how include slicing to manifest
0
0
Entering edit mode
dvortsov • 0
@dvortsov-15439
Last seen 6.1 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 • 651 views
ADD COMMENT

Login before adding your answer.

Traffic: 704 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6