get_clinical_data: Retrieve Clinical Information for a Cancer Study.

In dami82/TCGAretriever: Retrieve Genomic and Clinical Data from CBioPortal Including TCGA Data

Retrieve Clinical Information for a Cancer Study.

Description

Retrieve Clinical Information about the samples included in a cancer study of interest. For each sample/case, information about the corresponding cancer patient are returned. These may include sex, age, therapeutic regimen, tumor stage, survival status, as well as other information.

Usage

get_clinical_data(csid, case_list_id = NULL, dryrun = FALSE)

Arguments

csid	String corresponding to a TCGA Cancer Study identifier.
case_list_id	String corresponding to the case_list identifier of interest. This Can be NULL.
dryrun	Logical. If TRUE, all other arguments (if any) are ignored and a representative example is returned as output. No Internet connection is required for executing the operation when 'dryrun' is TRUE.

Value

data.frame including clinical information of a list of samples/cases of interest.

Author(s)

Damiano Fantini, [e-mail]

References

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

Examples

# Set `dryrun = FALSE` (default option) in production!
clinic_data <- get_clinical_data("blca_tcga", dryrun = TRUE)  
utils::head(clinic_data[, 1:7])
 

dami82/TCGAretriever documentation built on Feb. 2, 2024, 12:06 p.m.