Contents

library(gDRutils)
suppressPackageStartupMessages(library(MultiAssayExperiment))

1 Overview

gDRutils is part of the gDR suite. This package provides a bunch of tools for, among others:

2 Use cases

2.1 Data manipulation

The basic output of gDRcore package is the MultiAssayExperiment object. Function MAEpply allows for the data manipulation of this object, and can be used in a similar way as a basic function lapply.

mae <- get_synthetic_data("finalMAE_combo_matrix_small")
MAEpply(mae, dim)
#> $combination
#> [1] 6 2
#> 
#> $`single-agent`
#> [1] 5 2
MAEpply(mae, rowData)
#> $combination
#> DataFrame with 6 rows and 7 columns
#>                                                    Gnumber    DrugName
#>                                                <character> <character>
#> G00004_drug_004_moa_A_G00021_drug_021_moa_D_72      G00004    drug_004
#> G00004_drug_004_moa_A_G00026_drug_026_moa_E_72      G00004    drug_004
#> G00005_drug_005_moa_A_G00021_drug_021_moa_D_72      G00005    drug_005
#> G00005_drug_005_moa_A_G00026_drug_026_moa_E_72      G00005    drug_005
#> G00006_drug_006_moa_A_G00021_drug_021_moa_D_72      G00006    drug_006
#> G00006_drug_006_moa_A_G00026_drug_026_moa_E_72      G00006    drug_006
#>                                                   drug_moa   Gnumber_2
#>                                                <character> <character>
#> G00004_drug_004_moa_A_G00021_drug_021_moa_D_72       moa_A      G00021
#> G00004_drug_004_moa_A_G00026_drug_026_moa_E_72       moa_A      G00026
#> G00005_drug_005_moa_A_G00021_drug_021_moa_D_72       moa_A      G00021
#> G00005_drug_005_moa_A_G00026_drug_026_moa_E_72       moa_A      G00026
#> G00006_drug_006_moa_A_G00021_drug_021_moa_D_72       moa_A      G00021
#> G00006_drug_006_moa_A_G00026_drug_026_moa_E_72       moa_A      G00026
#>                                                 DrugName_2  drug_moa_2
#>                                                <character> <character>
#> G00004_drug_004_moa_A_G00021_drug_021_moa_D_72    drug_021       moa_D
#> G00004_drug_004_moa_A_G00026_drug_026_moa_E_72    drug_026       moa_E
#> G00005_drug_005_moa_A_G00021_drug_021_moa_D_72    drug_021       moa_D
#> G00005_drug_005_moa_A_G00026_drug_026_moa_E_72    drug_026       moa_E
#> G00006_drug_006_moa_A_G00021_drug_021_moa_D_72    drug_021       moa_D
#> G00006_drug_006_moa_A_G00026_drug_026_moa_E_72    drug_026       moa_E
#>                                                 Duration
#>                                                <numeric>
#> G00004_drug_004_moa_A_G00021_drug_021_moa_D_72        72
#> G00004_drug_004_moa_A_G00026_drug_026_moa_E_72        72
#> G00005_drug_005_moa_A_G00021_drug_021_moa_D_72        72
#> G00005_drug_005_moa_A_G00026_drug_026_moa_E_72        72
#> G00006_drug_006_moa_A_G00021_drug_021_moa_D_72        72
#> G00006_drug_006_moa_A_G00026_drug_026_moa_E_72        72
#> 
#> $`single-agent`
#> DataFrame with 5 rows and 4 columns
#>                              Gnumber    DrugName    drug_moa  Duration
#>                          <character> <character> <character> <numeric>
#> G00004_drug_004_moa_A_72      G00004    drug_004       moa_A        72
#> G00005_drug_005_moa_A_72      G00005    drug_005       moa_A        72
#> G00006_drug_006_moa_A_72      G00006    drug_006       moa_A        72
#> G00021_drug_021_moa_D_72      G00021    drug_021       moa_D        72
#> G00026_drug_026_moa_E_72      G00026    drug_026       moa_E        72

This function allows also for extraction of unified data across all the SummarizedExperiments inside MultiAssayExperiment, e.g.

