Simple demo patient information dataset. The information is related to the organoids present in the 'drugScreening' dataset.

Source: R/OrganoidsToolBox.R

Simple demo patient information dataset. The information is related to the organoids present in the 'drugScreening' dataset.

data(patientInfoMethoSet)

Format

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.

  • ancestry a character string representing the patient genetic ancestry.

  • BMI a character string representing the patient BMI class.

See also

  • 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.

Examples


## Load drug screen dataset for methotrexate dataset
data(drugScreening)

## Load patient information dataset for methotrexate dataset
data(patientInfoMethoSet)

## Retain unreplicated samples
cleanData <- selectNoReplicateOrganoids(drugScreening=drugScreeningMethoSet,
    patientInfo=patientInfoMethoSet)

## Calculate the extreme organoids for the methotrexate drug screening
## using a quantile of 1/3
results <- getClassOneDrug(drugScreening=cleanData,
    drugName="Methotrexate", study="MEGA-TEST", screenType="TEST-01",
    doseType="Averaged", quantile=1/4)

## The information of the extreme organoids is found it the 'extreme' entry
head(results$extreme)
#>   organoid_id relative_auc     group
#> 1       hT402     5.477998 SENSITIVE
#> 2       hT209    14.427644 SENSITIVE
#> 3       hT204    16.741371 SENSITIVE
#> 4       hT598    19.086306 SENSITIVE
#> 5       hT468    19.532156 SENSITIVE
#> 6       hT317    22.479160 SENSITIVE

## Fisher test on BMI
fisherT <- fisherCategoricalVariable(drugQuantile=results, category="BMI")

fisherT
#> $Fisher
#> 
#> 	Fisher's Exact Test for Count Data
#> 
#> data:  allTable
#> p-value = 2.201e-05
#> alternative hypothesis: two.sided
#> 
#> 
#> $table
#>           Normal Overweight Obese Underweight
#> SENSITIVE     25          2     3           3
#> RESISTANT     12         18     3           0
#> 
#> $category
#> [1] "BMI"
#>