TCGA, TCGAbiolink, gene expression

Question

[Rob]

Hi friends, I m using the following code to download STAR count of KIRP. How should I download just the primary tumor & just coding genes (not all genes)? Also, how should I download the corresponding clinical data? Thanks

query <- GDCquery(project = "TCGA-KIRP",
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification",
                  experimental.strategy = "RNA-Seq",
                  workflow.type = "STAR - Counts")


# Download data using api
GDCdownload(query, method = "api")

#Prepare data
data <- GDCprepare(query)
?assay()
#generate count matrix
rna_TCGA_STAR_KIRP <- as.data.frame(SummarizedExperiment::assay(data))
#rna_STAR_test <- as.data.frame(SummarizedExperiment::assay(data_TCGA_STAR_KIRP))

write.table(rna_TCGA_STAR_KIRP, "rna_TCGA_STAR_KIRP.txt", sep='\t')