3:        168 CL130742          T-47D   Breast                 T-47D   unknown
    #>    i.ReferenceDivisionTime
    #>                      <num>
    #> 1:                      30
    #> 2:                      70
    #> 3:                      60

# References

1. Song, K. W., Edgar, K. A., Hanan, E. J., Hafner, M., Oeh, J., Merchant, M., … & Friedman, L. S. (2022). RTK-dependent inducible degradation of mutant PI3K drives GDC-0077 (Inavolisib) efficacy. Cancer discovery, 12(1), 204-219.

    sessionInfo()
    #> R version 4.4.0 beta (2024-04-15 r86425 ucrt)
    #> Platform: x86_64-w64-mingw32/x64
    #> Running under: Windows Server 2022 x64 (build 20348)
    #>
    #> Matrix products: default
    #>
    #>
    #> locale:
    #> [1] LC_COLLATE=C
    #> [2] LC_CTYPE=English_United States.utf8
    #> [3] LC_MONETARY=English_United States.utf8
    #> [4] LC_NUMERIC=C
    #> [5] LC_TIME=English_United States.utf8
    #>
    #> time zone: America/New_York
    #> tzcode source: internal
    #>
    #> attached base packages:
    #> [1] stats4    stats     graphics  grDevices utils     datasets  methods
    #> [8] base
    #>
    #> other attached packages:
    #>  [1] MultiAssayExperiment_1.30.0 gDRimport_1.2.0
    #>  [3] PharmacoGx_3.8.0            CoreGx_2.8.0
    #>  [5] SummarizedExperiment_1.34.0 Biobase_2.64.0
    #>  [7] GenomicRanges_1.56.0        GenomeInfoDb_1.40.0
    #>  [9] IRanges_2.38.0              S4Vectors_0.42.0
    #> [11] MatrixGenerics_1.16.0       matrixStats_1.3.0
    #> [13] BiocGenerics_0.50.0
    #>
    #> loaded via a namespace (and not attached):
    #>   [1] bitops_1.0-7            rlang_1.1.3             magrittr_2.0.3
    #>   [4] shinydashboard_0.7.2    compiler_4.4.0          vctrs_0.6.5
    #>   [7] reshape2_1.4.4          relations_0.6-13        stringr_1.5.1
    #>  [10] pkgconfig_2.0.3         crayon_1.5.2            fastmap_1.1.1
    #>  [13] backports_1.4.1         XVector_0.44.0          caTools_1.18.2
    #>  [16] utf8_1.2.4              promises_1.3.0          rmarkdown_2.26
    #>  [19] UCSC.utils_1.0.0        coop_0.6-3              xfun_0.43
    #>  [22] zlibbioc_1.50.0         cachem_1.0.8            jsonlite_1.8.8
    #>  [25] SnowballC_0.7.1         later_1.3.2             DelayedArray_0.30.0
    #>  [28] BiocParallel_1.38.0     parallel_4.4.0          sets_1.0-25
    #>  [31] cluster_2.1.6           R6_2.5.1                stringi_1.8.3
    #>  [34] bslib_0.7.0             RColorBrewer_1.1-3      qs_0.26.1
    #>  [37] limma_3.60.0            boot_1.3-30             jquerylib_0.1.4
    #>  [40] Rcpp_1.0.12             knitr_1.46              downloader_0.4
    #>  [43] httpuv_1.6.15           Matrix_1.7-0            igraph_2.0.3
    #>  [46] tidyselect_1.2.1        abind_1.4-5             yaml_2.3.8
    #>  [49] stringfish_0.16.0       gplots_3.1.3.1          codetools_0.2-20
    #>  [52] lattice_0.22-6          tibble_3.2.1            plyr_1.8.9
    #>  [55] shiny_1.8.1.1           BumpyMatrix_1.12.0      evaluate_0.23
    #>  [58] RcppParallel_5.1.7      bench_1.1.3             pillar_1.9.0
    #>  [61] lsa_0.73.3              KernSmooth_2.23-22      checkmate_2.3.1
    #>  [64] DT_0.33                 shinyjs_2.1.0           piano_2.20.0
    #>  [67] generics_0.1.3          ggplot2_3.5.1           munsell_0.5.1
    #>  [70] scales_1.3.0            RApiSerialize_0.1.2     gtools_3.9.5
    #>  [73] xtable_1.8-4            marray_1.82.0           glue_1.7.0
    #>  [76] slam_0.1-50             tools_4.4.0             data.table_1.15.4
    #>  [79] gDRutils_1.2.0          fgsea_1.30.0            visNetwork_2.1.2
    #>  [82] fastmatch_1.1-4         cowplot_1.1.3           grid_4.4.0
    #>  [85] colorspace_2.1-0        GenomeInfoDbData_1.2.12 cli_3.6.2
    #>  [88] fansi_1.0.6             S4Arrays_1.4.0          dplyr_1.1.4
    #>  [91] gtable_0.3.5            sass_0.4.9              digest_0.6.35
    #>  [94] SparseArray_1.4.0       htmlwidgets_1.6.4       htmltools_0.5.8.1
    #>  [97] lifecycle_1.0.4         httr_1.4.7              statmod_1.5.0
    #> [100] mime_0.12