[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/69/"
[1] "op: MUTATION_RATE"
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/CESC-TP/13351545/iteration1/CESC-TP.patients.counts_and_rates.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CESC-TP/15076797/CESC-TP.merged_data.txt"
[1] "gv: ALL"
[1] "gfn: "
[1] "sfn: "
[1] "fv: ALL"
[1] "ofn: "
[1] "dx: "
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CESC-TP/15076797/CESC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=304, in expression file=194, common to both=194
Number of genes in original expression dataset=2
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                                  
 [2] "VITAL_STATUS"                                    
 [3] "DAYS_TO_DEATH"                                   
 [4] "DAYS_TO_LAST_FOLLOWUP"                           
 [5] "PRIMARY_SITE_OF_DISEASE"                         
 [6] "NEOPLASM_DISEASESTAGE"                           
 [7] "PATHOLOGY_T_STAGE"                               
 [8] "PATHOLOGY_N_STAGE"                               
 [9] "PATHOLOGY_M_STAGE"                               
[10] "DCC_UPLOAD_DATE"                                 
[11] "GENDER"                                          
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"            
[13] "HISTOLOGICAL_TYPE"                               
[14] "RADIATIONS_RADIATION_REGIMENINDICATION"          
[15] "NUMBER_PACK_YEARS_SMOKED"                        
[16] "NUMBER_OF_LYMPH_NODES"                           
[17] "RACE"                                            
[18] "ETHNICITY"                                       
[19] "BATCH_NUMBER"                                    
[20] "WEIGHT_KG_AT_DIAGNOSIS"                          
[21] "TUMOR_STATUS"                                    
[22] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[23] "NEOPLASM_HISTOLOGIC_GRADE"                       
[24] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[25] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[26] "TOBACCO_SMOKING_HISTORY"                         
[27] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[28] "RADIATION_TREATMENT_ADJUVANT"                    
[29] "RADIATION_TOTAL_DOSE"                            
[30] "RADIATION_THERAPY_TYPE"                          
[31] "RADIATION_THERAPY_STATUS"                        
[32] "RADIATION_THERAPY_SITE"                          
[33] "RADIATION_ADJUVANT_UNITS"                        
[34] "PREGNANCIES_COUNT_TOTAL"                         
[35] "PREGNANCIES_COUNT_STILLBIRTH"                    
[36] "PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[37] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[38] "PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[39] "PREGNANCIES_COUNT_ECTOPIC"                       
[40] "PATIENT_CERVICALCARCINOMAPELVICEXTENSIONTEXT"    
[41] "LYMPH_NODE_LOCATION"                             
[42] "POS_LYMPH_NODE_LOCATION"                         
[43] "MENOPAUSE_STATUS"                                
[44] "LYMPHOVASCULAR_INVOLVEMENT"                      
[45] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[46] "LYMPH_NODES_EXAMINED"                            
[47] "KERATINIZATION_SQUAMOUS_CELL"                    
[48] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[49] "HYSTERECTOMY_TYPE"                               
[50] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[51] "HEIGHT_CM_AT_DIAGNOSIS"                          
[52] "FEDPET_OR_CT_RESULTS"                            
[53] "CORPUS_INVOLVEMENT"                              
[54] "CHEMO_CONCURRENT_TYPE"                           
[55] "CERVIX_SUV_RESULTS"                              
[56] "CAUSE_OF_DEATH"                                  
[57] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[58] "AGE_AT_DIAGNOSIS"                                
[59] "STAGE_EVENT.CLINICAL_STAGE"                      

Input Data has 59 rows and 194 columns.

