TCGAbarcode: Parse data from TCGA barcode

In waldronlab/TCGAmisc: TCGA utility functions for data management

Parse data from TCGA barcode

Description

This function returns the specified snippet of information obtained from the TCGA barcode.

Usage

TCGAbarcode(
  barcodes,
  participant = TRUE,
  sample = FALSE,
  portion = FALSE,
  plate = FALSE,
  center = FALSE,
  index = NULL
)

Arguments

barcodes	A character vector of TCGA barcodes
participant	Logical (default TRUE) participant identifier chunk
sample	Logical (default FALSE) includes the numeric sample code of the barcode and the vial letter
portion	Logical (default FALSE) includes the portion and analyte codes of the barcode
plate	Logical (default FALSE) returns the plate value
center	Logical (default FALSE) returns a matrix with the plate and center codes
index	An optional numeric vector indicating barcode positions when split by the delimiter (i.e., hyphen '-'). For example, an index of c(1, 2) corresponds to 'TCGA-ZZ' in TCGA-ZZ-A1A1.

Value

A character vector or data matrix of TCGA barcode information

Author(s)

M. Ramos

Examples

barcodes <- c("TCGA-B0-5117-11A-01D-1421-08",
"TCGA-B0-5094-11A-01D-1421-08",
"TCGA-E9-A295-10A-01D-A16D-09")

## Patient identifiers
TCGAbarcode(barcodes)

## Sample identifiers
TCGAbarcode(barcodes, sample = TRUE)

waldronlab/TCGAmisc documentation built on Dec. 19, 2024, 2:10 p.m.