expand_cases: Samples Included in a List of Samples.

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

Samples Included in a List of Samples.

Description

Each study includes one or more "case lists". Each case list is a collection of samples that were analyzed using one or more platforms/assays. It is possible to obtain a list of all sample identifiers for each case list of interest.

Usage

expand_cases(csid, dryrun = FALSE)

Arguments

csid	String corresponding to a TCGA Cancer Study identifier.
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

list containing as many elements as TCGA case lists available for a given TCGA Study. Each element is named after a case list identifier. Also, each element is a character vector including all sample identifiers (case ids) corresponding to the corresponding case list identifier.

Author(s)

Damiano Fantini, [e-mail]

References

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

Examples

# Set `dryrun = FALSE` (default option) in production!
x <- expand_cases("blca_tcga", dryrun = TRUE)
lapply(x, utils::head)

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