MAEpply(mae, rowData, unify = TRUE)
#>     Gnumber DrugName drug_moa Gnumber_2 DrugName_2 drug_moa_2 Duration
#>      <char>   <char>   <char>    <char>     <char>     <char>    <num>
#>  1:  G00004 drug_004    moa_A    G00021   drug_021      moa_D       72
#>  2:  G00004 drug_004    moa_A    G00026   drug_026      moa_E       72
#>  3:  G00005 drug_005    moa_A    G00021   drug_021      moa_D       72
#>  4:  G00005 drug_005    moa_A    G00026   drug_026      moa_E       72
#>  5:  G00006 drug_006    moa_A    G00021   drug_021      moa_D       72
#>  6:  G00006 drug_006    moa_A    G00026   drug_026      moa_E       72
#>  7:  G00004 drug_004    moa_A      <NA>       <NA>       <NA>       72
#>  8:  G00005 drug_005    moa_A      <NA>       <NA>       <NA>       72
#>  9:  G00006 drug_006    moa_A      <NA>       <NA>       <NA>       72
#> 10:  G00021 drug_021    moa_D      <NA>       <NA>       <NA>       72
#> 11:  G00026 drug_026    moa_E      <NA>       <NA>       <NA>       72

2.2 Data extraction

All the metrics data are stored inside assays of SummarizedExperiment. For the downstream analyses we provide tools allowing for the extraction of the data into user-friendly data.table style.

There is a function working on the MultiAssayExperiment object as well as a set of functions working on the SummarizedExperiment object:

  • convert_mae_assay_to_dt
  • convert_se_assay_to_dt
  • convert_se_assay_to_custom_dt
  • convert_combo_data_to_dt
mdt <- convert_mae_assay_to_dt(mae, "Metrics")
#> Loading required namespace: BumpyMatrix
head(mdt, 3)
#>                                               rId
#>                                            <char>
#> 1: G00004_drug_004_moa_A_G00021_drug_021_moa_D_72
#> 2: G00004_drug_004_moa_A_G00021_drug_021_moa_D_72
#> 3: G00004_drug_004_moa_A_G00021_drug_021_moa_D_72
#>                                cId  x_mean  x_AOC x_AOC_range  xc50   x_max
#>                             <char>   <num>  <num>       <num> <num>   <num>
#> 1: CL00016_cellline_GB_tissue_y_46 -0.7046 1.7046      1.7046  -Inf -0.7046
#> 2: CL00016_cellline_GB_tissue_y_46 -0.7039 1.7039      1.7039  -Inf -0.7039
#> 3: CL00016_cellline_GB_tissue_y_46 -0.6920 1.6920      1.6920  -Inf -0.6920
#>     ec50   x_inf     x_0     h    r2 p_value   rss x_sd_avg
#>    <num>   <num>   <num> <num> <num>   <num> <num>    <num>
#> 1:     0 -0.7046 -0.7046 1e-04     0      NA    NA        0
#> 2:     0 -0.7039 -0.7039 1e-04     0      NA    NA        0
#> 3:     0 -0.6920 -0.6920 1e-04     0      NA    NA        0
#>                fit_type maxlog10Concentration N_conc normalization_type
#>                  <char>                 <num>  <int>             <char>
#> 1: DRCConstantFitResult             0.4996871      8                 GR
#> 2: DRCConstantFitResult             0.4996871      8                 GR
#> 3: DRCConstantFitResult             0.4996871      8                 GR
#>    fit_source cotrt_value ratio       source Gnumber DrugName drug_moa
#>        <char>       <num> <num>       <char>  <char>   <char>   <char>
#> 1:        gDR       3.160    NA row_fittings  G00004 drug_004    moa_A
#> 2:        gDR       1.000    NA row_fittings  G00004 drug_004    moa_A
#> 3:        gDR       0.316    NA row_fittings  G00004 drug_004    moa_A
#>    Gnumber_2 DrugName_2 drug_moa_2 Duration    clid CellLineName   Tissue
#>       <char>     <char>     <char>    <num>  <char>       <char>   <char>
#> 1:    G00021   drug_021      moa_D       72 CL00016  cellline_GB tissue_y
#> 2:    G00021   drug_021      moa_D       72 CL00016  cellline_GB tissue_y
#> 3:    G00021   drug_021      moa_D       72 CL00016  cellline_GB tissue_y
#>    ReferenceDivisionTime
#>                    <num>
#> 1:                    46
#> 2:                    46
#> 3:                    46

or alternatively for SummarizedExperiment object:

