This is a test version of Biostars. For the public version, visit https://www.biostars.org.
TCGA STAR count

Hi, all I want to download the TCGA-KIRC RNAseq using the following code. But I cannot get the data and instead I get error.

this is the code:

query <- GDCquery(
    project = "TCGA-KIRC",
    data.category = "Transcriptome Profiling",
    data.type = "Gene Expression Quantification",
    sample.type = "Primary Tumor",
    workflow.type = "STAR - Counts"
)

GDCdownload(query, method = "api")
rnaseq <- GDCprepare(query)  ##Here is the line causing error
rna_STAR_count <- as.data.frame(rnaseq@assays@data@listData)

this is the error :

Error in `fn()`:
! Join columns must be present in data.
x Problem with `#gene`.
Run `rlang::last_error()` to see where the error occurred.
There were 50 or more warnings (use warnings() to see the first 50)

it will be nice if anyone can help me with this.

star rnaseq expression gene count

0 answers

No answers yet.

Log in to answer this question.