# gDRimport

# Overview

The `gDRimport` package is a part of the gDR suite. It helps to prepare raw drug response data for downstream processing. It mainly contains helper functions for importing/loading/validating dose response data provided in different file formats.

# Use Cases

## Test Data

There are currently four test datasets that can be used to see what’s the expected input data for the gDRimport.

    # primary test data
    td1 <- get_test_data()
    summary(td1)

    ##        Length         Class          Mode
    ##             1 gdr_test_data            S4

    td1

    ## class: gdr_test_data
    ## slots: manifest_path result_path template_path ref_m_df ref_r1_r2 ref_r1 ref_t1_t2 ref_t1

    # test data in Tecan format
    td2 <- get_test_Tecan_data()
    summary(td2)

    ##          Length Class  Mode
    ## m_file   1      -none- character
    ## r_files  1      -none- character
    ## t_files  1      -none- character
    ## ref_m_df 1      -none- character
    ## ref_r_df 1      -none- character
    ## ref_t_df 1      -none- character

    # test data in D300 format
    td3 <- get_test_D300_data()
    summary(td3)

    ##        Length Class  Mode
    ## f_96w  6      -none- list
    ## f_384w 6      -none- list

    # test data obtained from EnVision
    td4 <- get_test_EnVision_data()
    summary(td4)

    ##            Length Class  Mode
    ## m_file      1     -none- character
    ## r_files    28     -none- character
    ## t_files     2     -none- character
    ## ref_l_path  1     -none- character

## Load data

The `load_data` is the key function. It wraps `load_manifest`, `load_templates` and `load_results` functions and supports different file formats.

    ml <- load_manifest(manifest_path(td1))
    summary(ml)

    ##         Length Class      Mode
    ## data     4     data.table list
    ## headers 27     -none-     list

    t_df <- load_templates(template_path(td1))
    summary(t_df)

    ##    WellRow           WellColumn          Gnumber          Concentration
    ##  Length:768         Length:768         Length:768         Length:768
    ##  Class :character   Class :character   Class :character   Class :character
    ##  Mode  :character   Mode  :character   Mode  :character   Mode  :character
    ##   Gnumber_2         Concentration_2      Template
    ##  Length:768         Length:768         Length:768
    ##  Class :character   Class :character   Class :character
    ##  Mode  :character   Mode  :character   Mode  :character

    r_df <- suppressMessages(load_results(result_path(td1)))
    summary(r_df)

    ##    Barcode            WellRow            WellColumn     ReadoutValue
    ##  Length:4587        Length:4587        Min.   : 1.00   Min.   :  12627
    ##  Class :character   Class :character   1st Qu.: 6.50   1st Qu.:  67905
    ##  Mode  :character   Mode  :character   Median :12.00   Median : 140865
    ##                                        Mean   :12.49   Mean   : 263996
    ##                                        3rd Qu.:18.00   3rd Qu.: 324707
    ##                                        Max.   :24.00   Max.   :2423054
    ##  BackgroundValue
    ##  Min.   :332.0
    ##  1st Qu.:351.0
    ##  Median :374.0
    ##  Mean   :453.2
    ##  3rd Qu.:570.0
    ##  Max.   :704.0

    l_tbl <-
      suppressMessages(
        load_data(manifest_path(td1), template_path(td1), result_path(td1)))
    summary(l_tbl)

    ##            Length Class      Mode
    ## manifest   4      data.table list
    ## treatments 7      data.table list
    ## data       5      data.table list

# PRISM

PRISM, the Multiplexed cancer cell line screening platform, facilitates rapid screening of a broad spectrum of drugs across more than 900 human cancer cell line models, employing a high-throughput, multiplexed approach. Publicly available PRISM data can be downloaded from the DepMap website (DepMap).

The `gDRimport` package provides support for processing PRISM data at two levels: LEVEL5 and LEVEL6.

- LEVEL5 Data: This format encapsulates all information about drugs, cell lines, and viability within a single file. To process LEVEL5 PRISM data, you can use the `convert_LEVEL5_prism_to_gDR_input()` function. This function not only transforms and cleans the data but also executes the gDR pipeline for further analysis.

- LEVEL6 Data: In LEVEL6, PRISM data is distributed across three separate files:

prism_data: containing collapsed log fold change data for viability assays. cell_line_data: providing information about cell lines. treatment_data: containing treatment data.

Processing LEVEL6 PRISM data can be accomplished using the `convert_LEVEL6_prism_to_gDR_input()` function, which requires paths to these three files as input arguments.

### Processing LEVEL5 PRISM Data

To process LEVEL5 PRISM data, you can use the following function:

    convert_LEVEL5_prism_to_gDR_input("path_to_file")

Replace “path_to_file” with the actual path to your LEVEL5 PRISM data file. This function will handle the transformation, cleaning, and execution of the gDR pipeline automatically.