se <- mae[[1]]
sdt <- convert_se_assay_to_dt(se, "Metrics")
head(sdt, 3)
#>                                               rId
#>                                            <char>
#> 1: G00004_drug_004_moa_A_G00021_drug_021_moa_D_72
#> 2: G00004_drug_004_moa_A_G00021_drug_021_moa_D_72
#> 3: G00004_drug_004_moa_A_G00021_drug_021_moa_D_72
#>                                cId  x_mean  x_AOC x_AOC_range  xc50   x_max
#>                             <char>   <num>  <num>       <num> <num>   <num>
#> 1: CL00016_cellline_GB_tissue_y_46 -0.7046 1.7046      1.7046  -Inf -0.7046
#> 2: CL00016_cellline_GB_tissue_y_46 -0.7039 1.7039      1.7039  -Inf -0.7039
#> 3: CL00016_cellline_GB_tissue_y_46 -0.6920 1.6920      1.6920  -Inf -0.6920
#>     ec50   x_inf     x_0     h    r2 p_value   rss x_sd_avg
#>    <num>   <num>   <num> <num> <num>   <num> <num>    <num>
#> 1:     0 -0.7046 -0.7046 1e-04     0      NA    NA        0
#> 2:     0 -0.7039 -0.7039 1e-04     0      NA    NA        0
#> 3:     0 -0.6920 -0.6920 1e-04     0      NA    NA        0
#>                fit_type maxlog10Concentration N_conc normalization_type
#>                  <char>                 <num>  <int>             <char>
#> 1: DRCConstantFitResult             0.4996871      8                 GR
#> 2: DRCConstantFitResult             0.4996871      8                 GR
#> 3: DRCConstantFitResult             0.4996871      8                 GR
#>    fit_source cotrt_value ratio       source Gnumber DrugName drug_moa
#>        <char>       <num> <num>       <char>  <char>   <char>   <char>
#> 1:        gDR       3.160    NA row_fittings  G00004 drug_004    moa_A
#> 2:        gDR       1.000    NA row_fittings  G00004 drug_004    moa_A
#> 3:        gDR       0.316    NA row_fittings  G00004 drug_004    moa_A
#>    Gnumber_2 DrugName_2 drug_moa_2 Duration    clid CellLineName   Tissue
#>       <char>     <char>     <char>    <num>  <char>       <char>   <char>
#> 1:    G00021   drug_021      moa_D       72 CL00016  cellline_GB tissue_y
#> 2:    G00021   drug_021      moa_D       72 CL00016  cellline_GB tissue_y
#> 3:    G00021   drug_021      moa_D       72 CL00016  cellline_GB tissue_y
#>    ReferenceDivisionTime
#>                    <num>
#> 1:                    46
#> 2:                    46
#> 3:                    46

2.3 Managing gDR identifiers

2.3.1 Overview

In gDR we require standard identifiers that should be visible in the input data, such as e.g. Gnumber, CLID, Concentration. However, user can define their own custom identifiers.

To display gDR default identifier they can use get_env_identifiers function:

get_env_identifiers()
#> $duration
#> [1] "Duration"
#> 
#> $cellline
#> [1] "clid"
#> 
#> $cellline_name
#> [1] "CellLineName"
#> 
#> $cellline_tissue
#> [1] "Tissue"
#> 
#> $cellline_ref_div_time
#> [1] "ReferenceDivisionTime"
#> 
#> $cellline_parental_identifier
#> [1] "parental_identifier"
#> 
#> $cellline_subtype
#> [1] "subtype"
#> 
#> $drug
#> [1] "Gnumber"
#> 
#> $drug_name
#> [1] "DrugName"
#> 
#> $drug_moa
#> [1] "drug_moa"
#> 
#> $untreated_tag
#> [1] "vehicle"   "untreated"
#> 
#> $masked_tag
#> [1] "masked"
#> 
#> $well_position
#> [1] "WellRow"    "WellColumn"
#> 
#> $concentration
#> [1] "Concentration"
#> 
#> $template
#> [1] "Template"  "Treatment"
#> 
#> $barcode
#> [1] "Barcode" "Plate"  
#> 
#> $drug2
#> [1] "Gnumber_2"
#> 
#> $drug_name2
#> [1] "DrugName_2"
#> 
#> $drug_moa2
#> [1] "drug_moa_2"
#> 
#> $concentration2
#> [1] "Concentration_2"
#> 
#> $drug3
#> [1] "Gnumber_3"
#> 
#> $drug_name3
#> [1] "DrugName_3"
#> 
#> $drug_moa3
#> [1] "drug_moa_3"
#> 
#> $concentration3
#> [1] "Concentration_3"
#> 
#> $data_source
#> [1] "data_source"
#> 
#> $replicate
#> [1] "Replicate"
#> 
#> $normalization_type
#> [1] "normalization_type"

