[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTPCPG-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PCPG-TP/10006138/PCPG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/10685824/transformed.cor.cli.txt"

nPatients in clinical file=61, in cluster file=178, common to both=61
[1] "Reduce the number of clustering variables from 9 to 4."
[1]  4 61
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
             5             56 
  HRAS MUTATED HRAS WILD-TYPE 
             5             56 
[1] "EPAS1 MUTATION ANALYSIS"
[1] 3
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              4              57 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              4              57 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
            7            54 
  NF1 MUTATED NF1 WILD-TYPE 
            7            54 
[1] "RET MUTATION ANALYSIS"
[1] 3
  RET MUTATED RET WILD-TYPE 
            4            57 
  RET MUTATED RET WILD-TYPE 
            4            57 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "RADIATIONTHERAPY"                      
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCHNUMBER"                           

Input Data has 11 rows and 61 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
         883           69           29          179          240         1094 
TCGA-PR-A5PH TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
         852          773          211           55           22          766 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RT-A6Y9 TCGA-RT-A6YA 
          70          134           24           29         2957         1249 
TCGA-RT-A6YC TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
         246          604           89          216         1013          724 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
          32           26           37          356          191         2214 
TCGA-RW-A7D0 TCGA-SP-A6QD TCGA-SP-A6QH TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
          54         3087         1857         2983          274         3013 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MR TCGA-SR-A6MS TCGA-SR-A6MT 
          43            3         1558         2020         2222         3247 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
        3362         3269           NA          456          345         1106 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HA 
         132          765          242          317          770           36 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A815 
         218          195          137          188           24          182 
TCGA-XG-A823 
         210 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 3:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER" "RACE"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 61 columns, 0 survival variables, and 3 non-survival variables.
AGE, nv=39, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = HRAS MUTATION ANALYSIS
D1V1, continuous
D1V2, binary
                cls
clus              0  1
  HRAS MUTATED    5  0
  HRAS WILD-TYPE 35 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      5    0
  HRAS WILD-TYPE   35   21
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE            5             35
  MALE              0             21
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HRAS MUTATED                                  0     0
  HRAS WILD-TYPE                                1     3
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED                           0     5
  HRAS WILD-TYPE                         7    43
D1V3, multiclass
                                  clus
vv                                 HRAS MUTATED HRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              3
  BLACK OR AFRICAN AMERICAN                   0              7
  WHITE                                       5             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = EPAS1 MUTATION ANALYSIS
D2V1, continuous
D2V2, binary
                 cls
clus               0  1
  EPAS1 MUTATED    2  2
  EPAS1 WILD-TYPE 38 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPAS1 MUTATED      2    2
  EPAS1 WILD-TYPE   38   19
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  FEMALE             2              38
  MALE               2              19
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPAS1 MUTATED                                  0     1
  EPAS1 WILD-TYPE                                1     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPAS1 MUTATED                           0     3
  EPAS1 WILD-TYPE                         7    45
D2V3, multiclass
                                  clus
vv                                 EPAS1 MUTATED EPAS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               2
  BLACK OR AFRICAN AMERICAN                    0               7
  WHITE                                        3              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = NF1 MUTATION ANALYSIS
D3V1, continuous
D3V2, binary
               cls
clus             0  1
  NF1 MUTATED    5  2
  NF1 WILD-TYPE 35 19
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      5    2
  NF1 WILD-TYPE   35   19
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE           5            35
  MALE             2            19
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF1 MUTATED                                  0     0
  NF1 WILD-TYPE                                1     3
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED                           0     7
  NF1 WILD-TYPE                         7    41
D3V3, multiclass
                                  clus
vv                                 NF1 MUTATED NF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             3
  BLACK OR AFRICAN AMERICAN                  0             7
  WHITE                                      7            41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RET MUTATION ANALYSIS
D4V1, continuous
D4V2, binary
               cls
clus             0  1
  RET MUTATED    3  1
  RET WILD-TYPE 37 20
[1] "tbl2"
               cls
clus            [,1] [,2]
  RET MUTATED      3    1
  RET WILD-TYPE   37   20
        clus
vv       RET MUTATED RET WILD-TYPE
  FEMALE           3            37
  MALE             1            20
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RET MUTATED                                  1     1
  RET WILD-TYPE                                0     2
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RET MUTATED                           1     1
  RET WILD-TYPE                         6    47
D4V3, multiclass
                                  clus
vv                                 RET MUTATED RET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      1             2
  BLACK OR AFRICAN AMERICAN                  1             6
  WHITE                                      1            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
