Hello, i'm very neewby to gdc and R, so i need your help.
I need to extract expression data for several proteins for tumor and normal tissues from the same patient. due to the bad internet connection i cannot download full raw data, so i need using slicing.
I've read the manual and the suggesting procedure for my task is:
x=files() %>% filter(~ cases.primary_site=='Lung' & cases.samples.sample_type== 'Primary Tumor') y = x %>% response_all() %>% ids() data = slicing(y,symbols=c("prot1", "prot2"))
As i can understand, slicing is already retrieving data, not just building request. In RStudio i cannot use slicing, because i haven't authority_token, just got HTTP 503 error. So i need construct manifest and then use it with gdc_client.exe, it can load public access data, ignoring restricted access ones.
So the question is: how construct gdcquery with slicing conditions to make manifest from it?