[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"        "-oTDLBC-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/DLBC-TP/11541278/DLBC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/11544212/transformed.cor.cli.txt"

nPatients in clinical file=35, in cluster file=48, common to both=35
[1] "Reduce the number of clustering variables from 80 to 37."
[1] 37 35
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                31 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                31 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3                32 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3                32 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                3                32 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                3                32 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                7                28 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                7                28 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                9                26 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                9                26 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                3                32 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                3                32 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                31 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                31 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                32 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                32 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               10                25 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               10                25 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                9                26 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                9                26 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4                31 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4                31 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4                31 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4                31 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 32 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 32 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 30 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 30 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 9                 26 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 9                 26 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                 31 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                 31 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 29 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 29 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                 32 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                 32 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 29 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 29 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 29 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 29 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 32 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 32 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                 26 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                 26 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                 25 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                 25 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                 32 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                 32 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                 28 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                 28 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                31 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                31 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                32 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                32 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                32 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                32 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                4                31 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                4                31 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                6                29 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                6                29 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                32 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                32 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 29 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 29 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 31 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 31 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 4                 31 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 4                 31 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 3                 32 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 3                 32 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 32 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 32 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                31 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                31 
[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] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[12] "RADIATIONTHERAPY"                      
[13] "HISTOLOGICALTYPE"                      
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"
[15] "RACE"                                  
[16] "ETHNICITY"                             
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 35 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
         132          132          456            6            6          410 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
          22           25           NA         1081          946          965 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
         751          126          832          679          298           NA 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
         791          385          139           NA         1581         1441 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
          NA           NA         3227         5980         4578         2983 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
        1099         1299         1334         1739          788 
Variable 1:'AGE':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=29,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=5,	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 35 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=26, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1Q GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    4  0
  1Q GAIN WILD-TYPE 25  5
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                30 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                0                 5 
$`1Q GAIN MUTATED`
TCGA-FM-8000 TCGA-G8-6325 TCGA-GR-7353 TCGA-GR-A4D9 
        4.57        51.98        98.07        57.17 

$`1Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        14.99         0.20         0.20        13.48 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        0.72         0.82        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       12.66        41.16        47.38       211.23        19.56       106.09 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-RQ-A68N 
      196.60       150.51        36.13        42.71        43.86        25.91 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             4.57              0.20 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            98.07            211.23 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           54.575            25.300 
[1] "4.6 - 98.1 (54.6)"  "0.2 - 211.2 (25.3)"
[1] "hr="     "2.6e+08"
D1V2, continuous
D1V3, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    2  2
  1Q GAIN WILD-TYPE 16 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2    2
  1Q GAIN WILD-TYPE   16   15
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               2                16
  MALE                 2                15
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       0                         0     4
  1Q GAIN WILD-TYPE    18                         1    12
D1V4, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   0                18
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                12
[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 = 2P GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    3  0
  2P GAIN WILD-TYPE 26  5
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3                31 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                0                 5 
$`2P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A82F TCGA-FF-8041 
       14.99         0.82        35.54 

$`2P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         0.20         0.20        13.48         0.72 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        36.13        42.71        43.86        57.17 
TCGA-RQ-A68N 
       25.91 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.82              0.20 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            35.54            211.23 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            14.99             26.01 
[1] "0.8 - 35.5 (15.0)"  "0.2 - 211.2 (26.0)"
[1] "hr="     "2.7e+07"
D2V2, continuous
D2V3, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    2  1
  2P GAIN WILD-TYPE 16 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2    1
  2P GAIN WILD-TYPE   16   16
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               2                16
  MALE                 1                16
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       3                         0     0
  2P GAIN WILD-TYPE    15                         1    16
D2V4, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   0                16
[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 = 2Q GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    3  0
  2Q GAIN WILD-TYPE 26  5
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                3                31 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                0                 5 
$`2Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A82F TCGA-FF-8041 
       14.99         0.82        35.54 

$`2Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         0.20         0.20        13.48         0.72 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        36.13        42.71        43.86        57.17 
TCGA-RQ-A68N 
       25.91 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.82              0.20 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            35.54            211.23 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            14.99             26.01 
[1] "0.8 - 35.5 (15.0)"  "0.2 - 211.2 (26.0)"
[1] "hr="     "2.7e+07"
D3V2, continuous
D3V3, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    2  1
  2Q GAIN WILD-TYPE 16 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2    1
  2Q GAIN WILD-TYPE   16   16
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               2                16
  MALE                 1                16
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       3                         0     0
  2Q GAIN WILD-TYPE    15                         1    16
D3V4, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   0                16
[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 = 3P GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    7  0
  3P GAIN WILD-TYPE 22  5
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                7                27 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                0                 5 
$`3P GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-A7CW TCGA-G8-6914 TCGA-GR-A4D6 
        0.20         0.82        31.10        26.01       196.60        43.86 
TCGA-RQ-A68N 
       25.91 

