[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/COAD-TP/15633943/COAD-TP.patients.counts_and_rates.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/COAD-TP/15076851/COAD-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/COAD-TP/15076851/COAD-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=453, in expression file=366, common to both=366
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] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "COMPLETENESS_OF_RESECTION"             
[18] "NUMBER_OF_LYMPH_NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCH_NUMBER"                          

Input Data has 21 rows and 366 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=62,	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=232,	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=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "2"     "364"  
freq.contrast "364"   "2"    
both >= 3     "FALSE" "FALSE"
Variable 17:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "1"                "197"                 
freq.contrast "197"              "1"                   
both >= 3     "FALSE"            "FALSE"               
Variable 21:'BATCH_NUMBER':	nDistinctValues=21,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 366 columns, 1 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"            "NEOPLASM_DISEASESTAGE"    
 [3] "PATHOLOGY_T_STAGE"         "PATHOLOGY_N_STAGE"        
 [5] "PATHOLOGY_M_STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL_TYPE"         "COMPLETENESS_OF_RESECTION"
 [9] "NUMBER_OF_LYMPH_NODES"     "RACE"                     
[1] "changed to 11 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=58, binary=FALSE, numeric=TRUE
AGE_mutation.rate, nv=58, binary=FALSE, numeric=TRUE
$MUTATIONRATE_NONSYNONYMOUS

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

Residuals:
       Min         1Q     Median         3Q        Max 
-1.515e-05 -1.065e-05 -8.557e-06 -3.018e-06  2.456e-04 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)   
(Intercept)  2.075e-05  7.384e-06   2.810  0.00522 **
vv          -9.956e-08  1.074e-07  -0.927  0.35479   
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 2.63e-05 on 363 degrees of freedom
  (1 observation deleted due to missingness)
Multiple R-squared: 0.002359,	Adjusted R-squared: -0.0003891 
F-statistic: 0.8584 on 1 and 363 DF,  p-value: 0.3548 


$MUTATIONRATE_SILENT

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

Residuals:
       Min         1Q     Median         3Q        Max 
-4.599e-06 -3.401e-06 -2.468e-06 -3.230e-07  6.297e-05 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)   
(Intercept)  5.658e-06  1.993e-06   2.840  0.00477 **
vv          -1.761e-08  2.900e-08  -0.607  0.54402   
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 7.098e-06 on 363 degrees of freedom
  (1 observation deleted due to missingness)
Multiple R-squared: 0.001015,	Adjusted R-squared: -0.001737 
F-statistic: 0.3688 on 1 and 363 DF,  p-value: 0.544 


NEOPLASM_DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY_T_STAGE"
[1] "num to class table"
vv1
 T1  T2  T3  T4 
  9  68 247  41 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY_N_STAGE"
[1] "num to class table"
vv1
 N0  N1  N2 
220  80  65 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=19, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
