[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/74/"
[1] "op: MUTATION_RATE"
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/PCPG-TP/22541474/PCPG-TP.patients.counts_and_rates.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PCPG-TP/22506925/PCPG-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/PCPG-TP/22506925/PCPG-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=179, in expression file=179, common to both=179
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] "TUMOR_TISSUE_SITE"                   
 [6] "GENDER"                              
 [7] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [8] "RADIATION_THERAPY"                   
 [9] "KARNOFSKY_PERFORMANCE_SCORE"         
[10] "HISTOLOGICAL_TYPE"                   
[11] "NUMBER_OF_LYMPH_NODES"               
[12] "RACE"                                
[13] "ETHNICITY"                           

Input Data has 13 rows and 179 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=6,	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=164,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 8:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 10:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'ETHNICITY':	nDistinctValues=2,	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] "****** SUMMARY ***** "
Output Data has 179 columns, 1 survival variables, and 9 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "TUMOR_TISSUE_SITE"          
[3] "GENDER"                      "RADIATION_THERAPY"          
[5] "KARNOFSKY_PERFORMANCE_SCORE" "HISTOLOGICAL_TYPE"          
[7] "NUMBER_OF_LYMPH_NODES"       "RACE"                       
[9] "ETHNICITY"                  
[1] "changed to 10 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=59, binary=FALSE, numeric=TRUE
AGE_mutation.rate, nv=59, binary=FALSE, numeric=TRUE
$MUTATIONRATE_NONSYNONYMOUS

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

Residuals:
       Min         1Q     Median         3Q        Max 
-3.853e-07 -1.149e-07 -2.553e-08  1.001e-07  6.495e-07 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)    
(Intercept) 1.819e-07  4.015e-08   4.530 1.08e-05 ***
vv          3.910e-09  8.083e-10   4.837 2.85e-06 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 1.631e-07 on 177 degrees of freedom
Multiple R-squared: 0.1168,	Adjusted R-squared: 0.1118 
F-statistic:  23.4 on 1 and 177 DF,  p-value: 2.853e-06 


$MUTATIONRATE_SILENT

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

Residuals:
       Min         1Q     Median         3Q        Max 
-1.301e-07 -5.186e-08 -1.359e-08  4.063e-08  1.957e-07 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)    
(Intercept) 4.626e-08  1.831e-08   2.527 0.012373 *  
vv          1.310e-09  3.685e-10   3.555 0.000486 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 7.435e-08 on 177 degrees of freedom
Multiple R-squared: 0.06663,	Adjusted R-squared: 0.06135 
F-statistic: 12.63 on 1 and 177 DF,  p-value: 0.0004857 


TUMOR_TISSUE_SITE, nv=2, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=4, binary=FALSE, numeric=TRUE
[1] "KARNOFSKY_PERFORMANCE_SCORE"
[1] "num to class table"
vv1
 70  80  90 100 
  1   2  13  46 
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=4, binary=FALSE, numeric=TRUE
[1] "NUMBER_OF_LYMPH_NODES"
[1] "num to class table"
vv1
 0  1  2 13 
16  3  1  1 
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
