Error with TCGA package - TCGAbiolinks
1
0
Entering edit mode
JAcky • 0
@d6b8183e
Last seen 10 hours ago
Israel

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()

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

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!

TCGAbiolinks RNASeq CancerData • 262 views
0
Entering edit mode

You can try the Genomic Data Commons Data Portal at

https://portal.gdc.cancer.gov/

or the GenomicDataCommons R/Bioconductor package

0
Entering edit mode
@tiagochst-7121
Last seen 6 days ago
Miami, US

It is working with the github version. Could you update please?

BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")