[1] "R version 2.15.3 (2013-03-01)"
[1] "dx" ""  
[1] "dx" " " 
[1] "dx" " " 
[1] "opt:  RPPA_EXPR"
[1] "vtyp==survival in table1 generation"
[1] "vtyp==continuous in table1 table 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==continuous in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==multiclass in table1 generation"
[1] "vtyp==binary in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==binary in table1 table generation"
[1] "vtyp==multiclass in table1 generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==binary in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==multiclass in table1 generation"
[1] "vtyp==multiclass in table1 generation"
[1] "vtyp==binary in table1 table generation"
[1] "vtyp==continuous in table1 table 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==continuous in table1 table generation"
[1] "vtyp==binary in table1 table generation"
[1] "vtyp==multiclass in table1 generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==multiclass in table1 generation"
                                     Clinical feature                      
DAYS_TO_DEATH_OR_LAST_FUP            "DAYS_TO_DEATH_OR_LAST_FUP"           
YEARS_TO_BIRTH                       "YEARS_TO_BIRTH"                      
PATHOLOGY_T_STAGE                    "PATHOLOGY_T_STAGE"                   
PATHOLOGY_N_STAGE                    "PATHOLOGY_N_STAGE"                   
PATHOLOGY_M_STAGE                    "PATHOLOGY_M_STAGE"                   
RADIATION_THERAPY                    "RADIATION_THERAPY"                   
HISTOLOGICAL_TYPE                    "HISTOLOGICAL_TYPE"                   
NUMBER_PACK_YEARS_SMOKED             "NUMBER_PACK_YEARS_SMOKED"            
NUMBER_OF_LYMPH_NODES                "NUMBER_OF_LYMPH_NODES"               
RACE                                 "RACE"                                
ETHNICITY                            "ETHNICITY"                           
WEIGHT_KG_AT_DIAGNOSIS               "WEIGHT_KG_AT_DIAGNOSIS"              
TUMOR_STATUS                         "TUMOR_STATUS"                        
NEOPLASM_HISTOLOGIC_GRADE            "NEOPLASM_HISTOLOGIC_GRADE"           
TOBACCO_SMOKING_YEAR_STOPPED         "TOBACCO_SMOKING_YEAR_STOPPED"        
TOBACCO_SMOKING_PACK_YEARS_SMOKED    "TOBACCO_SMOKING_PACK_YEARS_SMOKED"   
TOBACCO_SMOKING_HISTORY              "TOBACCO_SMOKING_HISTORY"             
AGEBEGANSMOKINGINYEARS               "AGEBEGANSMOKINGINYEARS"              
PREGNANCIES_COUNT_TOTAL              "PREGNANCIES_COUNT_TOTAL"             
PREGNANCIES_COUNT_STILLBIRTH         "PREGNANCIES_COUNT_STILLBIRTH"        
PREGNANCY_SPONTANEOUS_ABORTION_COUNT "PREGNANCY_SPONTANEOUS_ABORTION_COUNT"
PREGNANCIES_COUNT_LIVE_BIRTH         "PREGNANCIES_COUNT_LIVE_BIRTH"        
PREGNANCY_THERAPEUTIC_ABORTION_COUNT "PREGNANCY_THERAPEUTIC_ABORTION_COUNT"
PREGNANCIES_COUNT_ECTOPIC            "PREGNANCIES_COUNT_ECTOPIC"           
POS_LYMPH_NODE_LOCATION              "POS_LYMPH_NODE_LOCATION"             
MENOPAUSE_STATUS                     "MENOPAUSE_STATUS"                    
LYMPHOVASCULAR_INVOLVEMENT           "LYMPHOVASCULAR_INVOLVEMENT"          
LYMPH_NODES_EXAMINED_HE_COUNT        "LYMPH_NODES_EXAMINED_HE_COUNT"       
LYMPH_NODES_EXAMINED                 "LYMPH_NODES_EXAMINED"                
KERATINIZATION_SQUAMOUS_CELL         "KERATINIZATION_SQUAMOUS_CELL"        
INITIAL_PATHOLOGIC_DX_YEAR           "INITIAL_PATHOLOGIC_DX_YEAR"          
HISTORY_HORMONAL_CONTRACEPTIVES_USE  "HISTORY_HORMONAL_CONTRACEPTIVES_USE" 
HEIGHT_CM_AT_DIAGNOSIS               "HEIGHT_CM_AT_DIAGNOSIS"              
CORPUS_INVOLVEMENT                   "CORPUS_INVOLVEMENT"                  
CHEMO_CONCURRENT_TYPE                "CHEMO_CONCURRENT_TYPE"               
CERVIX_SUV_RESULTS                   "CERVIX_SUV_RESULTS"                  
AGE_AT_DIAGNOSIS                     "AGE_AT_DIAGNOSIS"                    
CLINICAL_STAGE                       "CLINICAL_STAGE"                      
                                     Statistical test           
DAYS_TO_DEATH_OR_LAST_FUP            "Cox regression test"      
YEARS_TO_BIRTH                       "Spearman correlation test"
PATHOLOGY_T_STAGE                    "Spearman correlation test"
PATHOLOGY_N_STAGE                    "Wilcoxon test"            
PATHOLOGY_M_STAGE                    "Wilcoxon test"            
RADIATION_THERAPY                    "Wilcoxon test"            
HISTOLOGICAL_TYPE                    "Kruskal-Wallis test"      
