I'm trying to download SKCM melanoma samples to R, using the package
TCGAbiolinks . The wanted data is RNA-seq expression matrix, along with the metadata. Pretty basic stuff.
This is the code right from the beginning:
library(TCGAbiolinks) GDCprojects = getGDCprojects() TCGAbiolinks:::getProjectSummary("TCGA-SKCM") query_TCGA = GDCquery( project = "TCGA-SKCM", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", experimental.strategy = "RNA-Seq", workflow.type = "STAR - Counts", sample.type = c("Primary Tumor")) # picked primary skcm_res = getResults(query_TCGA) # make results as table GDCdownload(query = query_TCGA) tcga_data = GDCprepare(query_TCGA)
However, I get this error:
> tcga_data = GDCprepare(query_TCGA) |=================================================================================|100% Completed after 24 s Error in `vectbl_as_col_location()`: ! Can't subset columns past the end. ℹ Locations 2, 3, and 4 don't exist. ℹ There is only 1 column. Run `rlang::last_error()` to see where the error occurred. There were 50 or more warnings (use warnings() to see the first 50)
What does this mean and how do I fix this error? thank you.
Note: Suggestions for other packages that might get the job done would be more than welcomed!