[1] "Batch" "19"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=144,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'BATCH_NUMBER':	nDistinctValues=19,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
Variable 20:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=66,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'TUMOR_SAMPLE_PROCUREMENT_COUNTRY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'NEOPLASM_HISTOLOGIC_GRADE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'TOBACCO_SMOKING_YEAR_STOPPED':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 27:'PATIENT.AGEBEGANSMOKINGINYEARS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 28:'RADIATION_TREATMENT_ADJUVANT':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_TREATMENT_ADJUVANT is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 29:'RADIATION_TOTAL_DOSE':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 30:'RADIATION_THERAPY_TYPE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 31:'RADIATION_THERAPY_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 32:'RADIATION_THERAPY_SITE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 33:'RADIATION_ADJUVANT_UNITS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 34:'PREGNANCIES_COUNT_TOTAL':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 35:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 36:'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 37:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 39:'PREGNANCIES_COUNT_ECTOPIC':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 40:'PATIENT_CERVICALCARCINOMAPELVICEXTENSIONTEXT':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATIENT_CERVICALCARCINOMAPELVICEXTENSIONTEXT excluded in the analysis because there is no case of (both >= 3) in the table below"
              CARCINOMA INVOLVES ALL SECTIONS OF THE CERVIX WITH DIRECT EXTENSION INTO THE MYOMETRIAL WALL, PARAMETRIAL TISSUES AND UPPER VAGINA.
freq.values   "1"                                                                                                                                
freq.contrast "6"                                                                                                                                
both >= 3     "FALSE"                                                                                                                            
              METASTASES TO RIGHT OVARY NO PELVIC SPREAD PELVIC SPREAD
freq.values   "1"                       "1"              "1"          
freq.contrast "6"                       "6"              "6"          
both >= 3     "FALSE"                   "FALSE"          "FALSE"      
              SEVERE SQUAMOUS DYSPLASIA (CIN3) EXTENDING TO THE VAGINAL MARGIN OF EXCISION
freq.values   "1"                                                                         
freq.contrast "6"                                                                         
both >= 3     "FALSE"                                                                     
              THE PELVIC NODULES SHOW CIRCUMSCRIBED AREA OF ADIPOSE TISSUE WITH LOCAL FAT NECROSIS. NO EVIDENCE OF MALIGNANCY WITHIN THIS PELVIC NODULE.
freq.values   "1"                                                                                                                                       
freq.contrast "6"                                                                                                                                       
both >= 3     "FALSE"                                                                                                                                   
              TUMOR EXTENDS 1.0CM INTO 1.3 CM THICK CERVICAL/LOWER UTERINE SEGMENT WALL
freq.values   "1"                                                                      
freq.contrast "6"                                                                      
both >= 3     "FALSE"                                                                  
Variable 41:'LYMPH_NODE_LOCATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "LYMPH_NODE_LOCATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 42:'POS_LYMPH_NODE_LOCATION':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 43:'MENOPAUSE_STATUS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 44:'LYMPHOVASCULAR_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 45:'LYMPH_NODES_EXAMINED_HE_COUNT':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 46:'LYMPH_NODES_EXAMINED':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 47:'KERATINIZATION_SQUAMOUS_CELL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 48:'INITIAL_PATHOLOGIC_DX_YEAR':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 49:'HYSTERECTOMY_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HYSTERECTOMY_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 50:'HISTORY_HORMONAL_CONTRACEPTIVES_USE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 51:'HEIGHT_CM_AT_DIAGNOSIS':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 52:'FEDPET_OR_CT_RESULTS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "FEDPET_OR_CT_RESULTS is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 53:'CORPUS_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 54:'CHEMO_CONCURRENT_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 55:'CERVIX_SUV_RESULTS':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 56:'CAUSE_OF_DEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CAUSE_OF_DEATH is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 57:'AJCC_TUMOR_PATHOLOGIC_PT':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 58:'AGE_AT_DIAGNOSIS':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 59:'STAGE_EVENT.CLINICAL_STAGE':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 194 columns, 1 survival variables, and 44 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                                  
 [2] "PATHOLOGY_T_STAGE"                               
 [3] "PATHOLOGY_N_STAGE"                               
 [4] "PATHOLOGY_M_STAGE"                               
 [5] "HISTOLOGICAL_TYPE"                               
 [6] "RADIATIONS_RADIATION_REGIMENINDICATION"          
 [7] "NUMBER_PACK_YEARS_SMOKED"                        
 [8] "NUMBER_OF_LYMPH_NODES"                           
 [9] "RACE"                                            
[10] "ETHNICITY"                                       
[11] "WEIGHT_KG_AT_DIAGNOSIS"                          
[12] "TUMOR_STATUS"                                    
[13] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[14] "NEOPLASM_HISTOLOGIC_GRADE"                       
[15] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[16] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[17] "TOBACCO_SMOKING_HISTORY"                         
[18] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[19] "RADIATION_TOTAL_DOSE"                            
[20] "RADIATION_THERAPY_TYPE"                          
[21] "RADIATION_THERAPY_STATUS"                        
[22] "RADIATION_THERAPY_SITE"                          
[23] "RADIATION_ADJUVANT_UNITS"                        
[24] "PREGNANCIES_COUNT_TOTAL"                         
[25] "PREGNANCIES_COUNT_STILLBIRTH"                    
[26] "PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[27] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[28] "PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[29] "PREGNANCIES_COUNT_ECTOPIC"                       
[30] "POS_LYMPH_NODE_LOCATION"                         
[31] "MENOPAUSE_STATUS"                                
[32] "LYMPHOVASCULAR_INVOLVEMENT"                      
[33] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[34] "LYMPH_NODES_EXAMINED"                            
[35] "KERATINIZATION_SQUAMOUS_CELL"                    
[36] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[37] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[38] "HEIGHT_CM_AT_DIAGNOSIS"                          
[39] "CORPUS_INVOLVEMENT"                              
[40] "CHEMO_CONCURRENT_TYPE"                           
[41] "CERVIX_SUV_RESULTS"                              
[42] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[43] "AGE_AT_DIAGNOSIS"                                
[44] "STAGE_EVENT.CLINICAL_STAGE"                      
[1] "changed to 45 non-survival variables adding another age variable for linear regression analysis on mutaion rate."
[1] "DAYS_TO_DEATH_OR_LAST_FUP"
[1] "DAYS_TO_DEATH_OR_LAST_FUP"
[1] "D"                         "DAYS_TO_DEATH_OR_LAST_FUP"
[3] "Month"                    
[1] "check if there is any case_to_report in survival time data or not"
[1] "alarming case(s) exist!"
[1] "[  1  ] case_to_report(s) is(are) excluded in survival analysis"
AGE, nv=57, binary=FALSE, numeric=TRUE
AGE_mutation.rate, nv=57, binary=FALSE, numeric=TRUE
$MUTATIONRATE_NONSYNONYMOUS

