Convert a MultiAssayExperiment assay to a long data.table — convert_mae_assay_to_dt • gDRutils

Convert an assay within a SummarizedExperiment object in a MultiAssayExperiment to a long data.table.

Usage

convert_mae_assay_to_dt(
  mae,
  assay_name,
  experiment_name = NULL,
  include_metadata = TRUE,
  retain_nested_rownames = FALSE,
  wide_structure = FALSE,
  drop_masked = TRUE,
  merge_additional_variables = FALSE
)

Arguments

mae: A MultiAssayExperiment object holding experiments with raw and/or processed dose-response data in its assays.
assay_name: String of name of the assay to transform within an experiment of the mae.
experiment_name: String of name of the experiment in mae whose assay_name should be converted. Defaults to NULL to indicate to convert assay in all experiments into one data.table object.
include_metadata: Boolean indicating whether or not to include rowData() and colData() in the returned data.table. Defaults to TRUE.
retain_nested_rownames: Boolean indicating whether or not to retain the rownames nested within a BumpyMatrix assay. Defaults to FALSE. If the assay_name is not of the BumpyMatrix class, this argument's value is ignored. If TRUE, the resulting column in the data.table will be named as "<assay_name>_rownames".
wide_structure: Boolean indicating whether or not to transform data.table into wide format. wide_structure = TRUE requires retain_nested_rownames = TRUE however that will be validated in convert_se_assay_to_dt function
drop_masked: Boolean indicating whether to drop masked values; TRUE by default.
merge_additional_variables: Boolean indicating whether to merge additional variables identified by get_additional_variables into the DrugName column. Defaults to FALSE.

Value

data.table representation of the data in assay_name.

Details

NOTE: to extract information about 'Control' data, simply call the function with the name of the assay holding data on controls.

