The function TODO
selectNoReplicateOrganoids(drugScreening, patientInfo)a data.frame that contains the drug screening
results. The column is 'organoid_id' is mandatory.
a data.frame containing the meta-data information
related to the organoids. The mandatory columns are: 'organoid_id'
and 'patient_id'.
a data.frame with the drug screening results filtered
to contain with only one organoid per patient. The extra columns from the
patient information dataset is added as extra columns to the final dataset.
## Load drug screen dataset for 1 drug
data(drugScreening)
## Load patient information dataset for 1 drug
data(patientInfo)
## Set seed to get reproducible results
set.seed(1212)
results <- selectNoReplicateOrganoids(drugScreening=drugScreening,
patientInfo=patientInfo)
## TODO
results
#> organoid_id Column1 plate passage_number timestamp study
#> hT102 hT102 4 Plate1 P14 2/2/1994 MEGA-TEST
#> hT1082 hT1082 3 Plate1 P13 2/2/1988 MEGA-TEST
#> hT192 hT192 4 Plate1 P11 2/2/1994 MEGA-TEST
#> hT2211 hT2211 3 Plate1 P14 1/1/1970 MEGA-TEST
#> hT2212 hT2212 3 Plate1 P29 1/1/1970 MEGA-TEST
#> hT2213 hT2213 5 Plate2 P12 1/1/1970 MEGA-TEST
#> hT2251 hT2251 3 Plate1 P13 1/1/1970 SUPER-TEST
#> hT322 hT322 5 Plate1 P11 1/1/2022 MEGA-TEST
#> hT3312 hT3312 3 Plate1 P12 1/1/1970 MEGA-TEST
#> hT999 hT999 5 Plate1 P9 2/2/1994 MEGA-TEST
#> screen_type z_prime drug_a drug_b drug_c drug_background
#> hT102 TEST-01 0.2882018 Methotrexate N/A N/A N/A
#> hT1082 TEST-01 0.2362953 Methotrexate N/A N/A N/A
#> hT192 TEST-01 0.2120181 Methotrexate N/A N/A N/A
#> hT2211 TEST-01 0.0728753 Methotrexate N/A N/A N/A
#> hT2212 TEST-01 0.0744753 Methotrexate N/A N/A N/A
#> hT2213 TEST-02 0.0718753 Methotrexate N/A N/A N/A
#> hT2251 TEST-01 0.2500374 Methotrexate N/A N/A N/A
#> hT322 TEST-01 0.4219293 Methotrexate N/A N/A N/A
#> hT3312 TEST-01 0.1628113 Methotrexate N/A N/A N/A
#> hT999 TEST-01 0.5520181 Methotrexate N/A N/A N/A
#> dosage_type dosage_concentration_a dosage_concentration_b
#> hT102 Averaged -0.1231304 0
#> hT1082 Averaged 1.9956352 0
#> hT192 Averaged -1.1180171 0
#> hT2211 Averaged -1.3027707 0
#> hT2212 Averaged 0.5051500 0
#> hT2213 Averaged -2.1132728 0
#> hT2251 Averaged 0.6518696 0
#> hT322 Averaged -1.2127707 0
#> hT3312 Averaged -1.3027707 0
#> hT999 Averaged 1.7446352 0
#> dosage_concentration_c dosage_concentration_background percent_viability
#> hT102 0 0 70.12445
#> hT1082 0 0 36.63934
#> hT192 0 0 76.11993
#> hT2211 0 0 67.49417
#> hT2212 0 0 46.14517
#> hT2213 0 0 93.53307
#> hT2251 0 0 43.36855
#> hT322 0 0 90.23416
#> hT3312 0 0 61.06084
#> hT999 0 0 95.22267
#> ic50 auc relative_auc patient_id
#> hT102 1.0002432 201.0053 46.11044 Patient_008
#> hT1082 3.3907678 285.6598 68.93726 Patient_001
#> hT192 0.9002432 187.0053 33.11044 Patient_009
#> hT2211 1.1417485 222.0073 53.57622 Patient_003
#> hT2212 0.8862142 246.3675 75.67628 Patient_004
#> hT2213 0.8162142 242.3675 71.67628 Patient_005
#> hT2251 1.5223589 248.8876 63.38033 Patient_006
#> hT322 14.1157419 931.1471 55.22300 Patient_007
#> hT3312 0.7672968 193.1456 46.61114 Patient_002
#> hT999 0.9880232 287.0054 97.31222 Patient_010