TCGAretriever (version 1.5)

get_clinical_data: Retrieve Clinical Information from a TCGA Study

Description

Retrieve Information about the Patients included in a TCGA Study of Interest. Each patient is associates with a case_id. Each case_id is accompained by a set of clinical information that may include sex, age, therapeutic regimen, Tumor Staging, vital status and others. NA are allowed.

Usage

get_clinical_data(case_id = NULL)

Value

data.frame including one row per patient/case/sample

Arguments

case_id

string corresponding to the case_list identifier of a specific list of cases of interest

Author

Damiano Fantini,

References

• http://www.biotechworld.it/bioinf/2016/07/11/tcga-data-via-tcgaretriever/

• https://www.data-pulse.com/dev_site/TCGAretriever/

Examples

clinic_data <- get_clinical_data("blca_tcga_all")
if (nrow(clinic_data) >= 6 & ncol(clinic_data) >= 5) {
  clinic_data[1:6,1:5]
  hist(as.numeric(clinic_data$AGE), 
  col = "darkorange", 
  xlab = "Age", 
  main = "Bladder Cancer, age of diagnosis")
}