See also

flatten convert_se_assay_to_dt

Author

Bartosz Czech czech.bartosz@external.gene.com

Examples

mae <- get_synthetic_data("finalMAE_small.qs2")
convert_mae_assay_to_dt(mae, "Metrics")
#>                           rId                             cId
#>                        <char>                          <char>
#>   1: G00002_drug_002_moa_A_72 CL00011_cellline_BA_tissue_x_26
#>   2: G00002_drug_002_moa_A_72 CL00011_cellline_BA_tissue_x_26
#>   3: G00003_drug_003_moa_A_72 CL00011_cellline_BA_tissue_x_26
#>   4: G00003_drug_003_moa_A_72 CL00011_cellline_BA_tissue_x_26
#>   5: G00004_drug_004_moa_A_72 CL00011_cellline_BA_tissue_x_26
#>  ---                                                         
#> 196: G00009_drug_009_moa_A_72 CL00020_cellline_KB_tissue_z_62
#> 197: G00010_drug_010_moa_A_72 CL00020_cellline_KB_tissue_z_62
#> 198: G00010_drug_010_moa_A_72 CL00020_cellline_KB_tissue_z_62
#> 199: G00011_drug_011_moa_B_72 CL00020_cellline_KB_tissue_z_62
#> 200: G00011_drug_011_moa_B_72 CL00020_cellline_KB_tissue_z_62
#>      normalization_type     x_mean     x_AOC x_AOC_range       x_max   x_sd_avg
#>                  <char>      <num>     <num>       <num>       <num>      <num>
#>   1:                 GR  0.4729298 0.5270702   0.6048472  0.33660000 0.03203268
#>   2:                 RV  0.4466890 0.5533110   0.6277120  0.32793333 0.02424423
#>   3:                 GR  0.3932199 0.6067801   0.7027714  0.25136667 0.03075240
#>   4:                 RV  0.3939872 0.6060128   0.6954994  0.27413333 0.02195104
#>   5:                 GR  0.8393271 0.1606729   0.1905009  0.76383333 0.02000573
#>  ---                                                                           
#> 196:                 RV  0.5045079 0.4954921   0.5777711  0.20156667 0.02298094
#> 197:                 GR  0.1991504 0.8008496   0.8915995 -0.78626667 0.06333498
#> 198:                 RV  0.5769999 0.4230001   0.4723104  0.07513333 0.03151223
#> 199:                 GR -0.1148134 1.1148134   1.3059605 -0.76026667 0.07007818
#> 200:                 RV  0.4117805 0.5882195   0.6900581  0.08603333 0.03335063
#>      N_conc maxlog10Concentration        ec50        xc50        h        r2
#>       <int>                 <num>       <num>       <num>    <num>     <num>
#>   1:      9                     1 0.004512560 0.008956223 1.911901 0.9884406
#>   2:      9                     1 0.003795893 0.007253171 1.827031 0.9924695
#>   3:      9                     1 0.004714084 0.006591468 2.270093 0.9905292
#>   4:      9                     1 0.003962986 0.005655581 2.349599 0.9958511
#>   5:      9                     1 0.017152797         Inf 3.143707 0.9914280
#>  ---                                                                        
#> 196:      9                     1 0.035484367 0.045034344 1.998935 0.9961207
#> 197:      9                     1 0.146270629 0.096729600 2.204685 0.9985705
#> 198:      9                     1 0.137152296 0.150209032 2.245643 0.9988156
#> 199:      9                     1 0.026434030 0.016239553 1.854308 0.9987249
#> 200:      9                     1 0.024485958 0.027440547 1.884916 0.9986615
#>               rss      p_value   x_0       x_inf               fit_type
#>             <num>        <num> <num>       <num>                 <char>
#>   1: 0.0045303452 1.660656e-07     1  0.36516781 DRC3pHillFitModelFixS0
#>   2: 0.0027788222 3.705769e-08     1  0.34682665 DRC3pHillFitModelFixS0
#>   3: 0.0056700663 8.267143e-08     1  0.26639679 DRC3pHillFitModelFixS0
#>   4: 0.0021823404 4.600131e-09     1  0.28319787 DRC3pHillFitModelFixS0
#>   5: 0.0007996589 5.831599e-08     1  0.76697772 DRC3pHillFitModelFixS0
#>  ---                                                                   
#> 196: 0.0042739653 3.636093e-09     1  0.18949638 DRC3pHillFitModelFixS0
#> 197: 0.0081610637 1.104466e-10     1 -0.74430401 DRC3pHillFitModelFixS0
#> 198: 0.0018424204 5.718652e-11     1  0.09235428 DRC3pHillFitModelFixS0
#> 199: 0.0064842414 7.403286e-11     1 -0.73401896 DRC3pHillFitModelFixS0
#> 200: 0.0018446214 8.773134e-11     1  0.09662172 DRC3pHillFitModelFixS0
#>      fit_source Gnumber DrugName drug_moa Duration    clid CellLineName
#>          <char>  <char>   <char>   <char>    <num>  <char>       <char>
#>   1:        gDR  G00002 drug_002    moa_A       72 CL00011  cellline_BA
#>   2:        gDR  G00002 drug_002    moa_A       72 CL00011  cellline_BA
#>   3:        gDR  G00003 drug_003    moa_A       72 CL00011  cellline_BA
#>   4:        gDR  G00003 drug_003    moa_A       72 CL00011  cellline_BA
#>   5:        gDR  G00004 drug_004    moa_A       72 CL00011  cellline_BA
#>  ---                                                                   
#> 196:        gDR  G00009 drug_009    moa_A       72 CL00020  cellline_KB
#> 197:        gDR  G00010 drug_010    moa_A       72 CL00020  cellline_KB
#> 198:        gDR  G00010 drug_010    moa_A       72 CL00020  cellline_KB
#> 199:        gDR  G00011 drug_011    moa_B       72 CL00020  cellline_KB
#> 200:        gDR  G00011 drug_011    moa_B       72 CL00020  cellline_KB
#>        Tissue ReferenceDivisionTime
#>        <char>                 <num>
#>   1: tissue_x                    26
#>   2: tissue_x                    26
#>   3: tissue_x                    26
#>   4: tissue_x                    26
#>   5: tissue_x                    26
#>  ---                               
#> 196: tissue_z                    62
#> 197: tissue_z                    62
#> 198: tissue_z                    62
#> 199: tissue_z                    62
#> 200: tissue_z                    62