how include slicing to manifest
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dvortsov • 0
@dvortsov-15439
Last seen 3.7 years ago

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?

gdcquery • 305 views