[1] "R version 2.15.3 (2013-03-01)"
[1] "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "dx" ""  
[1] "dx" " " 
[1] "dx" " " 
[1] "opt:  MUTATION_RATE"
[1] "vtyp==survival in table1 generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==multiclass in table1 generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==binary in table1 table generation"
[1] "vtyp==binary in table1 table generation"
[1] "vtyp==binary in table1 table generation"
[1] "vtyp==multiclass in table1 generation"
[1] "vtyp==binary in table1 table generation"
[1] "vtyp==binary in table1 table generation"
[1] "vtyp==multiclass in table1 generation"
[1] "vtyp==multiclass in table1 generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==binary in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==multiclass in table1 generation"
[1] "vtyp==binary in table1 table generation"
                                       Clinical feature                        
DAYS_TO_DEATH_OR_LAST_FUP              "DAYS_TO_DEATH_OR_LAST_FUP"             
AGE                                    "AGE"                                   
AGE_mutation.rate                      "AGE_mutation rate"                     
NEOPLASM_DISEASESTAGE                  "NEOPLASM_DISEASESTAGE"                 
PATHOLOGY_T_STAGE                      "PATHOLOGY_T_STAGE"                     
PATHOLOGY_N_STAGE                      "PATHOLOGY_N_STAGE"                     
PATHOLOGY_M_STAGE                      "PATHOLOGY_M_STAGE"                     
GENDER                                 "GENDER"                                
HISTOLOGICAL_TYPE                      "HISTOLOGICAL_TYPE"                     
RADIATIONS_RADIATION_REGIMENINDICATION "RADIATIONS_RADIATION_REGIMENINDICATION"
RADIATION_EXPOSURE                     "RADIATION_EXPOSURE"                    
EXTRATHYROIDAL_EXTENSION               "EXTRATHYROIDAL_EXTENSION"              
COMPLETENESS_OF_RESECTION              "COMPLETENESS_OF_RESECTION"             
NUMBER_OF_LYMPH_NODES                  "NUMBER_OF_LYMPH_NODES"                 
MULTIFOCALITY                          "MULTIFOCALITY"                         
TUMOR_SIZE                             "TUMOR_SIZE"                            
RACE                                   "RACE"                                  
ETHNICITY                              "ETHNICITY"                             
                                       Statistical test            
DAYS_TO_DEATH_OR_LAST_FUP              "Cox regression test"       
AGE                                    "Spearman correlation test" 
AGE_mutation.rate                      "Linear Regression Analysis"
NEOPLASM_DISEASESTAGE                  "Kruskal-Wallis test"       
PATHOLOGY_T_STAGE                      "Spearman correlation test" 
PATHOLOGY_N_STAGE                      "Wilcoxon test"             
PATHOLOGY_M_STAGE                      "Wilcoxon test"             
GENDER                                 "Wilcoxon test"             
HISTOLOGICAL_TYPE                      "Kruskal-Wallis test"       
RADIATIONS_RADIATION_REGIMENINDICATION "Wilcoxon test"             
RADIATION_EXPOSURE                     "Wilcoxon test"             
EXTRATHYROIDAL_EXTENSION               "Kruskal-Wallis test"       
COMPLETENESS_OF_RESECTION              "Kruskal-Wallis test"       
NUMBER_OF_LYMPH_NODES                  "Spearman correlation test" 
MULTIFOCALITY                          "Wilcoxon test"             
TUMOR_SIZE                             "Spearman correlation test" 
RACE                                   "Kruskal-Wallis test"       
ETHNICITY                              "Wilcoxon test"             
                                       Significant variables
DAYS_TO_DEATH_OR_LAST_FUP              "N=2"                
AGE                                    "N=2"                
AGE_mutation.rate                      "N=2"                
NEOPLASM_DISEASESTAGE                  "N=2"                
PATHOLOGY_T_STAGE                      "N=2"                
PATHOLOGY_N_STAGE                      "N=0"                
PATHOLOGY_M_STAGE                      "N=0"                
GENDER                                 "N=0"                
HISTOLOGICAL_TYPE                      "N=1"                
RADIATIONS_RADIATION_REGIMENINDICATION "N=0"                
RADIATION_EXPOSURE                     "N=0"                
EXTRATHYROIDAL_EXTENSION               "N=2"                
COMPLETENESS_OF_RESECTION              "N=2"                
NUMBER_OF_LYMPH_NODES                  "N=0"                
MULTIFOCALITY                          "N=0"                
TUMOR_SIZE                             "N=1"                
RACE                                   "N=0"                
ETHNICITY                              "N=0"                
                                       Associated with    
DAYS_TO_DEATH_OR_LAST_FUP              "shorter survival" 
AGE                                    "older"            
AGE_mutation.rate                      " "                
NEOPLASM_DISEASESTAGE                  " "                
