convert combo assays from SummarizedExperiments to the list of data.tables
Source:R/combo.R
convert_combo_data_to_dt.Rdconvert combo assays from SummarizedExperiments to the list of data.tables
Usage
convert_combo_data_to_dt(
se,
c_assays = get_combo_assay_names(),
normalization_type = c("RV", "GR"),
prettify = TRUE
)Arguments
- se
SummarizedExperimentobject with dose-response data- c_assays
charvec of combo assays to be used
- normalization_type
charvec of normalization_types expected in the data
- prettify
boolean flag indicating whether or not to prettify the colnames of the returned data
Author
Arkadiusz Gładki arkadiusz.gladki@contractors.roche.com
Examples
mae <- get_synthetic_data("finalMAE_combo_matrix_small.qs")
convert_combo_data_to_dt(mae[[1]])
#> $excess
#> r Id
#> <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
#> 4: G00004_drug_004_moa_A_G00021_drug_021_moa_D_72
#> 5: G00004_drug_004_moa_A_G00021_drug_021_moa_D_72
#> ---
#> 1940: G00006_drug_006_moa_A_G00026_drug_026_moa_E_72
#> 1941: G00006_drug_006_moa_A_G00026_drug_026_moa_E_72
#> 1942: G00006_drug_006_moa_A_G00026_drug_026_moa_E_72
#> 1943: G00006_drug_006_moa_A_G00026_drug_026_moa_E_72
#> 1944: G00006_drug_006_moa_A_G00026_drug_026_moa_E_72
#> c Id Concentration Concentration 2 Smooth
#> <char> <num> <num> <num>
#> 1: CL00016_cellline_GB_tissue_y_46 0.00 0.00000 1.0000000
#> 2: CL00016_cellline_GB_tissue_y_46 0.00 0.00000 1.0000000
#> 3: CL00016_cellline_GB_tissue_y_46 0.00 0.00100 1.0000000
#> 4: CL00016_cellline_GB_tissue_y_46 0.00 0.00100 1.0000000
#> 5: CL00016_cellline_GB_tissue_y_46 0.00 0.00316 1.0000000
#> ---
#> 1940: CL00017_cellline_HB_tissue_y_50 3.16 0.31600 0.1828034
#> 1941: CL00017_cellline_HB_tissue_y_50 3.16 1.00000 -0.4035902
#> 1942: CL00017_cellline_HB_tissue_y_50 3.16 1.00000 0.1918578
#> 1943: CL00017_cellline_HB_tissue_y_50 3.16 3.16000 -0.4008597
#> 1944: CL00017_cellline_HB_tissue_y_50 3.16 3.16000 0.1921170
#> Normalization Type HSA Excess Bliss Excess Gnumber Drug Name Drug MOA
#> <char> <num> <num> <char> <char> <char>
#> 1: GR NA NA G00004 drug_004 moa_A
#> 2: RV NA NA G00004 drug_004 moa_A
#> 3: GR NA NA G00004 drug_004 moa_A
#> 4: RV NA NA G00004 drug_004 moa_A
#> 5: GR NA NA G00004 drug_004 moa_A
#> ---
#> 1940: RV -0.001579471 -0.001579471 G00006 drug_006 moa_A
#> 1941: GR 0.003961392 0.003961392 G00006 drug_006 moa_A
#> 1942: RV -0.010633816 -0.010633816 G00006 drug_006 moa_A
#> 1943: GR 0.001230976 0.001230976 G00006 drug_006 moa_A
#> 1944: RV -0.010893026 -0.010893026 G00006 drug_006 moa_A
#> Gnumber 2 Drug Name 2 Drug MOA 2 Duration Clid Cell Line Name 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
#> 4: G00021 drug_021 moa_D 72 CL00016 cellline_GB tissue_y
#> 5: G00021 drug_021 moa_D 72 CL00016 cellline_GB tissue_y
#> ---
#> 1940: G00026 drug_026 moa_E 72 CL00017 cellline_HB tissue_y
#> 1941: G00026 drug_026 moa_E 72 CL00017 cellline_HB tissue_y
#> 1942: G00026 drug_026 moa_E 72 CL00017 cellline_HB tissue_y
#> 1943: G00026 drug_026 moa_E 72 CL00017 cellline_HB tissue_y
#> 1944: G00026 drug_026 moa_E 72 CL00017 cellline_HB tissue_y
#> Reference Division Time
