Extract biospecimen data from the TCGA barcode

This function uses the full TCGA barcode to return a data frame of the data pertinent to laboratory variables such as vials, portions, analytes, plates and the center.

Usage

TCGAbiospec(barcodes)

Arguments

barcodes

A character vector of TCGA barcodes

Value

A dataframe with sample type, sample code, portion, plate, and center columns.

Author

M. Ramos

Examples

example("TCGAbarcode")
#> 
#> TCGAbr> barcodes <- c("TCGA-B0-5117-11A-01D-1421-08",
#> TCGAbr+ "TCGA-B0-5094-11A-01D-1421-08",
#> TCGAbr+ "TCGA-E9-A295-10A-01D-A16D-09")
#> 
#> TCGAbr> ## Patient identifiers
#> TCGAbr> TCGAbarcode(barcodes)
#> [1] "TCGA-B0-5117" "TCGA-B0-5094" "TCGA-E9-A295"
#> 
#> TCGAbr> ## Sample identifiers
#> TCGAbr> TCGAbarcode(barcodes, sample = TRUE)
#> [1] "TCGA-B0-5117-11A" "TCGA-B0-5094-11A" "TCGA-E9-A295-10A"
TCGAbiospec(barcodes)
#>   submitter_id    sample_definition sample vial portion analyte plate center
#> 1 TCGA-B0-5117  Solid Tissue Normal     11    A      01       D  1421     08
#> 2 TCGA-B0-5094  Solid Tissue Normal     11    A      01       D  1421     08
#> 3 TCGA-E9-A295 Blood Derived Normal     10    A      01       D  A16D     09