PATHOLOGY_T_STAGE                      "higher stage"     
PATHOLOGY_N_STAGE                      " "                
PATHOLOGY_M_STAGE                      " "                
GENDER                                 " "                
HISTOLOGICAL_TYPE                      " "                
RADIATIONS_RADIATION_REGIMENINDICATION " "                
RADIATION_EXPOSURE                     " "                
EXTRATHYROIDAL_EXTENSION               " "                
COMPLETENESS_OF_RESECTION              " "                
NUMBER_OF_LYMPH_NODES                  " "                
MULTIFOCALITY                          " "                
TUMOR_SIZE                             "higher tumor_size"
RACE                                   " "                
ETHNICITY                              " "                
                                       &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
DAYS_TO_DEATH_OR_LAST_FUP              "N=2"                                                                                     
AGE                                    "N=2"                                                                                     
AGE_mutation.rate                      " "                                                                                       
NEOPLASM_DISEASESTAGE                  " "                                                                                       
PATHOLOGY_T_STAGE                      "N=2"                                                                                     
PATHOLOGY_N_STAGE                      " "                                                                                       
PATHOLOGY_M_STAGE                      " "                                                                                       
GENDER                                 " "                                                                                       
HISTOLOGICAL_TYPE                      " "                                                                                       
RADIATIONS_RADIATION_REGIMENINDICATION " "                                                                                       
RADIATION_EXPOSURE                     " "                                                                                       
EXTRATHYROIDAL_EXTENSION               " "                                                                                       
COMPLETENESS_OF_RESECTION              " "                                                                                       
NUMBER_OF_LYMPH_NODES                  " "                                                                                       
MULTIFOCALITY                          " "                                                                                       
TUMOR_SIZE                             "N=1"                                                                                     
RACE                                   " "                                                                                       
ETHNICITY                              " "                                                                                       
                                       Associated with         
DAYS_TO_DEATH_OR_LAST_FUP              "longer survival"  "N=0"
AGE                                    "younger"          "N=0"
AGE_mutation.rate                      " "                " "  
NEOPLASM_DISEASESTAGE                  " "                " "  
PATHOLOGY_T_STAGE                      "lower stage"      "N=0"
PATHOLOGY_N_STAGE                      " "                " "  
PATHOLOGY_M_STAGE                      " "                " "  
GENDER                                 " "                " "  
HISTOLOGICAL_TYPE                      " "                " "  
RADIATIONS_RADIATION_REGIMENINDICATION " "                " "  
RADIATION_EXPOSURE                     " "                " "  
EXTRATHYROIDAL_EXTENSION               " "                " "  
COMPLETENESS_OF_RESECTION              " "                " "  
NUMBER_OF_LYMPH_NODES                  " "                " "  
MULTIFOCALITY                          " "                " "  
TUMOR_SIZE                             "lower tumor_size" "N=0"
RACE                                   " "                " "  
ETHNICITY                              " "                " "  
[1] "vtyp==survival in basici table generation"
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==multiclass in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==binary in basici table generation"
[1] "vtyp==binary in basici table generation"
[1] "vtyp==binary in basici table generation"
[1] "vtyp==multiclass in basici table generation"
[1] "vtyp==binary in basici table generation"
[1] "vtyp==binary in basici table generation"
[1] "vtyp==multiclass in basici table generation"
[1] "vtyp==multiclass in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==binary in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==multiclass in basici table generation"
[1] "vtyp==binary in basici table generation"
