Open bioinfo-dirty-jobs opened 6 years ago
You'll need to do this in two steps.
gdc_clinical
. Give it a try and let me know if you need more direction. Great question!
@seandavi Thanks so much.... I try to figure out.. .. but I miss something Here you have what I found
q = cases() %>%
filter(~ project.project_id=='TCGA-OV' &
files.analysis.workflow_type == 'HTSeq - FPKM-UQ')
q %>% count()
file_ids = q %>% facet('files.cases.case_id') %>% response_all() %>%
ids()
So I suppose I have in file_ids How can retrive all the diagnosis data... If I have the bcr_patient_uuid how can download the expression data? Could you please make me some example? thanks so much for the help and patience
I'll write something up, but it may take me a few days--sorry for the delay. I really appreciate you working through this with us.
Dear @seandavi
I still try to resolve the problem... but I miss something.
So I found on cases I found this:
grep('files.cases.case_id',available_fields('cases'),value=TRUE)
but not on the expand field
q = cases() %>%
GenomicDataCommons::filter(~ project.project_id=='TCGA-OV' &
files.analysis.workflow_type == 'HTSeq - FPKM-UQ') %>%
GenomicDataCommons::expand("diagnoses") %>% facet()
q %>% results()
I want to download all the clinical data from the rnaseq data selected: