[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: "
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/SKCM-TM/14527800/SKCM-TM.rppa.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SKCM-TM/15087681/SKCM-TM.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/SKCM-TM/15087681/SKCM-TM.merged_data.txt"
[1] "ok3"

nSamples in clinical file=359, in expression file=169, common to both=169
Number of genes in original expression dataset=181
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "DAYS_TO_SUBMITTED_SPECIMEN_DX"         
 [6] "PRIMARY_SITE_OF_DISEASE"               
 [7] "NEOPLASM_DISEASESTAGE"                 
 [8] "PATHOLOGY_T_STAGE"                     
 [9] "PATHOLOGY_N_STAGE"                     
[10] "PATHOLOGY_M_STAGE"                     
[11] "MELANOMA_ULCERATION"                   
[12] "MELANOMA_PRIMARY_KNOWN"                
[13] "BRESLOW_THICKNESS"                     
[14] "DCC_UPLOAD_DATE"                       
[15] "GENDER"                                
[16] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[17] "RADIATION_THERAPY"                     
[18] "RADIATIONS_RADIATION_REGIMENINDICATION"
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCH_NUMBER"                          

Input Data has 21 rows and 169 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=94,	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=81,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'DAYS_TO_SUBMITTED_SPECIMEN_DX':	nDistinctValues=136,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 6:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'NEOPLASM_DISEASESTAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_T_STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_N_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA_ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MELANOMA_PRIMARY_KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BRESLOW_THICKNESS':	nDistinctValues=74,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 15:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 17:'RADIATION_THERAPY':	nDistinctValues=1,	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 18:'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   "1"     "168"  
freq.contrast "168"   "1"    
both >= 3     "FALSE" "FALSE"
Variable 19:'RACE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RACE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 20:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 21:'BATCH_NUMBER':	nDistinctValues=6,	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] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "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 169 columns, 2 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"          "PRIMARY_SITE_OF_DISEASE"
 [3] "NEOPLASM_DISEASESTAGE"   "PATHOLOGY_T_STAGE"      
 [5] "PATHOLOGY_N_STAGE"       "PATHOLOGY_M_STAGE"      
 [7] "MELANOMA_ULCERATION"     "MELANOMA_PRIMARY_KNOWN" 
 [9] "BRESLOW_THICKNESS"       "GENDER"                 
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[1] "S"                                         
[2] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[3] "Month"                                     
[1] "check if there is any case_to_report in survival time data or not"
[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"
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
PRIMARY_SITE_OF_DISEASE, nv=4, binary=FALSE, numeric=FALSE
NEOPLASM_DISEASESTAGE, nv=14, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY_T_STAGE"
[1] "num to class table"
vv1
T0 T1 T2 T3 T4 
15 21 37 28 31 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY_N_STAGE"
[1] "num to class table"
vv1
N0 N1 N2 N3 
85 24 26 21 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
MELANOMA_ULCERATION, nv=2, binary=FALSE, numeric=FALSE
MELANOMA_PRIMARY_KNOWN, nv=2, binary=FALSE, numeric=FALSE
BRESLOW_THICKNESS, nv=74, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
