[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"       "-oTUCS-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/UCS-TP/10006365/UCS-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCS-TP/10685778/transformed.cor.cli.txt"

nPatients in clinical file=57, in cluster file=57, common to both=57
[1] "Reduce the number of clustering variables from 15 to 13."
[1] 13 57
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            51              6 
  TP53 MUTATED TP53 WILD-TYPE 
            51              6 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             22              35 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             22              35 
[1] "PPP2R1A MUTATION ANALYSIS"
[1] 3
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               16                41 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               16                41 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            11             46 
  PTEN MUTATED PTEN WILD-TYPE 
            11             46 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             7             50 
  KRAS MUTATED KRAS WILD-TYPE 
             7             50 
[1] "ZBTB7B MUTATION ANALYSIS"
[1] 3
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
               6               51 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
               6               51 
[1] "CHD4 MUTATION ANALYSIS"
[1] 3
  CHD4 MUTATED CHD4 WILD-TYPE 
            10             47 
  CHD4 MUTATED CHD4 WILD-TYPE 
            10             47 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               6               51 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               6               51 
[1] "ARHGAP35 MUTATION ANALYSIS"
[1] 3
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 6                 51 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 6                 51 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              20               37 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              20               37 
[1] "MAMLD1 MUTATION ANALYSIS"
[1] 3
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
               4               53 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
               4               53 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
            6            51 
  RB1 MUTATED RB1 WILD-TYPE 
            6            51 
[1] "LYPLA2 MUTATION ANALYSIS"
[1] 3
  LYPLA2 MUTATED LYPLA2 WILD-TYPE 
               3               54 
  LYPLA2 MUTATED LYPLA2 WILD-TYPE 
               3               54 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 57 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
          NA           NA           NA         1806           NA           NA 
TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV 
        1053           NA           NA         2118           NA         1816 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE 
          NA           NA          530           NA           NA           NA 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B 
          NA         1209           NA           NA           NA          407 
TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP 
          NA           NA          829          812          781          471 
TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 
         572          295           NA           NA         1672         1089 
TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY 
         604           NA         2841         2262          833           NA 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC 
          NA           NA         2596           NA           NA          461 
TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU 
          NA          298          452           81           NA           NA 
TCGA-NG-A4VW TCGA-QM-A5NM TCGA-QN-A5NN 
          NA          165           NA 
Variable 1:'AGE':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"  "RACE"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 57 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=30, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   21 29
  TP53 WILD-TYPE  1  5
  TP53 MUTATED TP53 WILD-TYPE 
            50              6 
  TP53 MUTATED TP53 WILD-TYPE 
            29              5 
$`TP53 MUTATED`
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
      102.41        52.31         4.67        59.38        18.08         4.87 
TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV 
       34.62        22.52        29.95        69.63        50.17        59.70 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VF 
       14.70        11.87        17.42        19.63         9.57        17.16 
TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL 
       39.75         0.26        12.43        13.38        26.63        13.74 
TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S 
       27.25        26.70        25.68        15.48        18.81         9.70 
TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 
       21.93        67.17        54.97        35.80        19.86        15.81 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 
       93.40        74.37        27.39         3.75        17.79         6.67 
TCGA-ND-A4W6 TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP 
       10.42        15.16         9.80        14.86         2.66         5.49 
TCGA-NG-A4VU TCGA-QM-A5NM 
       14.53         5.42 

$`TP53 WILD-TYPE`
TCGA-N6-A4VD TCGA-N7-A4Y0 TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NG-A4VW 
        3.68        25.35        85.35        23.47         5.49        31.20 

  TP53 MUTATED TP53 WILD-TYPE 
          0.26           3.68 
  TP53 MUTATED TP53 WILD-TYPE 
        102.41          85.35 
  TP53 MUTATED TP53 WILD-TYPE 
        17.935         24.410 
[1] "0.3 - 102.4 (17.9)" "3.7 - 85.3 (24.4)" 
[1] "hr=" "1.4"
D1V2, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       2                         9    39
  TP53 WILD-TYPE     1                         0     5
D1V3, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                2              1
  BLACK OR AFRICAN AMERICAN            9              0
  WHITE                               39              5
[1] 3 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 = FBXW7 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2              0  1
  FBXW7 MUTATED    8 14
  FBXW7 WILD-TYPE 14 20
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             22              34 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             14              20 
$`FBXW7 MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS 
       52.31         4.67        18.08        34.62        22.52        29.95 
TCGA-N5-A4RT TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VG 
       69.63        11.87        19.63         3.68         9.57        39.75 
TCGA-N7-A4Y8 TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N9-A4Q7 TCGA-NA-A4QX 
       12.43        26.63        27.25        26.70        19.86        27.39 
TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NG-A4VU 
       15.16         5.49        14.86        14.53 

