Samples.Clinical_FH: Retrieve CDEs normalized by Firehose and selected for...
In mariodeng/FirebrowseR: An 'API' Client for Broads 'Firehose' Pipeline

This service returns patient-level clinical data elements (CDEs) that have been normalized by Firehose for use in analyses. Results may be selected by disease cohort, patient barcode or CDE name, but at least one cohort, barcode or CDE must be provided. When filtering by CDE note that only when a patient record contains one or more of the selected CDEs will it be returned. Visit <a href="http://gdac.broadinstitute.org/runs/info/clinical">this table of CDEs</a> to see what's available for every disase cohort; for more information on how these CDEs are processed see our <a href="https://confluence.broadinstitute.org/display/GDAC/Documentation#Documentation-ClinicalPipeline">pipeline documentation</a>.

1
2
3

Samples.Clinical_FH(format = "json", cohort = "",
  tcga_participant_barcode = "", fh_cde_name = "", page = "1",
  page_size = "250", sort_by = "cohort")

`format`	Format of result. Default value is json. While json,tsv,csv are available.
`cohort`	Narrow search to one or more TCGA disease cohorts from the scrollable list. Multiple values are allowed ACC,BLCA,BRCA,CESC,CHOL,COAD,COADREAD,DLBC,ESCA,FPPP,GBM,GBMLGG,HNSC,KICH,KIPAN,KIRC,KIRP,LAML,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,STES,TGCT,THCA,THYM,UCEC,UCS,UVM.
`tcga_participant_barcode`	Comma separated list of TCGA participant barcodes (e.g. TCGA-GF-A4EO). Multiple values are allowed .
`fh_cde_name`	Retrieve results only for the CDEs specified from the scrollable list. Multiple values are allowed age_at_diagnosis,age_began_smoking_in_years,Breslow_thickness,cause_of_death,cervical_carcinoma_pelvic_extension_text,cervix_suv_results,chemo_concurrent_type,clinical_stage,corpus_involvement,date_of_initial_pathologic_diagnosis,days_to_death,days_to_last_followup,days_to_last_known_alive,days_to_psa,days_to_submitted_specimen_dx,ethnicity,extrathyroidal_extension,gender,gleason_score,height_cm_at_diagnosis,histological_type,history_hormonal_contraceptives_use,hysterectomy_type,initial_pathologic_dx_year,karnofsky_performance_score,keratinization_squamous_cell,lymph_node_location,lymph_nodes_examined,lymph_nodes_examined_he_count,lymphovascular_involvement,melanoma_primary_known,melanoma_ulceration,menopause_status,multifocality,neoplasm_histologic_grade,number_of_lymph_nodes,number_pack_years_smoked,pathologic_stage,pathology_M_stage,pathology_N_stage,pathology_T_stage,pos_lymph_node_location,pregnancies_count_ectopic,pregnancies_count_live_birth,pregnancies_count_stillbirth,pregnancies_count_total,pregnancy_spontaneous_abortion_count,pregnancy_therapeutic_abortion_count,psa_value,race,radiation_exposure,radiation_therapy,radiation_therapy_status,residual_tumor,tobacco_smoking_history,tobacco_smoking_pack_years_smoked,tobacco_smoking_year_stopped,tumor_size,tumor_stage,tumor_status,tumor_tissue_site,vital_status,weight_kg_at_diagnosis,year_of_tobacco_smoking_onset,years_to_birth.
`page`	Which page (slice) of entire results set should be returned. Multiple values are allowed . Default value is 1.
`page_size`	Number of records per page of results. Max is 2000. Multiple values are allowed . Default value is 250.
`sort_by`	Which column in the results should be used for sorting paginated results? Default value is cohort. While tcga_participant_barcode,cohort,fh_cde_name are available.