Problem with GDCprepare of TARGET-NBL project

[mona-n]

Hi all,

I am trying to use GDCquery, GDCdownload and GDCprepare to download mutation data of the TARGET-NBL project. My version of TCGAbiolinks is 2.14.0 and R version is 3.6.2.

Below is my code and corresponding output:

> query_TARGET <- GDCquery("TARGET-NBL", 
                         data.category = "Simple Nucleotide Variation", 
                         data.type = "Masked Somatic Mutation", 
                         workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking", 
                         access = "open")

--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TARGET-NBL
--------------------
oo Filtering results
--------------------
ooo By access
ooo By data.type
ooo By workflow.type
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------

> GDCdownload(query_TARGET)

Downloading data for project TARGET-NBL
Of the 219 files for download 219 already exist.
All samples have been already downloaded

> query_TARGET_prepare <- GDCprepare(query_TARGET,
                                   save = TRUE,
                                   save.filename = paste0("TARGET-NBL/TARGET_NBL_mut_data/TARGET_NBL_mut_data.rda"))

Saving file:TARGET-NBL/TARGET_NBL_mut_data/TARGET_NBL_mut_data.rda
File saved
Warning message:
In if (grepl("Masked Somatic Mutation", query$results[[1]]$data_type,  :
  the condition has length > 1 and only the first element will be used

query_TARGET_prepare then looks like the following:

which does not look right and I assume it has something to do with the above warning message from the GDCprepare step. The same thing occurs when I use the TARGET-AML project. How can I solve this problem?

Thank you very much in advance for your help.

Best regards, Mona

[tiagochst]

@mona-n Sorry for the late reply. I just fixed the issue.