Overview
The gDRtestData package is intended to store and
generate example data that can be used through the gDR
suite.
Use Cases
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.
- Replicates
cl_rep <- add_data_replicates(cell_lines)
head(cl_rep)- 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:
- Hill coefficient
hill <- generate_hill_coef(cell_lines, drugs)- EC50 metric
ec50_met <- generate_ec50(cell_lines, drugs)- 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 |
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.
SessionInfo
sessionInfo()
#> R version 4.6.0 (2026-04-24)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.4 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
#> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: UTC
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] gDRtestData_1.11.5 BiocStyle_2.40.0
#>
#> loaded via a namespace (and not attached):
#> [1] cli_3.6.6 knitr_1.51 rlang_1.2.0
#> [4] xfun_0.58 otel_0.2.0 textshaping_1.0.5
#> [7] data.table_1.18.4 jsonlite_2.0.0 backports_1.5.1
#> [10] htmltools_0.5.9 ragg_1.5.2 sass_0.4.10
#> [13] rmarkdown_2.31 evaluate_1.0.5 jquerylib_0.1.4
#> [16] fastmap_1.2.0 yaml_2.3.12 lifecycle_1.0.5
#> [19] bookdown_0.46 BiocManager_1.30.27 compiler_4.6.0
#> [22] fs_2.1.0 systemfonts_1.3.2 digest_0.6.39
#> [25] R6_2.6.1 checkmate_2.3.4 bslib_0.11.0
#> [28] tools_4.6.0 pkgdown_2.2.0 cachem_1.1.0
#> [31] desc_1.4.3