Merge all the input data into a single data.table
Arguments
- manifest
a data.table with a manifest info
- treatments
a data.table with a treaatments info
- data
a data.table with a raw data info
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 20:27:29] Manifest loaded successfully
#> INFO [2024-11-15 20:27:29] Reading Template_7daytreated.xlsx with load_templates_xlsx
#> INFO [2024-11-15 20:27:29] Loading Template_7daytreated.xlsx
#> INFO [2024-11-15 20:27:29] Loading Template_Untreated.xlsx
#> INFO [2024-11-15 20:27:29] Templates loaded successfully!
#> INFO [2024-11-15 20:27:29] 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 20:27:29] Plate 201904190a read; 384 wells
#> INFO [2024-11-15 20:27:29] Plate 201904190b read; 384 wells
#> INFO [2024-11-15 20:27:29] Plate 201904190c read; 384 wells
#> INFO [2024-11-15 20:27:29] Plate 201904190d read; 384 wells
#> INFO [2024-11-15 20:27:29] Plate 201904190e read; 384 wells
#> INFO [2024-11-15 20:27:29] Plate 201904190f read; 384 wells
#> INFO [2024-11-15 20:27:29] File done
#> INFO [2024-11-15 20:27:29] 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 20:27:30] Plate 201904197a read; 384 wells
#> INFO [2024-11-15 20:27:30] Plate 201904197b read; 384 wells
#> INFO [2024-11-15 20:27:30] Plate 201904197c read; 384 wells
#> INFO [2024-11-15 20:27:30] Plate 201904197d read; 384 wells
#> INFO [2024-11-15 20:27:30] Plate 201904197e read; 384 wells
#> INFO [2024-11-15 20:27:30] Plate 201904197f read; 384 wells
#> INFO [2024-11-15 20:27:30] File done
merge_data(
l_tbl$manifest,
l_tbl$treatments,
l_tbl$data
)
#> INFO [2024-11-15 20:27:30] Merging data
#> INFO [2024-11-15 20:27:30] Merging the metadata (manifest and treatment files)
#> WARN [2024-11-15 20:27:30] 4608 well loaded, 768 wells discarded for lack of annotation,
#> 3840 data point selected
#>
#> 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