The gDRtestData package is intended to store and
generate example data that can be used through the gDR
suite.
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.
These base objects can be extended with additional information.
Or the user can do both with one function:
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:
Or the user can create full response data with one function (for single-agent):
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 |
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.
In inst/annotation_data the user can find
CSV files used in gDRcore for testing
annotation functions.
Other files which were not mentioned above are used for testing gDR suite functionality.
sessionInfo()
#> R version 4.6.1 (2026-06-24)
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#> attached base packages:
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#> [1] gDRtestData_1.10.0 BiocStyle_2.40.0
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#> [1] backports_1.5.1 digest_0.6.39 R6_2.6.1
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