Samples.Clinical_FH: Retrieve CDEs normalized by Firehose and selected for...

Description Usage Arguments

View source: R/Samples.Clinical_FH.R

Description

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>.

Usage

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

Arguments

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.


mariodeng/FirebrowseR documentation built on May 21, 2017, 6:48 p.m.