## ----------------------------------------------------------------------------- library(GenomicDataCommons,quietly = TRUE) ## ----------------------------------------------------------------------------- q = files() %>% GenomicDataCommons::filter( cases.project.project_id == 'TCGA-COAD' & data_type == 'Aligned Reads' & experimental_strategy == 'RNA-Seq' & data_format == 'BAM') ## ----------------------------------------------------------------------------- count(q) ## ----------------------------------------------------------------------------- manifest(q) ## ----------------------------------------------------------------------------- all_fields = available_fields(files()) ## ----------------------------------------------------------------------------- grep('race|ethnic',all_fields,value=TRUE) ## ----------------------------------------------------------------------------- available_values('files',"cases.demographic.ethnicity") available_values('files',"cases.demographic.race") ## ----------------------------------------------------------------------------- q_white_only = q %>% GenomicDataCommons::filter(cases.demographic.race=='white') count(q_white_only) manifest(q_white_only) ## ----------------------------------------------------------------------------- library(tibble) library(dplyr) library(GenomicDataCommons) cases() %>% GenomicDataCommons::filter(~ project.program.name=='TCGA' & files.experimental_strategy=='RNA-Seq') %>% facet(c("files.created_datetime")) %>% aggregations() %>% .[[1]] %>% as_tibble() %>% dplyr::arrange(dplyr::desc(key))