$`FBXW7 WILD-TYPE`
TCGA-N5-A4R8 TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E 
      102.41        59.38         4.87        50.17        59.70        14.70 
TCGA-N6-A4V9 TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PL 
       17.42        17.16        25.35         0.26        13.38        13.74 
TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 
       25.68        15.48        18.81         9.70        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY 
       54.97        35.80        15.81        93.40        74.37         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WU 
       17.79         6.67        85.35        10.42        23.47         9.80 
TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW TCGA-QM-A5NM 
        2.66         5.49        31.20         5.42 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           3.68            0.26 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          69.63          102.41 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         19.745          17.605 
[1] "3.7 - 69.6 (19.7)"  "0.3 - 102.4 (17.6)"
[1] "hr=" "1.2"
D2V2, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED       1                         3    17
  FBXW7 WILD-TYPE     2                         6    27
D2V3, multiclass
                           clus
vv                          FBXW7 MUTATED FBXW7 WILD-TYPE
  ASIAN                                 1               2
  BLACK OR AFRICAN AMERICAN             3               6
  WHITE                                17              27
[1] 3 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 = PPP2R1A MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  PPP2R1A MUTATED    8  8
  PPP2R1A WILD-TYPE 14 26
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               16                40 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
                8                26 
$`PPP2R1A MUTATED`
TCGA-N5-A4RF TCGA-N5-A4RU TCGA-N5-A59E TCGA-N6-A4VD TCGA-N8-A4PL TCGA-N8-A4PN 
       59.38        50.17        14.70         3.68        13.74        26.70 
TCGA-N8-A4PP TCGA-N9-A4Q3 TCGA-N9-A4Q7 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-ND-A4WC 
       15.48        54.97        19.86        74.37        27.39        15.16 
TCGA-ND-A4WF TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-QM-A5NM 
        5.49         2.66        14.53         5.42 

$`PPP2R1A WILD-TYPE`
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN 
      102.41        52.31         4.67        18.08         4.87        34.62 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 
       22.52        29.95        69.63        59.70        11.87        17.42 
TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 
       19.63         9.57        17.16        39.75        25.35         0.26 
TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A4PQ 
       12.43        13.38        26.63        27.25        25.68        18.81 
TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QV 
        9.70        21.93        67.17        35.80        15.81        93.40 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA 
        3.75        17.79         6.67        85.35        10.42        23.47 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VW 
        9.80        14.86         5.49        31.20 

  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
             2.66              0.26 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
            74.37            102.41 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
            15.32             19.22 
[1] "2.7 - 74.4 (15.3)"  "0.3 - 102.4 (19.2)"
[1] "hr=" "1.1"
D3V2, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPP2R1A MUTATED       1                         1    14
  PPP2R1A WILD-TYPE     2                         8    30
D3V3, multiclass
                           clus
vv                          PPP2R1A MUTATED PPP2R1A WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 8
  WHITE                                  14                30
[1] 3 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 = PTEN MUTATION ANALYSIS
D4V1, survival
                sevent
clus2             0  1
  PTEN MUTATED    4  7
  PTEN WILD-TYPE 18 27
  PTEN MUTATED PTEN WILD-TYPE 
            11             45 
  PTEN MUTATED PTEN WILD-TYPE 
             7             27 
$`PTEN MUTATED`
TCGA-N5-A4RF TCGA-N6-A4VD TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-NA-A4R1 
       59.38         3.68        17.16        25.35        26.63         6.67 
TCGA-ND-A4WC TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW TCGA-QM-A5NM 
       15.16         2.66         5.49        31.20         5.42 

