R/OrganoidsToolBox.R
patientInfo.RdSimple demo patient information dataset. The information is related to the organoids present in the 'drugScreening' dataset.
data(patientInfo)a data.frame with the following columns:
organoid_id a character string representing the
organoid identifier.
patient_id a character string representing the patient
identifier.
getClassOneDrug for selecting the samples
with sensitive and resistant behavior for a
specific drug screening dataset.
selectNoReplicateOrganoids for selecting
the unrelated samples (only one sample per patient) from a drug screening
dataset.
fisherCategoricalVariable for running Fisher tests
in the sensitive and resistant groups using a categorical value
from a drug screening dataset.
## Load drug screen dataset for 1 drug
data(drugScreening)
## Load patient information dataset for 1 drug
data(patientInfo)
## Select unrelated organoids in the drug screening
results <- selectNoReplicateOrganoids(drugScreening=drugScreening,
patientInfo=patientInfo)
## The drug screen dataset has been filtered
results
#> organoid_id Column1 plate passage_number timestamp study
#> hT1001 hT1001 3 Plate1 P16 2/2/1988 MEGA-TEST
#> hT102 hT102 4 Plate1 P14 2/2/1994 MEGA-TEST
#> hT1051 hT1051 5 Plate1 P11 1/1/1970 MEGA-TEST
#> hT192 hT192 3 Plate1 P11 2/2/1994 MEGA-TEST
#> hT2211 hT2211 5 Plate1 P14 1/1/1970 MEGA-TEST
#> hT2212 hT2212 3 Plate1 P29 1/1/1970 MEGA-TEST
#> hT2213 hT2213 3 Plate2 P12 1/1/1970 MEGA-TEST
#> hT2251 hT2251 3 Plate1 P13 1/1/1970 SUPER-TEST
#> hT322 hT322 3 Plate1 P11 1/1/2022 MEGA-TEST
#> hT999 hT999 3 Plate1 P9 2/2/1994 MEGA-TEST
#> screen_type z_prime drug_a drug_b drug_c drug_background
#> hT1001 TEST-01 0.2732018 Methotrexate N/A N/A N/A
#> hT102 TEST-01 0.2882018 Methotrexate N/A N/A N/A
#> hT1051 TEST-01 0.2500374 Abraxane 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 0.0733353 Methotrexate Abraxane 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
#> hT999 TEST-01 0.5520181 Methotrexate N/A N/A N/A
#> dosage_type dosage_concentration_a dosage_concentration_b
#> hT1001 Averaged -1.3027707 0
#> hT102 Averaged 1.4663183 0
#> hT1051 Averaged 0.8343696 0
#> hT192 Averaged -1.2100130 0
#> hT2211 Averaged -0.1481304 0
#> hT2212 Averaged -1.2222200 0
#> hT2213 Averaged -1.3316204 0
#> hT2251 Averaged -2.2481304 0
#> hT322 Averaged -0.7335800 0
#> hT999 Averaged -0.1231304 0
#> dosage_concentration_c dosage_concentration_background percent_viability
#> hT1001 0 0 75.732264
#> hT102 0 0 19.945501
#> hT1051 0 0 42.368545
#> hT192 0 0 79.322142
#> hT2211 0 0 80.904988
#> hT2212 0 0 8.620515
#> hT2213 0 0 85.624298
#> hT2251 0 0 75.598561
#> hT322 0 0 97.336119
#> hT999 0 0 97.664067
#> ic50 auc relative_auc patient_id
#> hT1001 1.0722432 218.00535 52.610445 Patient_001
#> hT102 1.0002432 201.00535 46.110445 Patient_008
#> hT1051 0.8666430 243.22110 73.212120 Patient_002
#> hT192 0.9002432 187.00535 33.110445 Patient_009
#> hT2211 1.1417485 222.00729 53.576219 Patient_003
#> hT2212 0.7444589 49.99956 6.330331 Patient_004
#> hT2213 0.8162142 242.36746 71.676280 Patient_005
#> hT2251 1.5223589 248.88756 63.380332 Patient_006
#> hT322 14.1157419 931.14714 55.223002 Patient_007
#> hT999 0.9880232 287.00535 97.312221 Patient_010