#> <num>
#> 1: 46
#> 2: 46
#> 3: 46
#> 4: 46
#> 5: 46
#> ---
#> 1940: 50
#> 1941: 50
#> 1942: 50
#> 1943: 50
#> 1944: 50
#>
#> $scores
#> r Id
#> <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_G00026_drug_026_moa_E_72
#> 4: G00004_drug_004_moa_A_G00026_drug_026_moa_E_72
#> 5: G00005_drug_005_moa_A_G00021_drug_021_moa_D_72
#> 6: G00005_drug_005_moa_A_G00021_drug_021_moa_D_72
#> 7: G00005_drug_005_moa_A_G00026_drug_026_moa_E_72
#> 8: G00005_drug_005_moa_A_G00026_drug_026_moa_E_72
#> 9: G00006_drug_006_moa_A_G00021_drug_021_moa_D_72
#> 10: G00006_drug_006_moa_A_G00021_drug_021_moa_D_72
#> 11: G00006_drug_006_moa_A_G00026_drug_026_moa_E_72
#> 12: G00006_drug_006_moa_A_G00026_drug_026_moa_E_72
#> 13: G00004_drug_004_moa_A_G00021_drug_021_moa_D_72
#> 14: G00004_drug_004_moa_A_G00021_drug_021_moa_D_72
#> 15: G00004_drug_004_moa_A_G00026_drug_026_moa_E_72
#> 16: G00004_drug_004_moa_A_G00026_drug_026_moa_E_72
#> 17: G00005_drug_005_moa_A_G00021_drug_021_moa_D_72
#> 18: G00005_drug_005_moa_A_G00021_drug_021_moa_D_72
#> 19: G00005_drug_005_moa_A_G00026_drug_026_moa_E_72
#> 20: G00005_drug_005_moa_A_G00026_drug_026_moa_E_72
#> 21: G00006_drug_006_moa_A_G00021_drug_021_moa_D_72
#> 22: G00006_drug_006_moa_A_G00021_drug_021_moa_D_72
#> 23: G00006_drug_006_moa_A_G00026_drug_026_moa_E_72
#> 24: G00006_drug_006_moa_A_G00026_drug_026_moa_E_72
#> r Id
#> c Id Normalization Type HSA Score
#> <char> <char> <num>
#> 1: CL00016_cellline_GB_tissue_y_46 GR 0.0191864677
#> 2: CL00016_cellline_GB_tissue_y_46 RV 0.0054825946
#> 3: CL00016_cellline_GB_tissue_y_46 GR 0.0008640793
#> 4: CL00016_cellline_GB_tissue_y_46 RV 0.0002808689
#> 5: CL00016_cellline_GB_tissue_y_46 GR 0.0212207295
#> 6: CL00016_cellline_GB_tissue_y_46 RV 0.0064007236
#> 7: CL00016_cellline_GB_tissue_y_46 GR 0.0282314859
#> 8: CL00016_cellline_GB_tissue_y_46 RV 0.0004152695
#> 9: CL00016_cellline_GB_tissue_y_46 GR 0.0142686221
#> 10: CL00016_cellline_GB_tissue_y_46 RV 0.0035563938
#> 11: CL00016_cellline_GB_tissue_y_46 GR 0.0006824548
#> 12: CL00016_cellline_GB_tissue_y_46 RV 0.0002571149
#> 13: CL00017_cellline_HB_tissue_y_50 GR 0.0195462845
#> 14: CL00017_cellline_HB_tissue_y_50 RV 0.0062733026
#> 15: CL00017_cellline_HB_tissue_y_50 GR 0.0047716696
#> 16: CL00017_cellline_HB_tissue_y_50 RV 0.0020015238
#> 17: CL00017_cellline_HB_tissue_y_50 GR 0.0241474816
#> 18: CL00017_cellline_HB_tissue_y_50 RV 0.0080926437
#> 19: CL00017_cellline_HB_tissue_y_50 GR 0.0084478065
#> 20: CL00017_cellline_HB_tissue_y_50 RV 0.0009734877
#> 21: CL00017_cellline_HB_tissue_y_50 GR 0.0550440010
#> 22: CL00017_cellline_HB_tissue_y_50 RV 0.0268261867
#> 23: CL00017_cellline_HB_tissue_y_50 GR 0.0344185361
#> 24: CL00017_cellline_HB_tissue_y_50 RV 0.0090907653
#> c Id Normalization Type HSA Score
#> Bliss Score CIScore 50 CIScore 80 Gnumber Drug Name Drug MOA Gnumber 2
#> <num> <num> <num> <char> <char> <char> <char>
#> 1: 0.0191864677 0.01747735 0.029337758 G00004 drug_004 moa_A G00021
#> 2: 0.0054825946 0.03485816 0.042184690 G00004 drug_004 moa_A G00021
#> 3: 0.0008640793 0.02293000 0.010300153 G00004 drug_004 moa_A G00026