$`PTEN WILD-TYPE`
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN 
      102.41        52.31         4.67        18.08         4.87        34.62 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E 
       22.52        29.95        69.63        50.17        59.70        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VG TCGA-N7-A4Y5 
       11.87        17.42        19.63         9.57        39.75         0.26 
TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO 
       12.43        13.38        13.74        27.25        26.70        25.68 
TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       15.48        18.81         9.70        21.93        67.17        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX 
       35.80        19.86        15.81        93.40        74.37        27.39 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
        3.75        17.79        85.35        10.42        23.47         5.49 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NG-A4VU 
        9.80        14.86        14.53 

  PTEN MUTATED PTEN WILD-TYPE 
          2.66           0.26 
  PTEN MUTATED PTEN WILD-TYPE 
         59.38         102.41 
  PTEN MUTATED PTEN WILD-TYPE 
         15.16          19.63 
[1] "2.7 - 59.4 (15.2)"  "0.3 - 102.4 (19.6)"
[1] "hr=" "1.6"
D4V2, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       1                         1     9
  PTEN WILD-TYPE     2                         8    35
D4V3, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                1              2
  BLACK OR AFRICAN AMERICAN            1              8
  WHITE                                9             35
[1] 3 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(5) Variable = KRAS MUTATION ANALYSIS
D5V1, survival
                sevent
clus2             0  1
  KRAS MUTATED    4  3
  KRAS WILD-TYPE 18 31
  KRAS MUTATED KRAS WILD-TYPE 
             7             49 
  KRAS MUTATED KRAS WILD-TYPE 
             3             31 
$`KRAS MUTATED`
TCGA-N5-A4RF TCGA-N5-A4RS TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N8-A4PL TCGA-N9-A4Q3 
       59.38        29.95        17.42        19.63        13.74        54.97 
TCGA-NF-A4WU 
        9.80 

$`KRAS WILD-TYPE`
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN 
      102.41        52.31         4.67        18.08         4.87        34.62 
TCGA-N5-A4RO TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F 
       22.52        69.63        50.17        59.70        14.70        11.87 
TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 
        3.68         9.57        17.16        39.75        25.35         0.26 
TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO 
       12.43        13.38        26.63        27.25        26.70        25.68 
TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q4 
       15.48        18.81         9.70        21.93        67.17        35.80 
TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY 
       19.86        15.81        93.40        74.37        27.39         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC 
       17.79         6.67        85.35        10.42        23.47        15.16 
TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
        5.49        14.86         2.66         5.49        14.53        31.20 
TCGA-QM-A5NM 
        5.42 

  KRAS MUTATED KRAS WILD-TYPE 
          9.80           0.26 
  KRAS MUTATED KRAS WILD-TYPE 
         59.38         102.41 
  KRAS MUTATED KRAS WILD-TYPE 
         19.63          18.08 
[1] "9.8 - 59.4 (19.6)"  "0.3 - 102.4 (18.1)"
[1] "hr=" "1.7"
D5V2, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       0                         0     7
  KRAS WILD-TYPE     3                         9    37
D5V3, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              9
  WHITE                                7             37
[1] 3 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(6) Variable = ZBTB7B MUTATION ANALYSIS
D6V1, survival
                  sevent
clus2               0  1
  ZBTB7B MUTATED    2  3
  ZBTB7B WILD-TYPE 20 31
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
               5               51 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
               3               31 
$`ZBTB7B MUTATED`
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RT TCGA-N6-A4VG TCGA-NG-A4VW 
      102.41        52.31        69.63        39.75        31.20 

$`ZBTB7B WILD-TYPE`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO 
        4.67        59.38        18.08         4.87        34.62        22.52 
TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 
       29.95        50.17        59.70        14.70        11.87        17.42 
TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 
       19.63         3.68         9.57        17.16        25.35         0.26 
TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN 
       12.43        13.38        26.63        13.74        27.25        26.70 
TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 
       25.68        15.48        18.81         9.70        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       54.97        35.80        19.86        15.81        93.40        74.37 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       27.39         3.75        17.79         6.67        85.35        10.42 
TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 
       23.47        15.16         5.49         9.80        14.86         2.66 
TCGA-NF-A5CP TCGA-NG-A4VU TCGA-QM-A5NM 
        5.49        14.53         5.42 