$`3P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        9.80        10.29        12.66         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 
       47.38       211.23        19.56       106.09       150.51        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
       36.13        42.71        57.17 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              0.2               0.2 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           196.60            211.23 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            26.01             24.69 
[1] "0.2 - 196.6 (26.0)" "0.2 - 211.2 (24.7)"
[1] "hr="     "2.7e+08"
D4V2, continuous
D4V3, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    4  3
  3P GAIN WILD-TYPE 14 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4    3
  3P GAIN WILD-TYPE   14   14
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               4                14
  MALE                 3                14
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       5                         0     2
  3P GAIN WILD-TYPE    13                         1    14
D4V4, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   5                13
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   2                14
[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 = 3Q GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    8  0
  3Q GAIN WILD-TYPE 21  5
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                26 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                0                 5 
$`3Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-A7CW TCGA-G8-6914 
        0.20         0.82        31.10         4.14        26.01       196.60 
TCGA-GR-A4D6 TCGA-RQ-A68N 
       43.86        25.91 

$`3Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       35.54        31.73        24.69        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       10.29        12.66         4.57        41.16        51.98        47.38 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 
      211.23        19.56       106.09       150.51        98.07        36.13 
TCGA-GR-A4D5 TCGA-GR-A4D9 
       42.71        57.17 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              0.2               0.2 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           196.60            211.23 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            25.96             26.02 
[1] "0.2 - 196.6 (26.0)" "0.2 - 211.2 (26.0)"
[1] "hr="     "2.7e+08"
D5V2, continuous
D5V3, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    6  3
  3Q GAIN WILD-TYPE 12 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6    3
  3Q GAIN WILD-TYPE   12   14
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               6                12
  MALE                 3                14
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       6                         0     3
  3Q GAIN WILD-TYPE    12                         1    13
D5V4, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   6                12
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                13
[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 = 5P GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    2  1
  5P GAIN WILD-TYPE 27  4
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                3                31 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                 4 
$`5P GAIN MUTATED`
TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-G8-6909 
        0.72        35.54       106.09 

$`5P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        14.99         0.20         0.20        13.48 
TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
        0.82        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 
       41.16        51.98        47.38       211.23        19.56       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        36.13        42.71        43.86        57.17 
TCGA-RQ-A68N 
       25.91 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.72              0.20 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           106.09            211.23 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            35.54             25.91 
[1] "0.7 - 106.1 (35.5)" "0.2 - 211.2 (25.9)"
[1] "hr=" "2.4"
D6V2, continuous
D6V3, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    2  1
  5P GAIN WILD-TYPE 16 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    1
  5P GAIN WILD-TYPE   16   16
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               2                16
  MALE                 1                16
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       2                         0     1
  5P GAIN WILD-TYPE    16                         1    15
D6V4, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   2                16
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   1                15
[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 = 6P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    4  0
  6P GAIN WILD-TYPE 25  5
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                30 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                0                 5 
$`6P GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-G8-6325 
        0.20         0.82        31.10        51.98 

$`6P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66         4.57        41.16 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       106.09       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
       98.07        36.13        42.71        43.86        57.17        25.91 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              0.2               0.2 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            51.98            211.23 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            15.96             25.96 
[1] "0.2 - 52.0 (16.0)"  "0.2 - 211.2 (26.0)"
[1] "hr="     "7.6e+07"
D7V2, continuous
D7V3, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    3  1
  6P GAIN WILD-TYPE 15 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3    1
  6P GAIN WILD-TYPE   15   16
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               3                15
  MALE                 1                16
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       3                         0     1
  6P GAIN WILD-TYPE    15                         1    15
D7V4, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   1                15
[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 = 6Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    3  0
  6Q GAIN WILD-TYPE 26  5
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                31 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                0                 5 
$`6Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 
        0.20         0.82        31.10 

$`6Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        36.13        42.71        43.86        57.17 
TCGA-RQ-A68N 
       25.91 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              0.2               0.2 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            31.10            211.23 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.82             26.01 
[1] "0.2 - 31.1 (0.8)"   "0.2 - 211.2 (26.0)"
[1] "hr="     "2.6e+07"
D8V2, continuous
D8V3, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    3  0
  6Q GAIN WILD-TYPE 15 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    0
  6Q GAIN WILD-TYPE   15   17
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               3                15
  MALE                 0                17
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       3                         0     0
  6Q GAIN WILD-TYPE    15                         1    16
D8V4, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   0                16
[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 = 7P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   10  0
  7P GAIN WILD-TYPE 19  5
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               10                24 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 5 
$`7P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-A7CW TCGA-FM-8000 
       14.99         0.20         0.82        31.10        26.01         4.57 
TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
      196.60        98.07        36.13        43.86 

