Using TCGABioLinks to query multiple cancer studies

Question

[ivykosater]

I have a list of cancer samples that I wish to download transcriptome data for using TCGABiolinks. I use the GDCquery() function for downloading data, however my list spans multiple TCGA projects. Here is my code

query <- GDCquery(project = "", data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification", 
                  workflow.type = "HTSeq - Counts",
                  barcode = acc_numbers)

I am unsure what to put in the project argument. I do not think there is an argument for the TCGA pan cancer atlas, so does anyone know what I should do here?

Answer 1

[Ashutosh Pandey]

https://rdrr.io/bioc/TCGAbiolinks/man/GDCquery.html

See example from the manual to perform query on more than one study:

query.met <- GDCquery(project = c("TCGA-GBM","TCGA-LGG"),
                      legacy = TRUE,
                      data.category = "DNA methylation",
                      platform = "Illumina Human Methylation 450")

If you want all to perform across all projects then you can replace list of projects with TCGAbiolinks:::getGDCprojects()$project_idor filter it as needed.