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.