NUMBER_PACK_YEARS_SMOKED             "Spearman correlation test"
NUMBER_OF_LYMPH_NODES                "Spearman correlation test"
RACE                                 "Kruskal-Wallis test"      
ETHNICITY                            "Wilcoxon test"            
WEIGHT_KG_AT_DIAGNOSIS               "Spearman correlation test"
TUMOR_STATUS                         "Wilcoxon test"            
NEOPLASM_HISTOLOGIC_GRADE            "Kruskal-Wallis test"      
TOBACCO_SMOKING_YEAR_STOPPED         "Spearman correlation test"
TOBACCO_SMOKING_PACK_YEARS_SMOKED    "Spearman correlation test"
TOBACCO_SMOKING_HISTORY              "Spearman correlation test"
AGEBEGANSMOKINGINYEARS               "Spearman correlation test"
PREGNANCIES_COUNT_TOTAL              "Spearman correlation test"
PREGNANCIES_COUNT_STILLBIRTH         "Wilcoxon test"            
PREGNANCY_SPONTANEOUS_ABORTION_COUNT "Spearman correlation test"
PREGNANCIES_COUNT_LIVE_BIRTH         "Spearman correlation test"
PREGNANCY_THERAPEUTIC_ABORTION_COUNT "Spearman correlation test"
PREGNANCIES_COUNT_ECTOPIC            "Spearman correlation test"
POS_LYMPH_NODE_LOCATION              "Kruskal-Wallis test"      
MENOPAUSE_STATUS                     "Kruskal-Wallis test"      
LYMPHOVASCULAR_INVOLVEMENT           "Wilcoxon test"            
LYMPH_NODES_EXAMINED_HE_COUNT        "Spearman correlation test"
LYMPH_NODES_EXAMINED                 "Spearman correlation test"
KERATINIZATION_SQUAMOUS_CELL         "Wilcoxon test"            
INITIAL_PATHOLOGIC_DX_YEAR           "Spearman correlation test"
HISTORY_HORMONAL_CONTRACEPTIVES_USE  "Kruskal-Wallis test"      
HEIGHT_CM_AT_DIAGNOSIS               "Spearman correlation test"
CORPUS_INVOLVEMENT                   "Wilcoxon test"            
CHEMO_CONCURRENT_TYPE                "Kruskal-Wallis test"      
CERVIX_SUV_RESULTS                   "Spearman correlation test"
AGE_AT_DIAGNOSIS                     "Spearman correlation test"
CLINICAL_STAGE                       "Kruskal-Wallis test"      
                                     Significant genes
DAYS_TO_DEATH_OR_LAST_FUP            "N=2"            
YEARS_TO_BIRTH                       "N=30"           
PATHOLOGY_T_STAGE                    "N=0"            
PATHOLOGY_N_STAGE                    "N=0"            
PATHOLOGY_M_STAGE                    "N=0"            
RADIATION_THERAPY                    "N=0"            
HISTOLOGICAL_TYPE                    "N=30"           
NUMBER_PACK_YEARS_SMOKED             "N=30"           
NUMBER_OF_LYMPH_NODES                "N=0"            
RACE                                 "N=0"            
ETHNICITY                            "N=0"            
WEIGHT_KG_AT_DIAGNOSIS               "N=0"            
TUMOR_STATUS                         "N=1"            
NEOPLASM_HISTOLOGIC_GRADE            "N=0"            
TOBACCO_SMOKING_YEAR_STOPPED         "N=0"            
TOBACCO_SMOKING_PACK_YEARS_SMOKED    "N=30"           
TOBACCO_SMOKING_HISTORY              "N=0"            
AGEBEGANSMOKINGINYEARS               "N=0"            
PREGNANCIES_COUNT_TOTAL              "N=0"            
PREGNANCIES_COUNT_STILLBIRTH         "N=0"            
PREGNANCY_SPONTANEOUS_ABORTION_COUNT "N=0"            
PREGNANCIES_COUNT_LIVE_BIRTH         "N=14"           
PREGNANCY_THERAPEUTIC_ABORTION_COUNT "N=7"            
PREGNANCIES_COUNT_ECTOPIC            "N=0"            
POS_LYMPH_NODE_LOCATION              "N=0"            
MENOPAUSE_STATUS                     "N=12"           
LYMPHOVASCULAR_INVOLVEMENT           "N=0"            
LYMPH_NODES_EXAMINED_HE_COUNT        "N=0"            
LYMPH_NODES_EXAMINED                 "N=17"           
KERATINIZATION_SQUAMOUS_CELL         "N=0"            
INITIAL_PATHOLOGIC_DX_YEAR           "N=5"            
HISTORY_HORMONAL_CONTRACEPTIVES_USE  "N=0"            
HEIGHT_CM_AT_DIAGNOSIS               "N=0"            
CORPUS_INVOLVEMENT                   "N=0"            
CHEMO_CONCURRENT_TYPE                "N=0"            
CERVIX_SUV_RESULTS                   "N=27"           
AGE_AT_DIAGNOSIS                     "N=30"           
CLINICAL_STAGE                       "N=0"            
                                     Associated with                              
DAYS_TO_DEATH_OR_LAST_FUP            " "                                          
YEARS_TO_BIRTH                       "older"                                      
PATHOLOGY_T_STAGE                    " "                                          
PATHOLOGY_N_STAGE                    " "                                          