#> 4: 0.0002808689 0.01554275 0.013571845 G00004 drug_004 moa_A G00026
#> 5: 0.0212207295 0.01476993 0.027160969 G00005 drug_005 moa_A G00021
#> 6: 0.0064007236 0.02046719 0.032236614 G00005 drug_005 moa_A G00021
#> 7: 0.0282314859 0.15986822 -0.048282180 G00005 drug_005 moa_A G00026
#> 8: 0.0004152695 0.01524069 0.022185871 G00005 drug_005 moa_A G00026
#> 9: 0.0142686221 0.02309152 0.027147952 G00006 drug_006 moa_A G00021
#> 10: 0.0035563938 0.02563107 0.021081550 G00006 drug_006 moa_A G00021
#> 11: 0.0006824548 0.02039404 0.019774471 G00006 drug_006 moa_A G00026
#> 12: 0.0002571149 0.02106643 0.020332834 G00006 drug_006 moa_A G00026
#> 13: 0.0195462845 0.02002235 0.015382530 G00004 drug_004 moa_A G00021
#> 14: 0.0062733026 0.01573286 0.014713425 G00004 drug_004 moa_A G00021
#> 15: 0.0047716696 0.02639060 0.021365113 G00004 drug_004 moa_A G00026
#> 16: 0.0020015238 0.02122847 0.016280462 G00004 drug_004 moa_A G00026
#> 17: 0.0241474816 0.02205106 -0.005903405 G00005 drug_005 moa_A G00021
#> 18: 0.0080926437 -0.00401062 -0.032211087 G00005 drug_005 moa_A G00021
#> 19: 0.0084478065 0.03074943 0.051788631 G00005 drug_005 moa_A G00026
#> 20: 0.0009734877 0.04725145 0.081596255 G00005 drug_005 moa_A G00026
#> 21: 0.0550440010 -0.01169389 -0.138659682 G00006 drug_006 moa_A G00021
#> 22: 0.0268261867 -0.07492990 -0.297592786 G00006 drug_006 moa_A G00021
#> 23: 0.0344185361 0.07855021 0.339741093 G00006 drug_006 moa_A G00026
#> 24: 0.0090907653 0.16251115 0.384075521 G00006 drug_006 moa_A G00026
#> Bliss Score CIScore 50 CIScore 80 Gnumber Drug Name Drug MOA Gnumber 2
#> Drug Name 2 Drug MOA 2 Duration Clid Cell Line Name Tissue
#> <char> <char> <num> <char> <char> <char>
#> 1: drug_021 moa_D 72 CL00016 cellline_GB tissue_y
#> 2: drug_021 moa_D 72 CL00016 cellline_GB tissue_y
#> 3: drug_026 moa_E 72 CL00016 cellline_GB tissue_y
#> 4: drug_026 moa_E 72 CL00016 cellline_GB tissue_y
#> 5: drug_021 moa_D 72 CL00016 cellline_GB tissue_y
#> 6: drug_021 moa_D 72 CL00016 cellline_GB tissue_y
#> 7: drug_026 moa_E 72 CL00016 cellline_GB tissue_y
#> 8: drug_026 moa_E 72 CL00016 cellline_GB tissue_y
#> 9: drug_021 moa_D 72 CL00016 cellline_GB tissue_y
#> 10: drug_021 moa_D 72 CL00016 cellline_GB tissue_y
#> 11: drug_026 moa_E 72 CL00016 cellline_GB tissue_y
#> 12: drug_026 moa_E 72 CL00016 cellline_GB tissue_y
#> 13: drug_021 moa_D 72 CL00017 cellline_HB tissue_y
#> 14: drug_021 moa_D 72 CL00017 cellline_HB tissue_y
#> 15: drug_026 moa_E 72 CL00017 cellline_HB tissue_y
#> 16: drug_026 moa_E 72 CL00017 cellline_HB tissue_y
#> 17: drug_021 moa_D 72 CL00017 cellline_HB tissue_y
#> 18: drug_021 moa_D 72 CL00017 cellline_HB tissue_y
#> 19: drug_026 moa_E 72 CL00017 cellline_HB tissue_y
#> 20: drug_026 moa_E 72 CL00017 cellline_HB tissue_y
#> 21: drug_021 moa_D 72 CL00017 cellline_HB tissue_y
#> 22: drug_021 moa_D 72 CL00017 cellline_HB tissue_y
#> 23: drug_026 moa_E 72 CL00017 cellline_HB tissue_y
#> 24: drug_026 moa_E 72 CL00017 cellline_HB tissue_y
#> Drug Name 2 Drug MOA 2 Duration Clid Cell Line Name Tissue
#> Reference Division Time
#> <num>
#> 1: 46
#> 2: 46
#> 3: 46
#> 4: 46
#> 5: 46
#> 6: 46