$`7P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FF-8041 
        4.34         4.34         0.20        13.48         0.72        35.54 
TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.73        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       10.29        12.66        41.16        51.98        47.38       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-RQ-A68N 
       19.56       106.09       150.51        42.71        57.17        25.91 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              0.2               0.2 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           196.60            211.23 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           28.555            25.300 
[1] "0.2 - 196.6 (28.6)" "0.2 - 211.2 (25.3)"
[1] "hr="   "3e+08"
D9V2, continuous
D9V3, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    6  4
  7P GAIN WILD-TYPE 12 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6    4
  7P GAIN WILD-TYPE   12   13
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               6                12
  MALE                 4                13
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       6                         0     4
  7P GAIN WILD-TYPE    12                         1    12
D9V4, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   6                12
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                12
[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 = 7Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED    9  0
  7Q GAIN WILD-TYPE 20  5
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                9                25 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 5 
$`7Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-A7CW TCGA-FM-8000 
       14.99         0.20         0.82        31.10        26.01         4.57 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
       98.07        36.13        43.86 

$`7Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FF-8041 
        4.34         4.34         0.20        13.48         0.72        35.54 
TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.73        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       10.29        12.66        41.16        51.98        47.38       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 
       19.56       106.09       196.60       150.51        42.71        57.17 
TCGA-RQ-A68N 
       25.91 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              0.2               0.2 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            98.07            211.23 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            26.01             25.91 
[1] "0.2 - 98.1 (26.0)"  "0.2 - 211.2 (25.9)"
[1] "hr="     "2.7e+08"
D10V2, continuous
D10V3, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    6  3
  7Q GAIN WILD-TYPE 12 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      6    3
  7Q GAIN WILD-TYPE   12   14
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               6                12
  MALE                 3                14
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       6                         0     3
  7Q GAIN WILD-TYPE    12                         1    13
D10V4, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   6                12
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                13
[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 = 9P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    4  0
  9P GAIN WILD-TYPE 25  5
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4                30 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                 5 
$`9P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-A7CQ TCGA-FF-A7CW 
       14.99        35.54         9.80        26.01 

$`9P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         0.20         0.20        13.48         0.72 
TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
        0.82        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       22.32        10.29        12.66         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       106.09       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
       98.07        36.13        42.71        43.86        57.17        25.91 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              9.8               0.2 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            35.54            211.23 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            20.50             26.63 
[1] "9.8 - 35.5 (20.5)"  "0.2 - 211.2 (26.6)"
[1] "hr="     "7.9e+07"
D11V2, continuous
D11V3, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    1  3
  9P GAIN WILD-TYPE 17 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1    3
  9P GAIN WILD-TYPE   17   14
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               1                17
  MALE                 3                14
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       4                         0     0
  9P GAIN WILD-TYPE    14                         1    16
D11V4, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   4                14
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   0                16
[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 = 9Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    4  0
  9Q GAIN WILD-TYPE 25  5
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4                30 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                 5 
$`9Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-A7CQ TCGA-FF-A7CW 
       14.99        35.54         9.80        26.01 

$`9Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         0.20         0.20        13.48         0.72 
TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
        0.82        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       22.32        10.29        12.66         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       106.09       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
       98.07        36.13        42.71        43.86        57.17        25.91 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              9.8               0.2 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            35.54            211.23 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            20.50             26.63 
[1] "9.8 - 35.5 (20.5)"  "0.2 - 211.2 (26.6)"
[1] "hr="     "7.9e+07"
D12V2, continuous
D12V3, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    1  3
  9Q GAIN WILD-TYPE 17 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1    3
  9Q GAIN WILD-TYPE   17   14
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               1                17
  MALE                 3                14
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       4                         0     0
  9Q GAIN WILD-TYPE    14                         1    16
D12V4, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   4                14
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   0                16
[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 = 10P GAIN MUTATION ANALYSIS
D13V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    3  0
  10P GAIN WILD-TYPE 26  5
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 31 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  5 
$`10P GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-GR-A4D4 
        0.20         0.82        36.13 