PATHOLOGY_M_STAGE                    " "                                          
RADIATION_THERAPY                    " "                                          
HISTOLOGICAL_TYPE                    " "                                          
NUMBER_PACK_YEARS_SMOKED             "higher number_pack_years_smoked"            
NUMBER_OF_LYMPH_NODES                " "                                          
RACE                                 " "                                          
ETHNICITY                            " "                                          
WEIGHT_KG_AT_DIAGNOSIS               " "                                          
TUMOR_STATUS                         "with tumor"                                 
NEOPLASM_HISTOLOGIC_GRADE            " "                                          
TOBACCO_SMOKING_YEAR_STOPPED         " "                                          
TOBACCO_SMOKING_PACK_YEARS_SMOKED    "higher tobacco_smoking_pack_years_smoked"   
TOBACCO_SMOKING_HISTORY              " "                                          
AGEBEGANSMOKINGINYEARS               " "                                          
PREGNANCIES_COUNT_TOTAL              " "                                          
PREGNANCIES_COUNT_STILLBIRTH         " "                                          
PREGNANCY_SPONTANEOUS_ABORTION_COUNT " "                                          
PREGNANCIES_COUNT_LIVE_BIRTH         "higher pregnancies_count_live_birth"        
PREGNANCY_THERAPEUTIC_ABORTION_COUNT "higher pregnancy_therapeutic_abortion_count"
PREGNANCIES_COUNT_ECTOPIC            " "                                          
POS_LYMPH_NODE_LOCATION              " "                                          
MENOPAUSE_STATUS                     " "                                          
LYMPHOVASCULAR_INVOLVEMENT           " "                                          
LYMPH_NODES_EXAMINED_HE_COUNT        " "                                          
LYMPH_NODES_EXAMINED                 "higher lymph_nodes_examined"                
KERATINIZATION_SQUAMOUS_CELL         " "                                          
INITIAL_PATHOLOGIC_DX_YEAR           "higher initial_pathologic_dx_year"          
HISTORY_HORMONAL_CONTRACEPTIVES_USE  " "                                          
HEIGHT_CM_AT_DIAGNOSIS               " "                                          
CORPUS_INVOLVEMENT                   " "                                          
CHEMO_CONCURRENT_TYPE                " "                                          
CERVIX_SUV_RESULTS                   "higher cervix_suv_results"                  
AGE_AT_DIAGNOSIS                     "higher age_at_diagnosis"                    
CLINICAL_STAGE                       " "                                          
                                     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
DAYS_TO_DEATH_OR_LAST_FUP            "N=NA"                                                                                    
YEARS_TO_BIRTH                       "N=14"                                                                                    
PATHOLOGY_T_STAGE                    " "                                                                                       
PATHOLOGY_N_STAGE                    " "                                                                                       
PATHOLOGY_M_STAGE                    " "                                                                                       
RADIATION_THERAPY                    " "                                                                                       
HISTOLOGICAL_TYPE                    " "                                                                                       
NUMBER_PACK_YEARS_SMOKED             "N=12"                                                                                    
NUMBER_OF_LYMPH_NODES                " "                                                                                       
RACE                                 " "                                                                                       
ETHNICITY                            " "                                                                                       
WEIGHT_KG_AT_DIAGNOSIS               " "                                                                                       
TUMOR_STATUS                         "N=1"                                                                                     