To change any of these identifiers user can use set_env_identifier, e.g.

set_env_identifier("concentration", "Dose")

and confirm, by displaying:

get_env_identifiers("concentration")
#> [1] "Dose"

To restore default identifiers user can use reset_env_identifiers.

reset_env_identifiers()
get_env_identifiers("concentration")
#> [1] "Concentration"

2.3.2 Validating identifiers

The validate_identifiers function checks if the specified identifier values exist in the data and (if needed) tries to modify them to pass validation.

# Example data.table
dt <- data.table::data.table(
  Barcode = c("A1", "A2", "A3"),
  Duration = c(24, 48, 72),
  Template = c("T1", "T2", "T3"),
  clid = c("C1", "C2", "C3")
)

# Validate identifiers
validated_identifiers <- validate_identifiers(
  dt,
  req_ids = c("barcode", "duration", "template", "cellline")
)

print(validated_identifiers)
#> $duration
#> [1] "Duration"
#> 
#> $cellline
#> [1] "clid"
#> 
#> $cellline_name
#> [1] "CellLineName"
#> 
#> $cellline_tissue
#> [1] "Tissue"
#> 
#> $cellline_ref_div_time
#> [1] "ReferenceDivisionTime"
#> 
#> $cellline_parental_identifier
#> [1] "parental_identifier"
#> 
#> $cellline_subtype
#> [1] "subtype"
#> 
#> $drug
#> [1] "Gnumber"
#> 
#> $drug_name
#> [1] "DrugName"
#> 
#> $drug_moa
#> [1] "drug_moa"
#> 
#> $untreated_tag
#> [1] "vehicle"   "untreated"
#> 
#> $masked_tag
#> [1] "masked"
#> 
#> $well_position
#> [1] "WellRow"    "WellColumn"
#> 
#> $concentration
#> [1] "Concentration"
#> 
#> $template
#> [1] "Template"
#> 
#> $barcode
#> [1] "Barcode"
#> 
#> $drug2
#> [1] "Gnumber_2"
#> 
#> $drug_name2
#> [1] "DrugName_2"
#> 
#> $drug_moa2
#> [1] "drug_moa_2"
#> 
#> $concentration2
#> [1] "Concentration_2"
#> 
#> $drug3
#> [1] "Gnumber_3"
#> 
#> $drug_name3
#> [1] "DrugName_3"
#> 
#> $drug_moa3
#> [1] "drug_moa_3"
#> 
#> $concentration3
#> [1] "Concentration_3"
#> 
#> $data_source
#> [1] "data_source"
#> 
#> $replicate
#> [1] "Replicate"
#> 
#> $normalization_type
#> [1] "normalization_type"

In detail, validate_identifiers wraps the following steps:

  • modify identifier values to reflect the data, handling many-to-one mappings via the .modify_polymapped_identifiers function
  • ensure that all required identifiers are present in the data via the .check_required_identifiers function
  • check for polymapped identifiers in the data via the .check_polymapped_identifiers function

2.3.3 Prettifying identifiers

Prettifying identifiers means making them more user-friendly and human-readable and is handled by the prettify_flat_metrics function. Please see the relevant section for more details.

# Example of prettifying identifiers
x <- c("CellLineName", "Tissue", "Concentration_2")
prettified_names <- prettify_flat_metrics(x, human_readable = TRUE)
print(prettified_names)
#> [1] "Cell Line Name"  "Tissue"          "Concentration 2"

2.4 Data validation

Applied custom changes in the gDR output can disrupt internal functions operation. Custom changes can be validated using validate_MAE

validate_MAE(mae)

or validate_SE.

validate_SE(se)
assay(se, "Normalized") <- NULL
validate_SE(se)
#> Error in validate_SE(se): Assertion on 'exp_assay_names' failed: Must be a subset of {'RawTreated','Controls','Averaged','excess','all_iso_points','isobolograms','scores','Metrics'}, but has additional elements {'Normalized'}.

