TCGAbarcode: Parse data from TCGA barcode
In waldronlab/BiocInterfaces: TCGA utility functions for data management

TCGAbarcode

R Documentation

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/BiocInterfaces documentation built on Dec. 19, 2024, 2:07 p.m.