Current steps
refining nested confounders
refining nested identifiers
splitting df_ into (per experiment) df_list
Arguments
- x
data.table with raw data or MAE object with dose-response data
- ...
additional parameters
Examples
td <- gDRimport::get_test_data()
l_tbl <- gDRimport::load_data(
manifest_file = gDRimport::manifest_path(td),
df_template_files = gDRimport::template_path(td),
results_file = gDRimport::result_path(td)
)
#> INFO [2024-11-15 20:27:31] Manifest loaded successfully
#> INFO [2024-11-15 20:27:31] Reading Template_7daytreated.xlsx with load_templates_xlsx
#> INFO [2024-11-15 20:27:31] Loading Template_7daytreated.xlsx
#> INFO [2024-11-15 20:27:31] Loading Template_Untreated.xlsx
#> INFO [2024-11-15 20:27:31] Templates loaded successfully!
#> INFO [2024-11-15 20:27:31] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
#> New names:
#> • `` -> `...1`
#> • `` -> `...2`
#> • `` -> `...3`
#> • `` -> `...4`
#> • `` -> `...5`
#> • `` -> `...6`
#> • `` -> `...7`
#> • `` -> `...8`
#> • `` -> `...9`
#> • `` -> `...10`
#> • `` -> `...11`
#> • `` -> `...12`
#> • `` -> `...13`
#> • `` -> `...14`
#> • `` -> `...15`
#> • `` -> `...16`
#> • `` -> `...17`
#> • `` -> `...18`
#> • `` -> `...19`
#> • `` -> `...20`
#> • `` -> `...21`
#> • `` -> `...22`
#> • `` -> `...23`
#> • `` -> `...24`
#> • `` -> `...25`
#> INFO [2024-11-15 20:27:31] Plate 201904190a read; 384 wells
#> INFO [2024-11-15 20:27:31] Plate 201904190b read; 384 wells
#> INFO [2024-11-15 20:27:31] Plate 201904190c read; 384 wells
#> INFO [2024-11-15 20:27:31] Plate 201904190d read; 384 wells
#> INFO [2024-11-15 20:27:31] Plate 201904190e read; 384 wells
#> INFO [2024-11-15 20:27:31] Plate 201904190f read; 384 wells
#> INFO [2024-11-15 20:27:31] File done
#> INFO [2024-11-15 20:27:31] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
#> New names:
#> • `` -> `...1`
#> • `` -> `...2`
#> • `` -> `...3`
#> • `` -> `...4`
#> • `` -> `...5`
#> • `` -> `...6`
#> • `` -> `...7`
#> • `` -> `...8`
#> • `` -> `...9`
#> • `` -> `...10`
#> • `` -> `...11`
#> • `` -> `...12`
#> • `` -> `...13`
#> • `` -> `...14`
#> • `` -> `...15`
#> • `` -> `...16`
#> • `` -> `...17`
#> • `` -> `...18`
#> • `` -> `...19`
#> • `` -> `...20`
#> • `` -> `...21`
#> • `` -> `...22`
#> • `` -> `...23`
#> • `` -> `...24`
#> • `` -> `...25`
#> INFO [2024-11-15 20:27:31] Plate 201904197a read; 384 wells
#> INFO [2024-11-15 20:27:31] Plate 201904197b read; 384 wells
#> INFO [2024-11-15 20:27:31] Plate 201904197c read; 384 wells
#> INFO [2024-11-15 20:27:31] Plate 201904197d read; 384 wells
#> INFO [2024-11-15 20:27:31] Plate 201904197e read; 384 wells
#> INFO [2024-11-15 20:27:31] Plate 201904197f read; 384 wells
#> INFO [2024-11-15 20:27:31] File done
df_ <- merge_data(
l_tbl$manifest,
l_tbl$treatments,
l_tbl$data
)
#> INFO [2024-11-15 20:27:31] Merging data
#> INFO [2024-11-15 20:27:31] Merging the metadata (manifest and treatment files)
#> WARN [2024-11-15 20:27:31] 4608 well loaded, 768 wells discarded for lack of annotation,
#> 3840 data point selected
#>
nested_confounders = intersect(
names(df_),
gDRutils::get_env_identifiers("barcode")
)
prepare_input(df_, nested_confounders, NULL)
#> $df_
#> CellLineName Tissue Duration DrugName Concentration DrugName_2
#> <char> <char> <num> <char> <num> <char>
#> 1: cellline_BA breast 0 vehicle 0 vehicle
#> 2: cellline_BA breast 0 vehicle 0 vehicle
#> 3: cellline_BA breast 0 vehicle 0 vehicle
#> 4: cellline_BA breast 0 vehicle 0 vehicle
#> 5: cellline_BA breast 0 vehicle 0 vehicle
#> ---
#> 3836: cellline_IB breast 168 vehicle 0 vehicle
#> 3837: cellline_IB breast 168 vehicle 0 vehicle