There is also a group of functions to validate data used in the gDR application:

  • is_combo_data
  • has_single_codrug_data
  • has_valid_codrug_data
  • get_additional_variables

2.5 Prettifying

Prettifying involves transforming data into a more descriptive and human-readable version. This is particularly useful for front-end applications where user-friendly names are preferred over technical or abbreviated terms.

In gdrplatform there are two entities that can be prettified:

  • colnames of data.tables
  • assay names

2.5.1 Colnames of data.table(s)

One can prettify the columns of the data.table(s) with a single function called prettify_flat_metrics.

dt <- get_testdata()[["raw_data"]]
colnames(dt)
prettify_flat_metrics(colnames(dt), human_readable = TRUE)

The prettify_flat_metrics function is in fact a wrapper for the following actions:

  • conversion of the normalization-specific metric names via the .convert_norm_specific_metrics function
  • moving the GDS source info to the end of the column name via the .prettify_GDS_columns
  • prettifying the metadata columns via the .prettify_metadata_columns function
  • prettifying the metric columns via the .prettify_metric_columns function
  • prettifying the co-treatment column names. via the .prettify_cotreatment_columns
  • minor corrections (removal of ‘gDR’ and “_” prefixes, removal of spaces at the end/beginning, other)

In case of data.table(s) with combo excess and score assays some of the columns are prettified with the dedicated helper functions instead of using prettify_flat_metrics:

  • get_combo_excess_field_names()
  • get_combo_score_field_names()

These helpers depend on the DATA_COMBO_INFO_TBL, (gDRutils) internal data.table.

2.5.2 Assay names

The function get_assay_names is the primary solution for obtaining prettified versions of the assay names. It wraps the get_env_assay_names function which depends on ASSAY_INFO_TBL, (gDRutils) internal data.table.

There are some functions that wrap the get_assay_names function for combo data:

  • get_combo_assay_names
  • get_combo_score_assay_names
  • get_combo_base_assay_names

SessionInfo

sessionInfo()
#> R Under development (unstable) (2024-10-21 r87258)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.1 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so 
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.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] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] MultiAssayExperiment_1.33.0 SummarizedExperiment_1.37.0
#>  [3] Biobase_2.67.0              GenomicRanges_1.59.0       
#>  [5] GenomeInfoDb_1.43.0         IRanges_2.41.0             
#>  [7] S4Vectors_0.45.0            BiocGenerics_0.53.1        
#>  [9] generics_0.1.3              MatrixGenerics_1.19.0      
#> [11] matrixStats_1.4.1           gDRutils_1.5.2             
#> [13] BiocStyle_2.35.0           
#> 
#> loaded via a namespace (and not attached):
#>  [1] sass_0.4.9              SparseArray_1.7.1       stringi_1.8.4          
#>  [4] lattice_0.22-6          magrittr_2.0.3          digest_0.6.37          
#>  [7] evaluate_1.0.1          grid_4.5.0              bookdown_0.41          
#> [10] fastmap_1.2.0           jsonlite_1.8.9          Matrix_1.7-1           
#> [13] backports_1.5.0         BiocManager_1.30.25     httr_1.4.7             
#> [16] UCSC.utils_1.3.0        jquerylib_0.1.4         RApiSerialize_0.1.4    
#> [19] abind_1.4-8             cli_3.6.3               rlang_1.1.4            
#> [22] crayon_1.5.3            XVector_0.47.0          cachem_1.1.0           
#> [25] DelayedArray_0.33.1     yaml_2.3.10             S4Arrays_1.7.1         
#> [28] tools_4.5.0             qs_0.27.2               checkmate_2.3.2        
#> [31] GenomeInfoDbData_1.2.13 R6_2.5.1                lifecycle_1.0.4        
#> [34] stringr_1.5.1           zlibbioc_1.53.0         stringfish_0.16.0      
#> [37] BumpyMatrix_1.15.0      RcppParallel_5.1.9      bslib_0.8.0            
#> [40] glue_1.8.0              data.table_1.16.2       Rcpp_1.0.13-1          
#> [43] xfun_0.49               knitr_1.48              htmltools_0.5.8.1      
#> [46] rmarkdown_2.29          compiler_4.5.0