Oncology Datasets from OncoDataSets Package

A collection of 55 oncology datasets imported from the OncoDataSets package for use in ClinicoPath analyses. These datasets cover various cancer types, study designs, and analysis scenarios commonly encountered in clinical pathology and oncology research.

Usage

# Load a specific dataset
data("Melanoma_df")

# View all available oncology datasets
data("oncology_datasets_summary")
View(oncology_datasets_summary)

# Example analyses:
# Survival analysis with Melanoma data
data("Melanoma_df")
# Use in jsurvival module

# ROC analysis with PSA data  
data("PSAProstateCancer_df")
# Use in meddecide module

# Descriptive statistics with Breast Cancer data
data("BreastCancerWI_df") 
# Use in ClinicoPathDescriptives module

Details

The datasets are organized into several categories:

Survival Analysis (5 datasets):

• Melanoma_df: Melanoma patient survival with tumor characteristics

• LeukemiaSurvival_df: Leukemia survival with treatment information

• ProstateSurvival_df: Prostate cancer survival by grade, stage, age

• NCCTGLungCancer_df: NCCTG lung cancer trial data

• OvarianCancer_df: Ovarian cancer trial survival data

Diagnostic/Decision Analysis (3 datasets):

• PSAProstateCancer_df: PSA levels and prostate cancer outcomes

• CA19PancreaticCancer_df: CA19-9 diagnostic accuracy studies

• LungNodulesDetected_df: Lung nodule characteristics and malignancy

Descriptive/Comparative Analysis (6 datasets):

• BreastCancerWI_df: Wisconsin Breast Cancer diagnostic features

• ChildCancer_df: Childhood cancer epidemiological data

• BladderCancer_df: Bladder cancer patient characteristics

• SmokingLungCancer_df: Smoking status and lung cancer relationship

• BrainCancerCases_df: Brain cancer case characteristics

• BrainCancerGeo_df: Brain cancer geographic distribution

Biomarker Analysis (5 datasets):

• BRCA1BreastCancer_df: BRCA1 mutations in breast cancer

• BRCA2BreastCancer_df: BRCA2 mutations in breast cancer

• BRCA1OvarianCancer_df: BRCA1 mutations in ovarian cancer

• BRCA2OvarianCancer_df: BRCA2 mutations in ovarian cancer

• CASP8BreastCancer_df: CASP8 gene variants in breast cancer

Additional categories include: Treatment Outcomes, Epidemiological, Molecular/Genomic, Experimental, Case-Control Studies, Risk Factors, Clinical Outcomes, and Specialized Studies.

References

Caceres Rossi, R. (2024). OncoDataSets: A Rich Collection of Data Focused on Cancer Research. R package version 0.1.0. https://CRAN.R-project.org/package=OncoDataSets

See also

• ClinicoPathDescriptives documentation

• jsurvival documentation

• meddecide documentation

• jjstatsplot documentation

Examples

if (FALSE) { # \dontrun{
# Load and explore melanoma survival data
data("Melanoma_df")
str(Melanoma_df)

# Create survival object
library(survival)
surv_obj <- Surv(Melanoma_df$time, Melanoma_df$status == 1)

# Load PSA data for ROC analysis
data("PSAProstateCancer_df")
# Create binary outcome
PSAProstateCancer_df$high_grade <- ifelse(PSAProstateCancer_df$gleason >= 7, 1, 0)

# Load breast cancer data for descriptive analysis
data("BreastCancerWI_df")
table(BreastCancerWI_df$diagnosis)
} # }