Question: How to find patient sample.type in TCGA-PRAD ?
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gravatar for Björn
2.7 years ago by
Björn50
Björn50 wrote:

Hi, I downloaded clinical- patient data for TCGA-PRAD. Following are the colnames

     colnames(cli_patient)

 [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"

PROBLEM The bcr_patient_barcode contains sample identifier as "TCGA-HC-A6AP-01A" except for last 3 digits. The last 3 digits indicates sample.type which is missing. How to know the sample type in "cli_patient" file as in hereTCGA_sampletypes

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Björn50

You can make a table that translates the numeric code to the sample types listed here.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by Noushin N590

The clinical- patient data, the bcr_patient_barcode contains only "TCGA-HC-A6AP" (without 01A) unlike in transcriptome data. So, from the list of clinical data, how to know sample.type. This was my question.

ADD REPLYlink written 2.7 years ago by Björn50
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