I've been experimenting with the GenomicDataCommons package to handle query work against the GDC API. For some reason there is an issue with timeouts for requests of a certain length. There doesn't seem to be a direct way around this using the piped syntax. Anyone else have luck with this?
There is a results(size = n) method, its syntax seems to allow only the first n records to be accessed.
Here is an example query (should return 400-500 records):
proj <- 'TCGA-COAD' case_data <- cases() %>% GenomicDataCommons::filter(~ project.project_id == proj) %>% GenomicDataCommons::expand('diagnoses') %>% results_all() %>% as_tibble()
Gives, after a few moments:
Error in is.response(x) : Internal Server Error (HTTP 500).