### Processing LEVEL6 PRISM Data

To process LEVEL6 PRISM data, you can use the following function:

    convert_LEVEL6_prism_to_gDR_input("prism_data_path", "cell_line_data_path", "treatment_data_path")

Replace “prism_data_path”, “cell_line_data_path”, and “treatment_data_path” with the respective paths to your LEVEL6 PRISM data files.

## Package installation

The function `installAllDeps` assists in installing package dependencies.

# SessionInfo

    sessionInfo()

    ## R version 4.5.2 (2025-10-31)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.3 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=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_US.UTF-8        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: Etc/UTC
    ## tzcode source: system (glibc)
    ##
    ## attached base packages:
    ## [1] stats4    stats     graphics  grDevices utils     datasets  methods
    ## [8] base
    ##
    ## other attached packages:
    ##  [1] BiocStyle_2.39.0            MultiAssayExperiment_1.37.2
    ##  [3] gDRimport_1.9.5             PharmacoGx_3.15.0
    ##  [5] CoreGx_2.15.0               SummarizedExperiment_1.41.0
    ##  [7] Biobase_2.71.0              GenomicRanges_1.63.1
    ##  [9] Seqinfo_1.1.0               IRanges_2.45.0
    ## [11] S4Vectors_0.49.0            MatrixGenerics_1.23.0
    ## [13] matrixStats_1.5.0           BiocGenerics_0.57.0
    ## [15] generics_0.1.4              rmarkdown_2.30
    ##
    ## loaded via a namespace (and not attached):
    ##   [1] bitops_1.0-9          formatR_1.14          readxl_1.4.5
    ##   [4] testthat_3.3.2        rlang_1.1.7           magrittr_2.0.4
    ##   [7] shinydashboard_0.7.3  otel_0.2.0            compiler_4.5.2
    ##  [10] vctrs_0.6.5           reshape2_1.4.5        relations_0.6-15
    ##  [13] stringr_1.6.0         pkgconfig_2.0.3       crayon_1.5.3
    ##  [16] fastmap_1.2.0         backports_1.5.0       XVector_0.51.0
    ##  [19] caTools_1.18.3        promises_1.5.0        coop_0.6-3
    ##  [22] xfun_0.55             cachem_1.1.0          jsonlite_2.0.0
    ##  [25] SnowballC_0.7.1       later_1.4.5           DelayedArray_0.37.0
    ##  [28] BiocParallel_1.45.0   parallel_4.5.2        sets_1.0-25
    ##  [31] cluster_2.1.8.1       R6_2.6.1              bslib_0.9.0
    ##  [34] stringi_1.8.7         RColorBrewer_1.1-3    qs_0.27.3
    ##  [37] limma_3.67.0          boot_1.3-32           cellranger_1.1.0
    ##  [40] brio_1.1.5            jquerylib_0.1.4       assertthat_0.2.1
    ##  [43] Rcpp_1.1.1            knitr_1.51            downloader_0.4.1
    ##  [46] httpuv_1.6.16         Matrix_1.7-4          igraph_2.2.1
    ##  [49] tidyselect_1.2.1      abind_1.4-8           yaml_2.3.12
    ##  [52] stringfish_0.17.0     gplots_3.3.0          codetools_0.2-20
    ##  [55] lattice_0.22-7        tibble_3.3.1          plyr_1.8.9
    ##  [58] withr_3.0.2           shiny_1.12.1          BumpyMatrix_1.19.0
    ##  [61] S7_0.2.1              evaluate_1.0.5        lambda.r_1.2.4
    ##  [64] futile.logger_1.4.9   RcppParallel_5.1.11-1 bench_1.1.4
    ##  [67] BiocManager_1.30.27   pillar_1.11.1         lsa_0.73.4
    ##  [70] KernSmooth_2.23-26    checkmate_2.3.3       DT_0.34.0
    ##  [73] shinyjs_2.1.0         piano_2.27.0          ggplot2_4.0.1
    ##  [76] scales_1.4.0          RApiSerialize_0.1.4   gtools_3.9.5
    ##  [79] xtable_1.8-4          marray_1.89.0         glue_1.8.0
    ##  [82] slam_0.1-55           maketools_1.3.2       tools_4.5.2
    ##  [85] sys_3.4.3             data.table_1.18.0     gDRutils_1.9.4
    ##  [88] fgsea_1.37.4          buildtools_1.0.0      visNetwork_2.1.4
    ##  [91] fastmatch_1.1-6       cowplot_1.2.0         grid_4.5.2
    ##  [94] cli_3.6.5             futile.options_1.0.1  S4Arrays_1.11.1
    ##  [97] rematch_2.0.0         dplyr_1.1.4           gtable_0.3.6
    ## [100] sass_0.4.10           digest_0.6.39         SparseArray_1.11.10
    ## [103] htmlwidgets_1.6.4     farver_2.1.2          htmltools_0.5.9
    ## [106] lifecycle_1.0.5       statmod_1.5.1         mime_0.13