  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
           31.20             0.26 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
          102.41            93.40 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
           52.31            17.42 
[1] "31.2 - 102.4 (52.3)" "0.3 - 93.4 (17.4)"  
[1] "hr=" "3.3"
D6V2, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZBTB7B MUTATED       1                         0     5
  ZBTB7B WILD-TYPE     2                         9    39
D6V3, multiclass
                           clus
vv                          ZBTB7B MUTATED ZBTB7B WILD-TYPE
  ASIAN                                  1                2
  BLACK OR AFRICAN AMERICAN              0                9
  WHITE                                  5               39
[1] 3 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(7) Variable = CHD4 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2             0  1
  CHD4 MUTATED    5  5
  CHD4 WILD-TYPE 17 29
  CHD4 MUTATED CHD4 WILD-TYPE 
            10             46 
  CHD4 MUTATED CHD4 WILD-TYPE 
             5             29 
$`CHD4 MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RT TCGA-N5-A4RV TCGA-N6-A4VE TCGA-N7-A4Y0 
        4.67        59.38        69.63        59.70         9.57        25.35 
TCGA-N8-A4PI TCGA-N8-A4PM TCGA-ND-A4WC TCGA-ND-A4WF 
       26.63        27.25        15.16         5.49 

$`CHD4 WILD-TYPE`
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO 
      102.41        52.31        18.08         4.87        34.62        22.52 
TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC 
       29.95        50.17        14.70        11.87        17.42        19.63 
TCGA-N6-A4VD TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B 
        3.68        17.16        39.75         0.26        12.43        13.38 
TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S 
       13.74        26.70        25.68        15.48        18.81         9.70 
TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 
       21.93        67.17        54.97        35.80        19.86        15.81 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 
       93.40        74.37        27.39         3.75        17.79         6.67 
TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 
       85.35        10.42        23.47         9.80        14.86         2.66 
TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
        5.49        14.53        31.20         5.42 

  CHD4 MUTATED CHD4 WILD-TYPE 
          4.67           0.26 
  CHD4 MUTATED CHD4 WILD-TYPE 
         69.63         102.41 
  CHD4 MUTATED CHD4 WILD-TYPE 
        25.990         17.935 
[1] "4.7 - 69.6 (26.0)"  "0.3 - 102.4 (17.9)"
[1] "hr=" "1.4"
D7V2, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHD4 MUTATED       1                         0     9
  CHD4 WILD-TYPE     2                         9    35
D7V3, multiclass
                           clus
vv                          CHD4 MUTATED CHD4 WILD-TYPE
  ASIAN                                1              2
  BLACK OR AFRICAN AMERICAN            0              9
  WHITE                                9             35
[1] 3 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(8) Variable = PIK3R1 MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2               0  1
  PIK3R1 MUTATED    1  4
  PIK3R1 WILD-TYPE 21 30
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               5               51 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               4               30 
$`PIK3R1 MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RS TCGA-N8-A4PI TCGA-N8-A4PN TCGA-NA-A4QX 
        4.67        29.95        26.63        26.70        27.39 

$`PIK3R1 WILD-TYPE`
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN 
      102.41        52.31        59.38        18.08         4.87        34.62 
TCGA-N5-A4RO TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F 
       22.52        69.63        50.17        59.70        14.70        11.87 
TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG 
       17.42        19.63         3.68         9.57        17.16        39.75 
TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PM 
       25.35         0.26        12.43        13.38        13.74        27.25 
TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 
       25.68        15.48        18.81         9.70        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       54.97        35.80        19.86        15.81        93.40        74.37 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA 
        3.75        17.79         6.67        85.35        10.42        23.47 
TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP 
       15.16         5.49         9.80        14.86         2.66         5.49 
TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
       14.53        31.20         5.42 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
            4.67             0.26 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           29.95           102.41 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           26.70            17.79 
[1] "4.7 - 29.9 (26.7)"  "0.3 - 102.4 (17.8)"
[1] "hr=" "1.2"
D8V2, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3R1 MUTATED       1                         0     5
  PIK3R1 WILD-TYPE     2                         9    39
D8V3, multiclass
                           clus
vv                          PIK3R1 MUTATED PIK3R1 WILD-TYPE
  ASIAN                                  1                2
  BLACK OR AFRICAN AMERICAN              0                9
  WHITE                                  5               39
[1] 3 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(9) Variable = ARHGAP35 MUTATION ANALYSIS
D9V1, survival
                    sevent
clus2                 0  1
  ARHGAP35 MUTATED    2  4
  ARHGAP35 WILD-TYPE 20 30
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 6                 50 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 4                 30 
$`ARHGAP35 MUTATED`
TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N8-A4PM TCGA-ND-A4WA TCGA-ND-A4WC TCGA-NG-A4VU 
       25.35         0.26        27.25        23.47        15.16        14.53 

