Download data by TCGAbiolinks

Question

[landscape95]

I'm getting familiar with TCGAbiolinks package, now I try to download BRCA data, data type is mRNA, sample type is tumor, could any help me with the code? Thanks in advance!

[venu]

Did you check the documentation?

http://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html

[landscape95]

yes, but I am a little confused of the data.category and data.type.

[GenoMax]

Why not try retrieving small portions of data and see what the difference is.

[venu]

could you also post the code you tried?

[landscape95]

Is this right?

library("TCGAbiolinks")
query = GDCquery(project = "TCGA-BRCA", data.category = "Raw Sequencing Data", experimental.strategy = "miRNA-Seq")

[venu]

Is this right?

Didn't you give a try?

There is no obvious error in the code (but I think you need to add other arguments also?). Execute it, if you get error, post it here.

[landscape95]

This has no error but I cannot download it since I don't have an authorized account. But I wonder is the above code is for the requirement above since I am new to TCGAbiolinks? My supervisor told me to download based on the requirements above and summarize the result to the matrix with columns are samples and rows are genes.

[GenoMax]

If all you need is a matrix of values then you could possibly get that from cBioPortal.

[landscape95]

Thank you very much, I got the information, but could we get it from biolinks.

[sandhana.krishnan]

I tried your code and it works fine. If you want to download then you have to use GDCdownload. Use the code below and you should be able to download the file. Ensure there is a lot of space in the hard disk where you have set your working directory to download the data.

query <- GDCquery(project = "TCGA-BRCA",
                  data.category = "Raw Sequencing Data",
                  experimental.strategy = "miRNA-Seq")

GDCdownload(query)

data <- GDCprepare(query)