NEOPLASM_HISTOLOGIC_GRADE            " "                                                                                       
TOBACCO_SMOKING_YEAR_STOPPED         " "                                                                                       
TOBACCO_SMOKING_PACK_YEARS_SMOKED    "N=12"                                                                                    
TOBACCO_SMOKING_HISTORY              " "                                                                                       
AGEBEGANSMOKINGINYEARS               " "                                                                                       
PREGNANCIES_COUNT_TOTAL              " "                                                                                       
PREGNANCIES_COUNT_STILLBIRTH         " "                                                                                       
PREGNANCY_SPONTANEOUS_ABORTION_COUNT " "                                                                                       
PREGNANCIES_COUNT_LIVE_BIRTH         "N=5"                                                                                     
PREGNANCY_THERAPEUTIC_ABORTION_COUNT "N=5"                                                                                     
PREGNANCIES_COUNT_ECTOPIC            " "                                                                                       
POS_LYMPH_NODE_LOCATION              " "                                                                                       
MENOPAUSE_STATUS                     " "                                                                                       
LYMPHOVASCULAR_INVOLVEMENT           " "                                                                                       
LYMPH_NODES_EXAMINED_HE_COUNT        " "                                                                                       
LYMPH_NODES_EXAMINED                 "N=11"                                                                                    
KERATINIZATION_SQUAMOUS_CELL         " "                                                                                       
INITIAL_PATHOLOGIC_DX_YEAR           "N=4"                                                                                     
HISTORY_HORMONAL_CONTRACEPTIVES_USE  " "                                                                                       
HEIGHT_CM_AT_DIAGNOSIS               " "                                                                                       
CORPUS_INVOLVEMENT                   " "                                                                                       
CHEMO_CONCURRENT_TYPE                " "                                                                                       
CERVIX_SUV_RESULTS                   "N=18"                                                                                    
AGE_AT_DIAGNOSIS                     "N=13"                                                                                    
CLINICAL_STAGE                       " "                                                                                       
                                     Associated with                             
DAYS_TO_DEATH_OR_LAST_FUP            " "                                         
YEARS_TO_BIRTH                       "younger"                                   
PATHOLOGY_T_STAGE                    " "                                         
PATHOLOGY_N_STAGE                    " "                                         
PATHOLOGY_M_STAGE                    " "                                         
RADIATION_THERAPY                    " "                                         
HISTOLOGICAL_TYPE                    " "                                         
NUMBER_PACK_YEARS_SMOKED             "lower number_pack_years_smoked"            
NUMBER_OF_LYMPH_NODES                " "                                         
RACE                                 " "                                         
ETHNICITY                            " "                                         
WEIGHT_KG_AT_DIAGNOSIS               " "                                         
TUMOR_STATUS                         "tumor free"                                
NEOPLASM_HISTOLOGIC_GRADE            " "                                         
TOBACCO_SMOKING_YEAR_STOPPED         " "                                         
