Dear Bioconductor,
I am working with TCGA data anaylsis. I want to download and analyze the TCGA data ( Project : TCGA-THCA).
using your TCGAbioconductort package, I could do practice in TCGA-LGG, GBM well.
but I can't do it again in TCGA-THCA because I don't know how to get the barcodes like as your protocol article(TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages https://www.ncbi.nlm.nih.gov/pubmed/28232861). and I have some questions.
Q1. can I know how to get the TCGA-THCA barcode numbers which should be in there as like bold letters in example below?
[ GDCdownload(query.met.gbm)
11 met.gbm.450 <– GDCprepare(query = query.met.gbm,
12 save = TRUE,
13 save.filename = "gbmDNAmet450k.rda" ,
14 summarizedExperiment = TRUE)
15 query.met.lgg <– GDCquery(project = "TCGA–LGG",
16 legacy = TRUE,
17 data.category = "DNA methylation ",
18 platform = "Illumina Human Methylation 450",
19 barcode = c("TCGA–HT–7879–01A–11D–2399–05", "TCGA–HT–8113–01A–11D–2399–05" )
)]
And I want to know the detailed meaning of each column in the barcode too, if possible.
Example of the above barcode : TCGA–HT–7879–01A–11D–2399–05
I think they might be matters of TCGA database but I can't find it anywhere. so please help me to start the anaylsis.
Thank you for your good tutorial here!
Sincerely,
Park
