Retrieve barcodes from TCGA using R

Question

[ravipriya11396]

How to retrieve sample barcode from patient barcode using R?

Thanks with regards in advance.

[Kevin Blighe]

Update, 12th May 2018

Since this post was made, a rapid way to interrogate the GDC data for the purposes of converting UUIDs to TCGA Barcodes was found using R Programming Language. See the thread here: Sample names for TCGA data from GDC-legacy archive

Kevin

Answer 1

[Chun-Jie Liu]

TCGA provide API to get the barcode from UUID. I wrote a python script to map file UUID barcode. Just input the manifest to the script.

Now, then. You want to use r to access GDC API, is the same as python. Use httr package in the r to post filters to return your result.

A simple example using file ID to retrieve info from GDC (GDC provides other end point, you can check it.)

require(httr)

files_endpt = "https://gdc-api.nci.nih.gov/files"

body = list("filters" = list("op" = "in", "content" = list('field'='files.file_id', 'value'='af5085c1-5b4e-4b88-9f5f-3c049cdd981f')), 'format' = 'TSV', 'fields'="file_id,file_name,cases.case_id,cases.submitter_id,cases.samples.sample_id,cases.samples.submitter_id,cases.samples.portions.analytes.aliquots.aliquot_id,cases.samples.portions.analytes.aliquots.submitter_id,cases.samples.sample_type,cases.samples.tissue_type,data_category,data_type", 'size' = 1)

r <- POST(url = files_endpt, body = body, encode = 'json')

content(r, 'parsed')

content(r)$cases_0_submitter_id

Answer 2

[Giovanni M Dall'Olio]

There is a bioconductor package called tcgaBiolinks. I've never used but it should have the function you are looking for.