$`ARHGAP35 WILD-TYPE`
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
      102.41        52.31         4.67        59.38        18.08         4.87 
TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV 
       34.62        22.52        29.95        69.63        50.17        59.70 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE 
       14.70        11.87        17.42        19.63         3.68         9.57 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL 
       17.16        39.75        12.43        13.38        26.63        13.74 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ 
       26.70        25.68        15.48        18.81         9.70        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV 
       67.17        54.97        35.80        19.86        15.81        93.40 
TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 
       74.37        27.39         3.75        17.79         6.67        85.35 
TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP 
       10.42         5.49         9.80        14.86         2.66         5.49 
TCGA-NG-A4VW TCGA-QM-A5NM 
       31.20         5.42 

  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
              0.26               2.66 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
             27.25             102.41 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
            19.315             18.445 
[1] "0.3 - 27.2 (19.3)"  "2.7 - 102.4 (18.4)"
[1] "hr=" "1.5"
D9V2, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP35 MUTATED       2                         0     4
  ARHGAP35 WILD-TYPE     1                         9    40
D9V3, multiclass
                           clus
vv                          ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                0                  9
  WHITE                                    4                 40
[1] 3 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(10) Variable = PIK3CA MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2               0  1
  PIK3CA MUTATED    5 15
  PIK3CA WILD-TYPE 17 19
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              20               36 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              15               19 
$`PIK3CA MUTATED`
TCGA-N5-A4R8 TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT 
      102.41        59.38        18.08        22.52        29.95        69.63 
TCGA-N6-A4VD TCGA-N6-A4VF TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PM 
        3.68        17.16         0.26        12.43        13.38        27.25 
TCGA-N9-A4PZ TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-ND-A4W6 TCGA-ND-A4WC TCGA-ND-A4WF 
       21.93         3.75        17.79        10.42        15.16         5.49 
TCGA-NF-A5CP TCGA-NG-A4VW 
        5.49        31.20 

$`PIK3CA WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RU TCGA-N5-A4RV 
       52.31         4.67         4.87        34.62        50.17        59.70 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VG 
       14.70        11.87        17.42        19.63         9.57        39.75 
TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP 
       25.35        26.63        13.74        26.70        25.68        15.48 
TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 
       18.81         9.70        67.17        54.97        35.80        19.86 
TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R1 TCGA-NA-A5I1 
       15.81        93.40        74.37        27.39         6.67        85.35 
TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-QM-A5NM 
       23.47         9.80        14.86         2.66        14.53         5.42 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.26             2.66 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          102.41            93.40 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          17.475           19.745 
[1] "0.3 - 102.4 (17.5)" "2.7 - 93.4 (19.7)" 
[1] "hr=" "1.6"
D10V2, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       1                         2    17
  PIK3CA WILD-TYPE     2                         7    27
D10V3, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  1                2
  BLACK OR AFRICAN AMERICAN              2                7
  WHITE                                 17               27
[1] 3 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(11) Variable = MAMLD1 MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2               0  1
  MAMLD1 MUTATED    2  2
  MAMLD1 WILD-TYPE 20 32
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
               4               52 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
               2               32 
$`MAMLD1 MUTATED`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-NA-A4QY TCGA-ND-A4WC 
       69.63         3.68         3.75        15.16 

$`MAMLD1 WILD-TYPE`
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
      102.41        52.31         4.67        59.38        18.08         4.87 
TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E 
       34.62        22.52        29.95        50.17        59.70        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG 
       11.87        17.42        19.63         9.57        17.16        39.75 
TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL 
       25.35         0.26        12.43        13.38        26.63        13.74 
TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S 
       27.25        26.70        25.68        15.48        18.81         9.70 
TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 
       21.93        67.17        54.97        35.80        19.86        15.81 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 
       93.40        74.37        27.39        17.79         6.67        85.35 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 
       10.42        23.47         5.49         9.80        14.86         2.66 
TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
        5.49        14.53        31.20         5.42 

