Parse data from TCGA barcode — TCGAbarcode • TCGAutils

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

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)
#> [1] "TCGA-B0-5117" "TCGA-B0-5094" "TCGA-E9-A295"

## Sample identifiers
TCGAbarcode(barcodes, sample = TRUE)
#> [1] "TCGA-B0-5117-11A" "TCGA-B0-5094-11A" "TCGA-E9-A295-10A"