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 for the samples, like tumour purity, LDH levels, and some more wanted features. Pretty basic.
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'm getting this error and I don't get what is the problem. I tried using metastatic samples instead of primary, and tried without entering the
data.type parameter, didn't work. So What does this mean and how do I fix this error? thank you.
> 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)
Note: if there is some other recommended way to download this type of data, using other packages for example, I'll be more than glad to hear. Thanks!