Question: How to find patient sample.type in TCGA-PRAD ?
0
gravatar for Björn
13 months ago by
Björn40
Björn40 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 12 months ago • written 13 months ago by Björn40

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

ADD REPLYlink modified 13 months ago • written 13 months ago by Noushin N550

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 12 months ago by Björn40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 534 users visited in the last hour