  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
            3.68             0.26 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
           69.63           102.41 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
           9.455           19.220 
[1] "3.7 - 69.6 (9.5)"   "0.3 - 102.4 (19.2)"
[1] "hr=" "1.2"
D11V2, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAMLD1 MUTATED       1                         0     3
  MAMLD1 WILD-TYPE     2                         9    41
D11V3, multiclass
                           clus
vv                          MAMLD1 MUTATED MAMLD1 WILD-TYPE
  ASIAN                                  1                2
  BLACK OR AFRICAN AMERICAN              0                9
  WHITE                                  3               41
[1] 3 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(12) Variable = RB1 MUTATION ANALYSIS
D12V1, survival
               sevent
clus2            0  1
  RB1 MUTATED    4  2
  RB1 WILD-TYPE 18 32
  RB1 MUTATED RB1 WILD-TYPE 
            6            50 
  RB1 MUTATED RB1 WILD-TYPE 
            2            32 
$`RB1 MUTATED`
TCGA-N5-A4RF TCGA-N5-A4RN TCGA-N5-A4RV TCGA-NA-A4R1 TCGA-ND-A4WC TCGA-NG-A4VW 
       59.38        34.62        59.70         6.67        15.16        31.20 

$`RB1 WILD-TYPE`
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO 
      102.41        52.31         4.67        18.08         4.87        22.52 
TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 
       29.95        69.63        50.17        14.70        11.87        17.42 
TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 
       19.63         3.68         9.57        17.16        39.75        25.35 
TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM 
        0.26        12.43        13.38        26.63        13.74        27.25 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ 
       26.70        25.68        15.48        18.81         9.70        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV 
       67.17        54.97        35.80        19.86        15.81        93.40 
TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 
       74.37        27.39         3.75        17.79        85.35        10.42 
TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP 
       23.47         5.49         9.80        14.86         2.66         5.49 
TCGA-NG-A4VU TCGA-QM-A5NM 
       14.53         5.42 

  RB1 MUTATED RB1 WILD-TYPE 
         6.67          0.26 
  RB1 MUTATED RB1 WILD-TYPE 
        59.70        102.41 
  RB1 MUTATED RB1 WILD-TYPE 
       32.910        17.935 
[1] "6.7 - 59.7 (32.9)"  "0.3 - 102.4 (17.9)"
[1] "hr=" "2.6"
D12V2, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED       1                         1     4
  RB1 WILD-TYPE     2                         8    40
D12V3, multiclass
                           clus
vv                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                               1             2
  BLACK OR AFRICAN AMERICAN           1             8
  WHITE                               4            40
[1] 3 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(13) Variable = LYPLA2 MUTATION ANALYSIS
D13V1, survival
                  sevent
clus2               0  1
  LYPLA2 MUTATED    1  2
  LYPLA2 WILD-TYPE 21 32
  LYPLA2 MUTATED LYPLA2 WILD-TYPE 
               3               53 
  LYPLA2 MUTATED LYPLA2 WILD-TYPE 
               2               32 
$`LYPLA2 MUTATED`
TCGA-N5-A4RT TCGA-N8-A4PL TCGA-NA-A4R0 
       69.63        13.74        17.79 

$`LYPLA2 WILD-TYPE`
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
      102.41        52.31         4.67        59.38        18.08         4.87 
TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E 
       34.62        22.52        29.95        50.17        59.70        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF 
       11.87        17.42        19.63         3.68         9.57        17.16 
TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI 
       39.75        25.35         0.26        12.43        13.38        26.63 
TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S 
       27.25        26.70        25.68        15.48        18.81         9.70 
TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 
       21.93        67.17        54.97        35.80        19.86        15.81 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 
       93.40        74.37        27.39         3.75         6.67        85.35 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX 
       10.42        23.47        15.16         5.49         9.80        14.86 
TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
        2.66         5.49        14.53        31.20         5.42 

  LYPLA2 MUTATED LYPLA2 WILD-TYPE 
           13.74             0.26 
  LYPLA2 MUTATED LYPLA2 WILD-TYPE 
           69.63           102.41 
  LYPLA2 MUTATED LYPLA2 WILD-TYPE 
           17.79            18.81 
[1] "13.7 - 69.6 (17.8)" "0.3 - 102.4 (18.8)"
[1] "hr=" "1"  
D13V2, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LYPLA2 MUTATED       0                         0     3
  LYPLA2 WILD-TYPE     3                         9    41
D13V3, multiclass
                           clus
vv                          LYPLA2 MUTATED LYPLA2 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                9
  WHITE                                  3               41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
