diff --git a/DESCRIPTION b/DESCRIPTION index 3263669..cfc5bd8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,9 +1,9 @@ Package: gDRtestData Title: gDRtestData - R data package with testing dose response data -Version: 1.9.1 -Date: 2025-10-30 +Version: 1.9.2 +Date: 2026-04-13 Description: R package with internal dose-response test data. Package provides functions to generate - input testing data that can be used as the input for gDR pipeline. It also contains qs files + input testing data that can be used as the input for gDR pipeline. It also contains qs2 files with MAE data processed by gDR. Authors@R: c(person("Aleksander", "Chlebowski", role=c("aut")), person("Bartosz", "Czech", role=c("aut"), @@ -27,7 +27,7 @@ Suggests: BiocStyle, gDRstyle (>= 1.7.1), knitr, - qs, + qs2, reshape2, rmarkdown, SummarizedExperiment, diff --git a/NEWS.md b/NEWS.md index 1d2d8ea..f1f8b1c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,6 @@ +## gDRtestData 1.9.2 - 2026-04-13 +* migrate test data files from `.qs` to `.qs2` format + ## gDRtestData 1.9.1 - 2025-10-30 * synchronize Bioconductor and GitHub versioning diff --git a/R/get_test_datasets.R b/R/get_test_datasets.R index 297324e..8fa40df 100644 --- a/R/get_test_datasets.R +++ b/R/get_test_datasets.R @@ -4,7 +4,7 @@ #' #' @param datasets_dir path to directory with datasets (default \code{NULL}). #' If \code{NULL}, then \code{inst/testdata} directory from \code{gDRtestData} will be used. -#' @param pattern used to: (1) filter to qs files from the dataset_dir path +#' @param pattern used to: (1) filter to qs2 files from the dataset_dir path #' and (2) prettify the labels of the files #' @keywords generate_test_data #' @@ -33,8 +33,8 @@ get_test_dataset_paths <- checkmate::assert_string(pattern, min.chars = 1) - epaths <- list.files(datasets_dir, pattern = pattern, full.names = TRUE) - enames <- gsub(pattern, "", gsub(".qs", "", basename(epaths))) + epaths <- list.files(datasets_dir, pattern = paste0(pattern, ".*\\.qs2$"), full.names = TRUE) + enames <- gsub(pattern, "", gsub("\\.qs2$", "", basename(epaths))) structure(epaths, names = enames) } diff --git a/README.md b/README.md index 9d3dfe9..d73fbb4 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ gDRtestData - R data package with testing dose response data to be used by all g # Available data -- `inst/testdata/` directory with R datasets provided in the package in qs format +- `inst/testdata/` directory with R datasets provided in the package in qs2 format - `inst/annotation_data/` annotation data provided in the package diff --git a/inst/testdata/P_999.qs2 b/inst/testdata/P_999.qs2 new file mode 100644 index 0000000..b123ce6 Binary files /dev/null and b/inst/testdata/P_999.qs2 differ diff --git a/inst/testdata/finalMAE_combo_2dose_nonoise.qs2 b/inst/testdata/finalMAE_combo_2dose_nonoise.qs2 new file mode 100644 index 0000000..f674196 Binary files /dev/null and b/inst/testdata/finalMAE_combo_2dose_nonoise.qs2 differ diff --git a/inst/testdata/finalMAE_combo_2dose_nonoise2.qs2 b/inst/testdata/finalMAE_combo_2dose_nonoise2.qs2 new file mode 100644 index 0000000..fb9a9be Binary files /dev/null and b/inst/testdata/finalMAE_combo_2dose_nonoise2.qs2 differ diff --git a/inst/testdata/finalMAE_combo_2dose_nonoise3.qs2 b/inst/testdata/finalMAE_combo_2dose_nonoise3.qs2 new file mode 100644 index 0000000..02c0969 Binary files /dev/null and b/inst/testdata/finalMAE_combo_2dose_nonoise3.qs2 differ diff --git a/inst/testdata/finalMAE_combo_codilution.qs2 b/inst/testdata/finalMAE_combo_codilution.qs2 new file mode 100644 index 0000000..efb9aca Binary files /dev/null and b/inst/testdata/finalMAE_combo_codilution.qs2 differ diff --git a/inst/testdata/finalMAE_combo_codilution_small.qs2 b/inst/testdata/finalMAE_combo_codilution_small.qs2 new file mode 100644 index 0000000..0ce4265 Binary files /dev/null and b/inst/testdata/finalMAE_combo_codilution_small.qs2 differ diff --git a/inst/testdata/finalMAE_combo_matrix.qs2 b/inst/testdata/finalMAE_combo_matrix.qs2 new file mode 100644 index 0000000..414473e Binary files /dev/null and b/inst/testdata/finalMAE_combo_matrix.qs2 differ diff --git a/inst/testdata/finalMAE_combo_matrix_small.qs2 b/inst/testdata/finalMAE_combo_matrix_small.qs2 new file mode 100644 index 0000000..59ca8ba Binary files /dev/null and b/inst/testdata/finalMAE_combo_matrix_small.qs2 differ diff --git a/inst/testdata/finalMAE_combo_triple.qs2 b/inst/testdata/finalMAE_combo_triple.qs2 new file mode 100644 index 0000000..4fb7778 Binary files /dev/null and b/inst/testdata/finalMAE_combo_triple.qs2 differ diff --git a/inst/testdata/finalMAE_medium.qs2 b/inst/testdata/finalMAE_medium.qs2 new file mode 100644 index 0000000..f03cc2a Binary files /dev/null and b/inst/testdata/finalMAE_medium.qs2 differ diff --git a/inst/testdata/finalMAE_small.qs2 b/inst/testdata/finalMAE_small.qs2 new file mode 100644 index 0000000..52e5284 Binary files /dev/null and b/inst/testdata/finalMAE_small.qs2 differ diff --git a/inst/testdata/finalMAE_small_no_noise.qs2 b/inst/testdata/finalMAE_small_no_noise.qs2 new file mode 100644 index 0000000..cdfedb0 Binary files /dev/null and b/inst/testdata/finalMAE_small_no_noise.qs2 differ diff --git a/inst/testdata/finalMAE_wLigand.qs2 b/inst/testdata/finalMAE_wLigand.qs2 new file mode 100644 index 0000000..e84f4b8 Binary files /dev/null and b/inst/testdata/finalMAE_wLigand.qs2 differ diff --git a/inst/testdata/metaprojects.qs2 b/inst/testdata/metaprojects.qs2 new file mode 100644 index 0000000..de263b3 Binary files /dev/null and b/inst/testdata/metaprojects.qs2 differ diff --git a/inst/testdata/projects.qs2 b/inst/testdata/projects.qs2 new file mode 100644 index 0000000..dabd28d Binary files /dev/null and b/inst/testdata/projects.qs2 differ diff --git a/inst/testdata/synthetic_list.yml b/inst/testdata/synthetic_list.yml index f986b64..fc2ad02 100644 --- a/inst/testdata/synthetic_list.yml +++ b/inst/testdata/synthetic_list.yml @@ -1,72 +1,72 @@ combo_2dose_nonoise: name: finalMAE_combo_2dose_nonoise - file: finalMAE_combo_2dose_nonoise.qs + file: finalMAE_combo_2dose_nonoise.qs2 script: generateComboNoNoiseData imported_as_example: TRUE description: "3 drugs x 2 co-treatment (1 drug at 2 doses) by 3 cell lines; co-treatment drug occurs also as a primary drug" combo_2dose_nonoise2: name: finalMAE_combo_2dose_nonoise2 - file: finalMAE_combo_2dose_nonoise2.qs + file: finalMAE_combo_2dose_nonoise2.qs2 script: generateComboNoNoiseData2 imported_as_example: FALSE description: "3 drugs x 2 co-treatment (1 drug at 2 doses) by 3 cell lines; co-treatment drug occurs also as a primary drug" combo_2dose_nonoise3: name: finalMAE_combo_2dose_nonoise3 - file: finalMAE_combo_2dose_nonoise3.qs + file: finalMAE_combo_2dose_nonoise3.qs2 script: generateComboNoNoiseData3 imported_as_example: FALSE description: "3 drugs x 2 co-treatment (1 drug at 2 doses) by 3 lines; co-treatment drug does NOT have single agent response" combo_codilution_small: name: finalMAE_combo_codilution_small - file: finalMAE_combo_codilution_small.qs + file: finalMAE_combo_codilution_small.qs2 script: generateCodilutionSmall imported_as_example: FALSE description: "4 x 1 drugs (co-dilution) for 2 cell lines; no noise" combo_codilution: name: finalMAE_combo_codilution - file: finalMAE_combo_codilution.qs + file: finalMAE_combo_codilution.qs2 script: