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")
#> 2024-10-29 17:28:33 Building assay index...
#> 2024-10-29 17:28:33 Joining rowData to assayIndex...
#> 2024-10-29 17:28:33 Joining colData to assayIndex...
#> 2024-10-29 17:28:34 Joining assays to assayIndex...
#> 2024-10-29 17:28:35 Setting assayIndex key...
#> 2024-10-29 17:28:36 Building LongTable...

We can now view the PharmacoSet object.

pset
#> <PharmacoSet>
#> Name: Kyung2022 
#> Date Created: Tue Oct 29 17:28:36 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 Under development (unstable) (2024-10-21 r87258)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.1 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so 
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB              LC_COLLATE=C              
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: America/New_York
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] MultiAssayExperiment_1.33.0 gDRimport_1.5.0            
#>  [3] PharmacoGx_3.11.0           CoreGx_2.11.0              
#>  [5] SummarizedExperiment_1.37.0 Biobase_2.67.0             
#>  [7] GenomicRanges_1.59.0        GenomeInfoDb_1.43.0        
#>  [9] IRanges_2.41.0              S4Vectors_0.45.0           
#> [11] MatrixGenerics_1.19.0       matrixStats_1.4.1          
#> [13] BiocGenerics_0.53.0        
#> 
#> loaded via a namespace (and not attached):
#>   [1] bitops_1.0-9            rlang_1.1.4             magrittr_2.0.3         
#>   [4] shinydashboard_0.7.2    compiler_4.5.0          vctrs_0.6.5            
#>   [7] reshape2_1.4.4          relations_0.6-13        stringr_1.5.1          
#>  [10] pkgconfig_2.0.3         crayon_1.5.3            fastmap_1.2.0          
#>  [13] backports_1.5.0         XVector_0.47.0          caTools_1.18.3         
#>  [16] utf8_1.2.4              promises_1.3.0          rmarkdown_2.28         
#>  [19] UCSC.utils_1.3.0        coop_0.6-3              xfun_0.48              
#>  [22] zlibbioc_1.53.0         cachem_1.1.0            jsonlite_1.8.9         
#>  [25] SnowballC_0.7.1         later_1.3.2             DelayedArray_0.33.0    
#>  [28] BiocParallel_1.41.0     parallel_4.5.0          sets_1.0-25            
#>  [31] cluster_2.1.6           R6_2.5.1                stringi_1.8.4          
#>  [34] bslib_0.8.0             RColorBrewer_1.1-3      qs_0.27.2              
#>  [37] limma_3.63.0            boot_1.3-31             jquerylib_0.1.4        
#>  [40] Rcpp_1.0.13             knitr_1.48              downloader_0.4         
#>  [43] httpuv_1.6.15           Matrix_1.7-1            igraph_2.1.1           
#>  [46] tidyselect_1.2.1        abind_1.4-8             yaml_2.3.10            
#>  [49] stringfish_0.16.0       gplots_3.2.0            codetools_0.2-20       
#>  [52] lattice_0.22-6          tibble_3.2.1            plyr_1.8.9             
#>  [55] shiny_1.9.1             BumpyMatrix_1.15.0      evaluate_1.0.1         
#>  [58] RcppParallel_5.1.9      bench_1.1.3             pillar_1.9.0           
#>  [61] lsa_0.73.3              KernSmooth_2.23-24      checkmate_2.3.2        
#>  [64] DT_0.33                 shinyjs_2.1.0           piano_2.23.0           
#>  [67] generics_0.1.3          ggplot2_3.5.1           munsell_0.5.1          
#>  [70] scales_1.3.0            RApiSerialize_0.1.4     gtools_3.9.5           
#>  [73] xtable_1.8-4            marray_1.85.0           glue_1.8.0             
#>  [76] slam_0.1-54             tools_4.5.0             data.table_1.16.2      
#>  [79] gDRutils_1.5.0          fgsea_1.33.0            visNetwork_2.1.2       
#>  [82] fastmatch_1.1-4         cowplot_1.1.3           grid_4.5.0             
#>  [85] colorspace_2.1-1        GenomeInfoDbData_1.2.13 cli_3.6.3              
#>  [88] fansi_1.0.6             S4Arrays_1.7.0          dplyr_1.1.4            
#>  [91] gtable_0.3.6            sass_0.4.9              digest_0.6.37          
#>  [94] SparseArray_1.7.0       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