#> 3838: cellline_IB breast 168 vehicle 0 vehicle
#> 3839: cellline_IB breast 168 vehicle 0 vehicle
#> 3840: cellline_IB breast 168 vehicle 0 vehicle
#> Concentration_2 drug_moa drug_moa_2 parental_identifier subtype
#> <num> <char> <char> <char> <char>
#> 1: 0 vehicle vehicle cellline_BA unknown
#> 2: 0 vehicle vehicle cellline_BA unknown
#> 3: 0 vehicle vehicle cellline_BA unknown
#> 4: 0 vehicle vehicle cellline_BA unknown
#> 5: 0 vehicle vehicle cellline_BA unknown
#> ---
#> 3836: 0 vehicle vehicle cellline_IB unknown
#> 3837: 0 vehicle vehicle cellline_IB unknown
#> 3838: 0 vehicle vehicle cellline_IB unknown
#> 3839: 0 vehicle vehicle cellline_IB unknown
#> 3840: 0 vehicle vehicle cellline_IB unknown
#> Barcode Template ReadoutValue BackgroundValue
#> <char> <char> <num> <num>
#> 1: 201904190a Template_Untreated.xlsx 91452 570
#> 2: 201904190a Template_Untreated.xlsx 126448 570
#> 3: 201904190a Template_Untreated.xlsx 91461 570
#> 4: 201904190a Template_Untreated.xlsx 126449 570
#> 5: 201904190a Template_Untreated.xlsx 91459 570
#> ---
#> 3836: 201904197f Template_7daytreated.xlsx 788743 395
#> 3837: 201904197f Template_7daytreated.xlsx 359748 395
#> 3838: 201904197f Template_7daytreated.xlsx 405491 395
#> 3839: 201904197f Template_7daytreated.xlsx 575063 395
#> 3840: 201904197f Template_7daytreated.xlsx 854686 395
#> ReferenceDivisionTime clid Gnumber Gnumber_2 WellRow WellColumn
#> <num> <char> <char> <char> <char> <char>
#> 1: 26 CL00011 vehicle vehicle A 3
#> 2: 26 CL00011 vehicle vehicle B 3
#> 3: 26 CL00011 vehicle vehicle C 3
#> 4: 26 CL00011 vehicle vehicle D 3
#> 5: 26 CL00011 vehicle vehicle E 3
#> ---
#> 3836: 54 CL00018 vehicle vehicle D 22
#> 3837: 54 CL00018 vehicle vehicle I 22
#> 3838: 54 CL00018 vehicle vehicle J 22
#> 3839: 54 CL00018 vehicle vehicle K 22
#> 3840: 54 CL00018 vehicle vehicle L 22
#> record_id type
#> <int> <char>
#> 1: 1 control
#> 2: 2 control
#> 3: 3 control
#> 4: 4 control
#> 5: 5 control
#> ---
#> 3836: 3836 control
#> 3837: 3837 control
#> 3838: 3838 control
#> 3839: 3839 control
#> 3840: 3840 control
#>
#> $df_list
#> $df_list$combination
#> CellLineName Tissue Duration DrugName Concentration DrugName_2
#> <char> <char> <num> <char> <num> <char>
#> 1: cellline_BA breast 168 drug_002 0.001524158 drug_011
#> 2: cellline_BA breast 168 drug_002 0.001524158 drug_011
#> 3: cellline_BA breast 168 drug_002 0.001524158 drug_011
#> 4: cellline_BA breast 168 drug_002 0.001524158 drug_011
#> 5: cellline_BA breast 168 drug_002 0.001524158 drug_011
#> ---
#> 3836: cellline_IB breast 168 drug_011 0.149999911 vehicle
#> 3837: cellline_IB breast 168 drug_011 0.149999911 vehicle
#> 3838: cellline_IB breast 168 drug_011 0.149999911 vehicle
#> 3839: cellline_IB breast 168 drug_011 0.149999911 vehicle
#> 3840: cellline_IB breast 168 drug_011 0.149999911 vehicle
#> Concentration_2 drug_moa drug_moa_2 parental_identifier subtype
#> <num> <char> <char> <char> <char>
#> 1: 0.1499999 moa_A moa_B cellline_BA unknown
#> 2: 0.1499999 moa_A moa_B cellline_BA unknown
#> 3: 0.1499999 moa_A moa_B cellline_BA unknown
#> 4: 0.1499999 moa_A moa_B cellline_BA unknown
#> 5: 0.1499999 moa_A moa_B cellline_BA unknown
#> ---
#> 3836: 0.0000000 moa_B vehicle cellline_IB unknown
#> 3837: 0.0000000 moa_B vehicle cellline_IB unknown
#> 3838: 0.0000000 moa_B vehicle cellline_IB unknown
#> 3839: 0.0000000 moa_B vehicle cellline_IB unknown
#> 3840: 0.0000000 moa_B vehicle cellline_IB unknown
#> Barcode Template ReadoutValue BackgroundValue
#> <char> <char> <num> <num>
#> 1: 201904197a Template_7daytreated.xlsx 102301 570
