GDC_Gene expression quantification values for matched tumor normal

Question

[kirti.gondkar]

Hi All,

i want to download Gene expression quantification data for tumor and matched normal pairs from GDC portal. Can someone suggest how can I do d same.

Thank you in advance

Answer 1

[thomaskuilman]

In R you can use the fantastic TCGAbiolinks package. You can find a thorough explanation here at the Bioconductor webpage. I have used the following script to do just what you want to do:

library("TCGAbiolinks")
library("SummarizedExperiment")

DIRPREFIX <- "/PATH/"

## Download raw counts for indicated sets
## Example of TCGA.data.sets: c("TCGA-LUAD", "TCGA-SKCM")
for (id in TCGA.data.sets){
    query <- GDCquery(project = id,
        ## get data.category using for instance TCGAbiolinks:::getProjectSummary("TCGA-LUAD")
        data.category = "Transcriptome Profiling",
        ## see link above for data.types and workflow.types
        data.type="Gene Expression Quantification",
        workflow.type = "HTSeq - Counts")
    GDCdownload(query, method = "client", directory = "~/Downloads/")
    data <- GDCprepare(query, directory = "~/Downloads/")
    save(data, file = file.path(DIRPREFIX, paste0(id, ".Rdata")), compress = "xz")
}