TOBACCO_SMOKING_PACK_YEARS_SMOKED    "lower tobacco_smoking_pack_years_smoked"   
TOBACCO_SMOKING_HISTORY              " "                                         
AGEBEGANSMOKINGINYEARS               " "                                         
PREGNANCIES_COUNT_TOTAL              " "                                         
PREGNANCIES_COUNT_STILLBIRTH         " "                                         
PREGNANCY_SPONTANEOUS_ABORTION_COUNT " "                                         
PREGNANCIES_COUNT_LIVE_BIRTH         "lower pregnancies_count_live_birth"        
PREGNANCY_THERAPEUTIC_ABORTION_COUNT "lower pregnancy_therapeutic_abortion_count"
PREGNANCIES_COUNT_ECTOPIC            " "                                         
POS_LYMPH_NODE_LOCATION              " "                                         
MENOPAUSE_STATUS                     " "                                         
LYMPHOVASCULAR_INVOLVEMENT           " "                                         
LYMPH_NODES_EXAMINED_HE_COUNT        " "                                         
LYMPH_NODES_EXAMINED                 "lower lymph_nodes_examined"                
KERATINIZATION_SQUAMOUS_CELL         " "                                         
INITIAL_PATHOLOGIC_DX_YEAR           "lower initial_pathologic_dx_year"          
HISTORY_HORMONAL_CONTRACEPTIVES_USE  " "                                         
HEIGHT_CM_AT_DIAGNOSIS               " "                                         
CORPUS_INVOLVEMENT                   " "                                         
CHEMO_CONCURRENT_TYPE                " "                                         
CERVIX_SUV_RESULTS                   "lower cervix_suv_results"                  
AGE_AT_DIAGNOSIS                     "lower age_at_diagnosis"                    
CLINICAL_STAGE                       " "                                         
                                           
DAYS_TO_DEATH_OR_LAST_FUP            "N=NA"
YEARS_TO_BIRTH                       "N=16"
PATHOLOGY_T_STAGE                    " "   
PATHOLOGY_N_STAGE                    " "   
PATHOLOGY_M_STAGE                    " "   
RADIATION_THERAPY                    " "   
HISTOLOGICAL_TYPE                    " "   
NUMBER_PACK_YEARS_SMOKED             "N=18"
NUMBER_OF_LYMPH_NODES                " "   
RACE                                 " "   
ETHNICITY                            " "   
WEIGHT_KG_AT_DIAGNOSIS               " "   
TUMOR_STATUS                         "N=0" 
NEOPLASM_HISTOLOGIC_GRADE            " "   
TOBACCO_SMOKING_YEAR_STOPPED         " "   
TOBACCO_SMOKING_PACK_YEARS_SMOKED    "N=18"
TOBACCO_SMOKING_HISTORY              " "   
AGEBEGANSMOKINGINYEARS               " "   
PREGNANCIES_COUNT_TOTAL              " "   
PREGNANCIES_COUNT_STILLBIRTH         " "   
PREGNANCY_SPONTANEOUS_ABORTION_COUNT " "   
PREGNANCIES_COUNT_LIVE_BIRTH         "N=9" 
PREGNANCY_THERAPEUTIC_ABORTION_COUNT "N=2" 
PREGNANCIES_COUNT_ECTOPIC            " "   
POS_LYMPH_NODE_LOCATION              " "   
MENOPAUSE_STATUS                     " "   
LYMPHOVASCULAR_INVOLVEMENT           " "   
LYMPH_NODES_EXAMINED_HE_COUNT        " "   
LYMPH_NODES_EXAMINED                 "N=6" 
KERATINIZATION_SQUAMOUS_CELL         " "   
INITIAL_PATHOLOGIC_DX_YEAR           "N=1" 
HISTORY_HORMONAL_CONTRACEPTIVES_USE  " "   
HEIGHT_CM_AT_DIAGNOSIS               " "   
CORPUS_INVOLVEMENT                   " "   
CHEMO_CONCURRENT_TYPE                " "   
CERVIX_SUV_RESULTS                   "N=9" 
AGE_AT_DIAGNOSIS                     "N=17"
CLINICAL_STAGE                       " "   
[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==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==continuous 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"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==binary in basici table generation"
[1] "vtyp==multiclass in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==continuous 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==continuous in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==multiclass in basici table generation"
[1] "vtyp==multiclass in basici table generation"
[1] "vtyp==binary in basici table generation"
[1] "vtyp==continuous 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==continuous in basici table generation"
[1] "vtyp==binary in basici table generation"
[1] "vtyp==multiclass in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==multiclass in basici table generation"
