Question: TCGA patient variable data dictionary
0
gravatar for Björn
12 months ago by
Björn40
Björn40 wrote:

Hi, I downloaded miRNA seq and patient data from TCGA-PRAD. Is there a way to find out the explanation /dictionary on patient/clinical variable

colnames(tcga-prad)

 [1] "bcr_patient_barcode"                              "additional_studies"                              
 [3] "tumor_tissue_site"                                "other_dx"                                        
 [5] "gender"                                           "vital_status"                                    
 [7] "days_to_birth"                                    "days_to_death"                                   
 [9] "days_to_last_followup"                            "race_list"                                       
[11] "tissue_source_site"                               "patient_id"                                      
[13] "bcr_patient_uuid"                                 "history_of_neoadjuvant_treatment"                
[15] "informed_consent_verified"                        "icd_o_3_site"                                    
[17] "icd_o_3_histology"                                "icd_10"                                          
[19] "tissue_prospective_collection_indicator"          "tissue_retrospective_collection_indicator"       
[21] "days_to_initial_pathologic_diagnosis"             "age_at_initial_pathologic_diagnosis"             
[23] "year_of_initial_pathologic_diagnosis"             "person_neoplasm_cancer_status"                   
[25] "ethnicity"                                        "day_of_form_completion"                          
[27] "month_of_form_completion"                         "year_of_form_completion"                         
[29] "histological_type"                                "histological_type_other"                         
[31] "zone_of_origin"                                   "laterality"                                      
[33] "tumor_levels"                                     "initial_pathologic_diagnosis_method"             
[35] "days_to_bone_scan_performed"                      "bone_scan_results"                               
[37] "diagnostic_ct_abd_pelvis_performed"               "days_to_diagnostic_computed_tomography_performed"
[39] "diagnostic_ct_abd_pelvis_results"                 "diagnostic_mri_performed"                        
[41] "days_to_diagnostic_mri_performed"                 "diagnostic_mri_results"                          
[43] "lymphnodes_examined"                              "number_of_lymphnodes_examined"                   
[45] "number_of_lymphnodes_positive_by_he"              "residual_tumor"                                  
[47] "patient_death_reason"                             "source_of_patient_death_reason"                  
[49] "postoperative_rx_tx"                              "radiation_therapy"                               
[51] "primary_therapy_outcome_success"                  "biochemical_recurrence"                          
[53] "days_to_first_biochemical_recurrence"             "has_new_tumor_events_information"                
[55] "has_drugs_information"                            "has_radiations_information"                      
[57] "has_follow_ups_information"                       "stage_event_system_version"                      
[59] "stage_event_clinical_stage"                       "stage_event_pathologic_stage"                    
[61] "stage_event_tnm_categories"                       "stage_event_psa"                                 
[63] "stage_event_gleason_grading"                      "stage_event_ann_arbor"                           
[65] "stage_event_serum_markers"                        "stage_event_igcccg_stage"                        
[67] "stage_event_masaoka_stage"
mirna tcga • 847 views
ADD COMMENTlink modified 12 months ago by Kevin Blighe49k • written 12 months ago by Björn40

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

ADD REPLYlink written 12 months ago by RamRS24k
0
gravatar for Kevin Blighe
12 months ago by
Kevin Blighe49k
Kevin Blighe49k wrote:

There are different ways to do this.

first way

First, see my previous answers, here:

In a nutshell, if you want more comprehensive information on these terms, you should go by the Common Data Elements (CDE) ID of each. You should have the CDE ID, which likely appears in the third row of the data that you downloaded.

With the CDE ID, do the following:

  1. Go to CDE Browser
  2. Go to Public ID Search tab
  3. Put the numerical CDE ID into the Public ID search box
  4. Click on Search

second way

Just go to the GDC Data Dictionary (in particular, the Viewer), and you can find descriptions there, too).

Kevin

ADD COMMENTlink written 12 months ago by Kevin Blighe49k
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