I provide below query:
query <- GDCquery(project = "TCGA-SARC",sample.type = "Primary solid Tumor", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification",workflow.type = "HTSeq - FPKM-UQ");
after that for downloading my data, I run below code:
GDCdownload(query, method= "api", directory = "mydata")
So I tried the GDCdownloads, it starts downloading, but it gives me an error saying the file or directory does not exist:
"<simpleWarning in file.create(to[okay]): cannot create file 'GDCdata/TCGA-SKCM/harmonized/Transcriptome_Profiling/Gene_Expression_Quantification/3c9fe8ef-e394-4d7a-9189-de6ce2169c45/50bbf24f-b914-4e53-98ee-0cf22b2d9f01.htseq.counts.gz', reason 'No such file or directory'>
I appreciate if anybody share his/ her comment with me.