#> 7: 46
#> 8: 46
#> 9: 46
#> 10: 46
#> 11: 46
#> 12: 46
#> 13: 50
#> 14: 50
#> 15: 50
#> 16: 50
#> 17: 50
#> 18: 50
#> 19: 50
#> 20: 50
#> 21: 50
#> 22: 50
#> 23: 50
#> 24: 50
#> Reference Division Time
#>
#> $isobolograms
#> r Id
#> <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
#> 4: G00004_drug_004_moa_A_G00021_drug_021_moa_D_72
#> 5: G00004_drug_004_moa_A_G00021_drug_021_moa_D_72
#> ---
#> 12990: G00006_drug_006_moa_A_G00026_drug_026_moa_E_72
#> 12991: G00006_drug_006_moa_A_G00026_drug_026_moa_E_72
#> 12992: G00006_drug_006_moa_A_G00026_drug_026_moa_E_72
#> 12993: G00006_drug_006_moa_A_G00026_drug_026_moa_E_72
#> 12994: G00006_drug_006_moa_A_G00026_drug_026_moa_E_72
#> c Id Iso Level Pos x Pos y
#> <char> <char> <num> <num>
#> 1: CL00016_cellline_GB_tissue_y_46 -0.05 -3.6757783 -2.283728
#> 2: CL00016_cellline_GB_tissue_y_46 -0.05 -3.1612132 -2.280315
#> 3: CL00016_cellline_GB_tissue_y_46 -0.05 -3.0184836 -2.279007
#> 4: CL00016_cellline_GB_tissue_y_46 -0.05 -2.8761652 -2.278110
#> 5: CL00016_cellline_GB_tissue_y_46 -0.05 -2.7335957 -2.276962
#> ---
#> 12990: CL00017_cellline_HB_tissue_y_50 0.8 0.7382477 -3.126321
#> 12991: CL00017_cellline_HB_tissue_y_50 0.8 0.7382477 -3.000234
#> 12992: CL00017_cellline_HB_tissue_y_50 0.8 0.7382477 -2.984900
#> 12993: CL00017_cellline_HB_tissue_y_50 0.8 0.7382477 -2.858813
#> 12994: CL00017_cellline_HB_tissue_y_50 0.8 0.7382477 -2.843478
#> Pos x Ref Pos y Ref Log10 Ratio Conc Log2 CI Normalization Type
#> <num> <num> <num> <num> <char>
#> 1: -3.6757783 -2.283728 -0.9843283 0.00000000 GR
#> 2: -3.1646556 -2.283758 -0.6228889 0.01152660 GR
#> 3: -3.0232457 -2.283769 -0.5228889 0.01721126 GR
#> 4: -2.8818402 -2.283785 -0.4228889 0.02231182 GR
#> 5: -2.7404408 -2.283807 -0.3228889 0.03271470 GR
#> ---
#> 12990: 0.7382477 -3.161643 2.9175283 0.00000000 RV
#> 12991: 0.7382477 -3.065879 2.8283715 0.16819143 GR
#> 12992: 0.7382477 -3.033195 2.8175283 0.12396001 RV
#> 12993: 0.7382477 -2.947395 2.7283715 0.14361810 GR
#> 12994: 0.7382477 -2.909123 2.7175283 0.15685335 RV
#> Gnumber Drug Name Drug MOA Gnumber 2 Drug Name 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 G00021 drug_021 moa_D 72
#> 3: G00004 drug_004 moa_A G00021 drug_021 moa_D 72
#> 4: G00004 drug_004 moa_A G00021 drug_021 moa_D 72
#> 5: G00004 drug_004 moa_A G00021 drug_021 moa_D 72
#> ---
#> 12990: G00006 drug_006 moa_A G00026 drug_026 moa_E 72
#> 12991: G00006 drug_006 moa_A G00026 drug_026 moa_E 72
#> 12992: G00006 drug_006 moa_A G00026 drug_026 moa_E 72
#> 12993: G00006 drug_006 moa_A G00026 drug_026 moa_E 72
#> 12994: G00006 drug_006 moa_A G00026 drug_026 moa_E 72
#> Clid Cell Line Name Tissue Reference Division Time
#> <char> <char> <char> <num>
#> 1: CL00016 cellline_GB tissue_y 46
#> 2: CL00016 cellline_GB tissue_y 46
#> 3: CL00016 cellline_GB tissue_y 46
#> 4: CL00016 cellline_GB tissue_y 46
#> 5: CL00016 cellline_GB tissue_y 46
#> ---
#> 12990: CL00017 cellline_HB tissue_y 50
#> 12991: CL00017 cellline_HB tissue_y 50
#> 12992: CL00017 cellline_HB tissue_y 50
#> 12993: CL00017 cellline_HB tissue_y 50
#> 12994: CL00017 cellline_HB tissue_y 50
#>