#> 2: 201904197a Template_7daytreated.xlsx 76966 570
#> 3: 201904197a Template_7daytreated.xlsx 461220 570
#> 4: 201904197a Template_7daytreated.xlsx 497047 570
#> 5: 201904197a Template_7daytreated.xlsx 64611 570
#> ---
#> 3836: 201904197f Template_7daytreated.xlsx 383366 395
#> 3837: 201904197f Template_7daytreated.xlsx 133207 395
#> 3838: 201904197f Template_7daytreated.xlsx 204959 395
#> 3839: 201904197f Template_7daytreated.xlsx 323669 395
#> 3840: 201904197f Template_7daytreated.xlsx 387380 395
#> ReferenceDivisionTime clid Gnumber Gnumber_2 WellRow WellColumn
#> <num> <char> <char> <char> <char> <char>
#> 1: 26 CL00011 G00002 G00011 E 19
#> 2: 26 CL00011 G00002 G00011 F 19
#> 3: 26 CL00011 G00002 G00011 G 19
#> 4: 26 CL00011 G00002 G00011 H 19
#> 5: 26 CL00011 G00002 G00011 E 20
#> ---
#> 3836: 54 CL00018 G00011 vehicle H 22
#> 3837: 54 CL00018 G00011 vehicle M 22
#> 3838: 54 CL00018 G00011 vehicle N 22
#> 3839: 54 CL00018 G00011 vehicle O 22
#> 3840: 54 CL00018 G00011 vehicle P 22
#> record_id
#> <int>
#> 1: 321
#> 2: 322
#> 3: 323
#> 4: 324
#> 5: 325
#> ---
#> 3836: 3820
#> 3837: 3821
#> 3838: 3822
#> 3839: 3823
#> 3840: 3824
#>
#> $df_list$`single-agent`
#> CellLineName Tissue Duration DrugName Concentration drug_moa
#> <char> <char> <num> <char> <num> <char>
#> 1: cellline_BA breast 168 drug_002 0.001524158 moa_A
#> 2: cellline_BA breast 168 drug_002 0.001524158 moa_A
#> 3: cellline_BA breast 168 drug_002 0.001524158 moa_A
#> 4: cellline_BA breast 168 drug_002 0.001524158 moa_A
#> 5: cellline_BA breast 168 drug_002 0.001524158 moa_A
#> ---
#> 2972: cellline_IB breast 168 vehicle 0.000000000 vehicle
#> 2973: cellline_IB breast 168 vehicle 0.000000000 vehicle
#> 2974: cellline_IB breast 168 vehicle 0.000000000 vehicle
#> 2975: cellline_IB breast 168 vehicle 0.000000000 vehicle
#> 2976: cellline_IB breast 168 vehicle 0.000000000 vehicle
#> parental_identifier subtype Barcode Template
#> <char> <char> <char> <char>
#> 1: cellline_BA unknown 201904197a Template_7daytreated.xlsx
#> 2: cellline_BA unknown 201904197a Template_7daytreated.xlsx
#> 3: cellline_BA unknown 201904197a Template_7daytreated.xlsx
#> 4: cellline_BA unknown 201904197a Template_7daytreated.xlsx
#> 5: cellline_BA unknown 201904197a Template_7daytreated.xlsx
#> ---
#> 2972: cellline_IB unknown 201904197f Template_7daytreated.xlsx
#> 2973: cellline_IB unknown 201904197f Template_7daytreated.xlsx
#> 2974: cellline_IB unknown 201904197f Template_7daytreated.xlsx
#> 2975: cellline_IB unknown 201904197f Template_7daytreated.xlsx
#> 2976: cellline_IB unknown 201904197f Template_7daytreated.xlsx
#> ReadoutValue BackgroundValue ReferenceDivisionTime clid Gnumber
#> <num> <num> <num> <char> <char>
#> 1: 159679 570 26 CL00011 G00002
#> 2: 165488 570 26 CL00011 G00002
#> 3: 1169641 570 26 CL00011 G00002
#> 4: 1346753 570 26 CL00011 G00002
#> 5: 112168 570 26 CL00011 G00002
#> ---
#> 2972: 788743 395 54 CL00018 vehicle
#> 2973: 359748 395 54 CL00018 vehicle
#> 2974: 405491 395 54 CL00018 vehicle
#> 2975: 575063 395 54 CL00018 vehicle
#> 2976: 854686 395 54 CL00018 vehicle
#> WellRow WellColumn record_id
#> <char> <char> <int>
#> 1: A 19 329
#> 2: B 19 330
#> 3: C 19 331
#> 4: D 19 332
#> 5: A 20 333
#> ---
#> 2972: D 22 3836
#> 2973: I 22 3837
#> 2974: J 22 3838
#> 2975: K 22 3839
#> 2976: L 22 3840
#>
#>
#> $nested_confounders
#> [1] "Barcode"
#>
#> $nested_identifiers_l
#> $nested_identifiers_l$`single-agent`
#> [1] "Concentration"
#>
#> $nested_identifiers_l$combination
#> [1] "Concentration" "Concentration_2"
#>
#>
#> $exps
#> $exps$combination
#> NULL
#>
#> $exps$`single-agent`
#> NULL
#>
#>