GDCprepare Issue

[ZaraForbrigger]

If I run the following code block on TCGAbiolinks version 2.37.3/2.38.0 I receive the error:

query_TCGA = GDCquery(project = "TARGET-WT",
data.category = "Transcriptome Profiling",
experimental.strategy = "RNA-Seq",
workflow.type = "STAR - Counts",
data.type = "Gene Expression Quantification")

GDCdownload(query_TCGA)

data.rna <- GDCprepare(query_TCGA)

"Error in dplyr::select():
! Can't select columns that don't exist.
✖ Column disease_response doesn't exist.
Run rlang::last_trace() to see where the error occurred."

If I use an older version of TCGAbiolinks, version 2.34, I do not get this error and I am able to run the full block.

Any help would be appreciated. Thanks!

[danmonyak]

I also just started getting that error. I forked my own version where I commented out lines 1979 and 1986 and then it worked.

[liu-zhiyang]

I also just started getting that error. I forked my own version where I commented out lines 1979 and 1986 and then it worked.

@danmonyak That's really helpful!
BTW, there are still two lines to be commented out in clinical.R -- line 320 and 327, for querying clinical data using GDCquery_clinic().
Also, an error occured when using GDCprepare() to get clinical data: Error in if (data.type == "Clinical data") { : missing value where TRUE/FALSE needed. It seems that there is an missing data.type of "Clinical data" because there is no such data.type currently.