[1] "terrence_modification_tag"
[1] TRUE
[1] "dfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/HNSC-TP/5956311/HNSC-TP.rppa.txt"
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/HNSC-TP/6154476/HNSC-TP.merged_data.txt"
[1] "gv"
[1] "ALL"
[1] "gfn"
[1] "ALL"
[1] "sfn"
[1] ""
[1] "fv"
[1] "ALL"
[1] "ofn"
[1] ""
[1] "dx"
[1] ""
[1] "sfn"
[1] ""
[1] FALSE
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/HNSC-TP/6154476/HNSC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=379, in expression file=212, common to both=212
Number of genes in original expression dataset=160
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBERPACKYEARSSMOKED"                 
[18] "YEAROFTOBACCOSMOKINGONSET"             
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "GLEASON_SCORE"                         
[21] "PSA_VALUE"                             
[22] "DAYS_TO_PSA"                           
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 212 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         461          276          248          722         1287         1761 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 
         520          725          623         1747          644          450 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BB-4217 TCGA-CN-4722 TCGA-CN-4723 
          63          395          113          186          192          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         485          142          194          613          156          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         693          642          226          642          395          541 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         436         1055          810         1085          397          488 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
         512          261          377         1081          193          252 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
         493          351          360          352          380           NA 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
         683          274          448          424          371          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         315          433           45          391           97          276 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         201          424          224           42          177           83 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 
         119           NA          114          100           46         1465 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1207          654           NA         1659         1422          896 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 
        1399          317          128          870           NA           NA 
TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
        1000         1160          984           NA           NA           NA 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
         814         1006         1308         4240          522         3930 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        3295          584          546         3270         2885         2326 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        2783         2437          519          406          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
        1478         1840          215         1315         1246          640 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
        1899           NA           NA           NA           NA           NA 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
          NA           NA           NA           NA           NA         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
          NA           NA           NA         3836         3380           NA 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
          NA           NA           NA           NA         3496         1724 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
          NA         1444         1095          953          797           NA 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 
        1099           NA           NA           NA           NA           NA 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
          NA           NA           NA           NA           NA         4334 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CX-7085 
          NA           NA           NA           NA           NA          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
         236          828           NA          773          292          700 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-7591 TCGA-DQ-7592 
          77          490          153          567          621          299 
TCGA-IQ-7630 TCGA-IQ-7632 
         485          441 
Variable 1:'AGE':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=110,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=126,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=81,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBERPACKYEARSSMOKED':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "NEOPLASM.DISEASESTAGE"                 
[3] "PATHOLOGY.T.STAGE"                     
[4] "PATHOLOGY.N.STAGE"                     
[5] "GENDER"                                
[6] "RADIATIONS.RADIATION.REGIMENINDICATION"
[7] "NUMBERPACKYEARSSMOKED"                 
[8] "YEAROFTOBACCOSMOKINGONSET"             
[9] "NUMBER.OF.LYMPH.NODES"                 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 212 columns, 1 survival variables, and 9 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=50, binary=FALSE, numeric=TRUE
CAV1|CAVEOLIN-1-R-V 
                 36 
NEOPLASM.DISEASESTAGE, nv=5, binary=FALSE, numeric=FALSE
ARID1A|ARID1A-M-V 
               12 
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
ARID1A|ARID1A-M-V 
               12 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
 1  2  3  4 
13 59 53 79 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
SRC|SRC_PY416-R-C 
              123 
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
 0  1  2  3 
72 21 79  4 
GENDER, nv=2, binary=FALSE, numeric=FALSE
MAPK14|P38_PT180_Y182-R-V 
                      155 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
BCL2|BCL-2-M-V 
            22 
NUMBERPACKYEARSSMOKED, nv=47, binary=FALSE, numeric=TRUE
TP63|P63-R-E 
         157 
YEAROFTOBACCOSMOKINGONSET, nv=46, binary=FALSE, numeric=TRUE
TP63|P63-R-E 
         157 
NUMBER.OF.LYMPH.NODES, nv=22, binary=FALSE, numeric=TRUE
ANXA1|ANNEXIN_I-R-V 
                 18 
[1] "saved param, results, example.expr in analysis.result.Rdata "