Call:
lm(formula = as.numeric(i) ~ vv)

Residuals:
       Min         1Q     Median         3Q        Max 
-6.733e-06 -3.177e-06 -1.931e-06 -4.460e-07  5.245e-05 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)  
(Intercept) -3.018e-07  2.161e-06  -0.140   0.8891  
vv           1.054e-07  4.403e-08   2.393   0.0177 *
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 8.052e-06 on 188 degrees of freedom
  (4 observations deleted due to missingness)
Multiple R-squared: 0.02957,	Adjusted R-squared: 0.0244 
F-statistic: 5.728 on 1 and 188 DF,  p-value: 0.01768 


$MUTATIONRATE_SILENT

Call:
lm(formula = as.numeric(i) ~ vv)

Residuals:
       Min         1Q     Median         3Q        Max 
-2.085e-06 -1.041e-06 -6.075e-07 -1.173e-07  1.570e-05 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)  
(Intercept) 2.248e-08  6.437e-07   0.035    0.972  
vv          3.129e-08  1.312e-08   2.386    0.018 *
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 2.399e-06 on 188 degrees of freedom
  (4 observations deleted due to missingness)
Multiple R-squared: 0.02939,	Adjusted R-squared: 0.02422 
F-statistic: 5.692 on 1 and 188 DF,  p-value: 0.01804 


PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY_T_STAGE"
[1] "num to class table"
vv1
 T1  T2  T3  T4 
104  40   3   2 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=6, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=28, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=10, binary=FALSE, numeric=TRUE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
WEIGHT_KG_AT_DIAGNOSIS, nv=66, binary=FALSE, numeric=TRUE
TUMOR_STATUS, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SAMPLE_PROCUREMENT_COUNTRY, nv=5, binary=FALSE, numeric=FALSE
NEOPLASM_HISTOLOGIC_GRADE, nv=5, binary=FALSE, numeric=FALSE
TOBACCO_SMOKING_YEAR_STOPPED, nv=18, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_PACK_YEARS_SMOKED, nv=28, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_HISTORY, nv=5, binary=FALSE, numeric=FALSE
PATIENT.AGEBEGANSMOKINGINYEARS, nv=22, binary=FALSE, numeric=TRUE
RADIATION_TOTAL_DOSE, nv=27, binary=FALSE, numeric=TRUE
RADIATION_THERAPY_TYPE, nv=5, binary=FALSE, numeric=FALSE
RADIATION_THERAPY_STATUS, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY_SITE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_ADJUVANT_UNITS, nv=2, binary=FALSE, numeric=FALSE
PREGNANCIES_COUNT_TOTAL, nv=14, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_STILLBIRTH, nv=3, binary=FALSE, numeric=TRUE
[1] "PREGNANCIES_COUNT_STILLBIRTH"
[1] "num to class table"
vv1
 0  1  3 
95  5  1 
PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT, nv=4, binary=FALSE, numeric=TRUE
[1] "PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[1] "num to class table"
vv1
 0  1  2  3 
81 25  3  1 
PREGNANCIES_COUNT_LIVE_BIRTH, nv=10, binary=FALSE, numeric=TRUE
PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT, nv=8, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_ECTOPIC, nv=3, binary=FALSE, numeric=TRUE
[1] "PREGNANCIES_COUNT_ECTOPIC"
[1] "num to class table"
vv1
 0  1  2 
93  9  1 
POS_LYMPH_NODE_LOCATION, nv=5, binary=FALSE, numeric=FALSE
MENOPAUSE_STATUS, nv=4, binary=FALSE, numeric=FALSE
LYMPHOVASCULAR_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
LYMPH_NODES_EXAMINED_HE_COUNT, nv=10, binary=FALSE, numeric=TRUE
LYMPH_NODES_EXAMINED, nv=47, binary=FALSE, numeric=TRUE
KERATINIZATION_SQUAMOUS_CELL, nv=2, binary=FALSE, numeric=FALSE
INITIAL_PATHOLOGIC_DX_YEAR, nv=20, binary=FALSE, numeric=TRUE
HISTORY_HORMONAL_CONTRACEPTIVES_USE, nv=3, binary=FALSE, numeric=FALSE
HEIGHT_CM_AT_DIAGNOSIS, nv=31, binary=FALSE, numeric=TRUE
CORPUS_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
CHEMO_CONCURRENT_TYPE, nv=3, binary=FALSE, numeric=FALSE
CERVIX_SUV_RESULTS, nv=10, binary=FALSE, numeric=TRUE
AJCC_TUMOR_PATHOLOGIC_PT, nv=13, binary=FALSE, numeric=FALSE
AGE_AT_DIAGNOSIS, nv=57, binary=FALSE, numeric=TRUE
STAGE_EVENT.CLINICAL_STAGE, nv=16, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