generateCodilution imported_as_example: FALSE description: "12 x 1 drugs (co-dilution) for 8 cell lines; no noise" combo_matrix_small: name: finalMAE_combo_matrix_small - file: finalMAE_combo_matrix_small.qs + file: finalMAE_combo_matrix_small.qs2 script: generateComboMatrixSmall imported_as_example: FALSE description: "3 x 2 drugs (matrix) for 2 cell lines; no noise" combo_matrix: name: finalMAE_combo_matrix - file: finalMAE_combo_matrix.qs + file: finalMAE_combo_matrix.qs2 script: generateComboMatrix imported_as_example: TRUE description: "6 x 3 drugs (matrix) for 8 cell lines" combo_triple: name: finalMAE_combo_triple - file: finalMAE_combo_triple.qs + file: finalMAE_combo_triple.qs2 script: generateTripleComboMatrix imported_as_example: TRUE description: "2 x 3 x 2 drugs (triple matrix) for 4 cell lines" medium: name: finalMAE_medium - file: finalMAE_medium.qs + file: finalMAE_medium.qs2 script: generateMediumData imported_as_example: TRUE description: "40 drugs (6 different drug_moa) by 15 lines (3 tissues); single agent" small_no_noise: name: finalMAE_small_no_noise - file: finalMAE_small_no_noise.qs + file: finalMAE_small_no_noise.qs2 script: generateNoNoiseRawData imported_as_example: FALSE description: "10 drugs (3 different drug_moa) by 10 lines (3 tissues); single agent - no noise in the data" small: name: finalMAE_small - file: finalMAE_small.qs + file: finalMAE_small.qs2 script: generateNoiseRawData imported_as_example: TRUE description: "10 drugs (3 different drug_moa) by 10 lines (3 tissues); single agent" wLigand: name: finalMAE_wLigand - file: finalMAE_wLigand.qs + file: finalMAE_wLigand.qs2 script: generateLigandData imported_as_example: TRUE description: "3 drugs by 4 lines (3 tissues); `Ligand = 0.1` as reference; single agent" diff --git a/man/gDRtestData-package.Rd b/man/gDRtestData-package.Rd index 7dddb9f..da23245 100644 --- a/man/gDRtestData-package.Rd +++ b/man/gDRtestData-package.Rd @@ -9,7 +9,7 @@ package help page } \description{ -R package with internal dose-response test data. Package provides functions to generate input testing data that can be used as the input for gDR pipeline. It also contains qs files with MAE data processed by gDR. +R package with internal dose-response test data. Package provides functions to generate input testing data that can be used as the input for gDR pipeline. It also contains qs2 files with MAE data processed by gDR. } \note{ To learn more about functions start with \code{help(package = "gDRtestData")} diff --git a/man/get_test_dataset_paths.Rd b/man/get_test_dataset_paths.Rd index 17a5a3b..85177ad 100644 --- a/man/get_test_dataset_paths.Rd +++ b/man/get_test_dataset_paths.Rd @@ -10,7 +10,7 @@ get_test_dataset_paths(datasets_dir = NULL, pattern = "finalMAE_") \item{datasets_dir}{path to directory with datasets (default \code{NULL}). If \code{NULL}, then \code{inst/testdata} directory from \code{gDRtestData} will be used.} -\item{pattern}{used to: (1) filter to qs files from the dataset_dir path +\item{pattern}{used to: (1) filter to qs2 files from the dataset_dir path and (2) prettify the labels of the files} } \value{ diff --git a/vignettes/gDRtestData.Rmd b/vignettes/gDRtestData.Rmd index 3e5d825..42b8d5a 100644 --- a/vignettes/gDRtestData.Rmd +++ b/vignettes/gDRtestData.Rmd @@ -109,7 +109,7 @@ head(response_data) 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 `qs` 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: +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: ```{r echo=FALSE} yml_path <- system.file(package = "gDRtestData", "testdata", "synthetic_list.yml") cat(paste0("* ", names(yaml::read_yaml(yml_path)), collapse = ", \n"), ".")