arguments imply differing number of rows: GDCquery_clinic

[aysenuroner]

Hi everyone,

I'm trying to get clinical data but I got error for a few cases.

cTCGA <- GDCquery_clinic(project = "CGCI-HTMCP-CC" , type = "clinical")

When I run this code then I got this error

Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 212, 214

You can find the name of the studies I got these errors below:

"CGCI-BLGSP"

"HCMI-CMDC"

"TARGET-NBL"

I really appreciate your help in solving this error. I want to use every study as much as possible.

[tiagochst]

HTMCP-03-06-02061 seems to have two diagnosis for the same patient. https://portal.gdc.cancer.gov/cases/c5e55e09-1a50-4415-95e8-0db66771a2db.

• [ ] Add exception code to handle those cases. Probable solution: merge each column separated by ;

[tiagochst]

@aysenuroner I updated the package to handle the case. Please, do you mind installing the updated version of TCGAbiolinks from github with BiocManager::install("BioinformaticsFMRP/TCGAbiolinks") and see if it is working as expected ?

[aysenuroner]

I just updated the package and now it seems working. Thanks a million