Author: gDR team
Date: 2026-04-23

# gDRtestData

gDR team

#### 23 April 2026

# Contents

# 1 Overview

The `gDRtestData` package is intended to store and generate example data that can be used through the `gDR` suite.

# 2 Use Cases

## 2.1 Synthetic data generation

Since gDR is a computational suite for drug response data from any experiment, a synthetic dataset is also needed for testing and exploration.

The basis of this package are two functions to generate the synthetic sets of cell lines and drugs.

    cell_lines <- create_synthetic_cell_lines()
    drugs <- create_synthetic_drugs()

These base objects can be extended with additional information.

1. Replicates

    cl_rep <- add_data_replicates(cell_lines)
    head(cl_rep)

2. Concentration

    cl_conc <- add_concentration(cell_lines)
    head(cl_conc)

Or the user can do both with one function:

    df_layout <- prepareData(cell_lines, drugs)
    head(df_layout)

Additionally, the user may fill in the full response data with the day 0 part.

    df_layout_small <- prepareData(cell_lines[seq_len(2), ], drugs[seq_len(4), ])
    df_layout_small$Duration <- 72
    df_layout_small$ReadoutValue <- 0
    df_layout_small_with_Day0 <- add_day0_data(df_layout_small)
    head(df_layout_small_with_Day0)

In a further step, the user may generate a set of synthetic results:

1. Hill coefficient

    hill <- generate_hill_coef(cell_lines, drugs)

2. EC50 metric

    ec50_met <- generate_ec50(cell_lines, drugs)

3. E inf metric

    einf_met <- generate_e_inf(cell_lines, drugs)

Or the user can create full response data with one function (for single-agent):

    response_data <- prepareMergedData(cell_lines, drugs)
    head(response_data)

SUMMARY

Step | Function | Output (`data.table`)
--- | --- | ---
0 | create_synthetic_cell_lines() | synthetic cell lines
0 | create_synthetic_drugs() | synthetic drugs
1 | prepareData() | cell lines and drug merged with replicates and concentration
2 | prepareMergedData() | full response data for single-agent
2 | prepareComboMergedData() | full response data for combo
2 | prepareCodilutionData () | full response data for co-dilution

## 2.2 Synthetic object of gDR data model

The gDR data model is built on the MultiAssayExperiments (MAE) structure. A detailed description of the gDR data model can be found in `gDRcore` package vignette.

In `inst/testdata` the user may find a set of `qs2` files that are examples of gDR data model for different data types. In the file `synthetic_list.yml` one can find a list of these datasets. Currently available are:

    #> * combo_2dose_nonoise,
    #> * combo_2dose_nonoise2,
    #> * combo_2dose_nonoise3,
    #> * combo_codilution_small,
    #> * combo_codilution,
    #> * combo_matrix_small,
    #> * combo_matrix,
    #> * combo_triple,
    #> * medium,
    #> * small_no_noise,
    #> * small,
    #> * wLigand .

The script `generate_example_data.R` which shows how to generate and process above-mentioned datasets is in `inst/scripts` dir. All key functions can be found in package `gDRcore` in script `generate_wrappers.R`.

## 2.3 Annotation data

In `inst/annotation_data` the user can find `CSV` files used in `gDRcore` for testing annotation functions.

## 2.4 Other

Other files which were not mentioned above are used for testing gDR suite functionality.

# SessionInfo

    sessionInfo()
    #> R version 4.6.0 RC (2026-04-17 r89917)
    #> Platform: x86_64-pc-linux-gnu
    #> Running under: Ubuntu 24.04.4 LTS
    #>
    #> Matrix products: default
    #> BLAS:   /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so
    #> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 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] stats     graphics  grDevices utils     datasets  methods   base
    #>
    #> other attached packages:
    #> [1] gDRtestData_1.9.2 BiocStyle_2.39.0
    #>
    #> loaded via a namespace (and not attached):
    #>  [1] backports_1.5.1     digest_0.6.39       R6_2.6.1
    #>  [4] bookdown_0.46       fastmap_1.2.0       xfun_0.57
    #>  [7] cachem_1.1.0        knitr_1.51          htmltools_0.5.9
    #> [10] rmarkdown_2.31      lifecycle_1.0.5     cli_3.6.6
    #> [13] sass_0.4.10         data.table_1.18.2.1 jquerylib_0.1.4
    #> [16] compiler_4.6.0      tools_4.6.0         checkmate_2.3.4
    #> [19] evaluate_1.0.5      bslib_0.10.0        yaml_2.3.12
    #> [22] otel_0.2.0          BiocManager_1.30.27 jsonlite_2.0.0
    #> [25] rlang_1.2.0