$`10P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       35.54        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       211.23        19.56       106.09 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60       150.51        98.07        42.71        43.86        57.17 
TCGA-RQ-A68N 
       25.91 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               0.2                0.2 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             36.13             211.23 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.82              26.01 
[1] "0.2 - 36.1 (0.8)"   "0.2 - 211.2 (26.0)"
[1] "hr="     "2.6e+07"
D13V2, continuous
D13V3, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    3  0
  10P GAIN WILD-TYPE 15 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3    0
  10P GAIN WILD-TYPE   15   17
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                3                 15
  MALE                  0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       2                         0     1
  10P GAIN WILD-TYPE    16                         1    15
D13V4, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 15
[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(14) Variable = 11P GAIN MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    5  0
  11P GAIN WILD-TYPE 24  5
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 29 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                  5 
$`11P GAIN MUTATED`
TCGA-FA-A82F TCGA-FF-8043 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-RQ-A68N 
        0.82        31.73        42.71        57.17        25.91 

$`11P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        14.99         0.20         0.20        13.48 
TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
        0.72        35.54        31.10        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       211.23        19.56       106.09 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
      196.60       150.51        98.07        36.13        43.86 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.82               0.20 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             57.17             211.23 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             31.73              24.69 
[1] "0.8 - 57.2 (31.7)"  "0.2 - 211.2 (24.7)"
[1] "hr="     "2.4e+08"
D14V2, continuous
D14V3, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    4  1
  11P GAIN WILD-TYPE 14 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4    1
  11P GAIN WILD-TYPE   14   16
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                4                 14
  MALE                  1                 16
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       2                         0     3
  11P GAIN WILD-TYPE    16                         1    13
D14V4, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 13
[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(15) Variable = 11Q GAIN MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    9  0
  11Q GAIN WILD-TYPE 20  5
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 9                 25 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                  5 
$`11Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8043 TCGA-GR-7351 TCGA-GR-7353 
       14.99         0.82        35.54        31.73       150.51        98.07 
TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-RQ-A68N 
       42.71        57.17        25.91 

$`11Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         0.20         0.20        13.48         0.72 
TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.10        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       10.29        26.01        12.66         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-A4D4 
       47.38       211.23        19.56       106.09       196.60        36.13 
TCGA-GR-A4D6 
       43.86 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.82               0.20 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            150.51             211.23 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             35.54              22.32 
[1] "0.8 - 150.5 (35.5)" "0.2 - 211.2 (22.3)"
[1] "hr="     "9.2e+08"
D15V2, continuous
D15V3, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    6  3
  11Q GAIN WILD-TYPE 12 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    3
  11Q GAIN WILD-TYPE   12   14
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                6                 12
  MALE                  3                 14
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       4                         0     5
  11Q GAIN WILD-TYPE    14                         1    11
D15V4, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    4                 14
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 11
[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(16) Variable = 12P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    4  0
  12P GAIN WILD-TYPE 25  5
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                 30 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  5 
$`12P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-GR-A4D5 
       14.99         0.72        35.54        42.71 

$`12P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F 
        4.34         4.34         0.20         0.20        13.48         0.82 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
      150.51        98.07        36.13        43.86        57.17        25.91 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.72               0.20 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             42.71             211.23 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            25.265             25.960 
[1] "0.7 - 42.7 (25.3)"  "0.2 - 211.2 (26.0)"
[1] "hr="     "7.8e+07"
D16V2, continuous
D16V3, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    3  1
  12P GAIN WILD-TYPE 15 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3    1
  12P GAIN WILD-TYPE   15   16
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                3                 15
  MALE                  1                 16
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       3                         0     1
  12P GAIN WILD-TYPE    15                         1    15
D16V4, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 15
[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(17) Variable = 12Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    5  1
  12Q GAIN WILD-TYPE 24  4
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 28 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                  4 
$`12Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-FF-A7CR TCGA-GR-A4D5 TCGA-RQ-A68N 
       14.99         0.72        35.54        10.29        42.71        25.91 

$`12Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F 
        4.34         4.34         0.20         0.20        13.48         0.82 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        9.80        26.01        12.66         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       106.09       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 
       98.07        36.13        43.86        57.17 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.72               0.20 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             42.71             211.23 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             20.45              26.68 
[1] "0.7 - 42.7 (20.4)"  "0.2 - 211.2 (26.7)"
[1] "hr=" "3"  
D17V2, continuous
D17V3, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    3  3
  12Q GAIN WILD-TYPE 15 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3    3
  12Q GAIN WILD-TYPE   15   14
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                3                 15
  MALE                  3                 14
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       4                         0     2
  12Q GAIN WILD-TYPE    14                         1    14
D17V4, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    4                 14
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 14
[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(18) Variable = 13Q GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    3  0
  13Q GAIN WILD-TYPE 26  5
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                 31 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                  5 
$`13Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-FF-8046 TCGA-FF-A7CX 
        0.20        24.69        12.66 

$`13Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 
        0.82        35.54        31.10        31.73         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FM-8000 TCGA-G8-6324 
       22.32         9.80        10.29        26.01         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        36.13        42.71        43.86        57.17 
TCGA-RQ-A68N 
       25.91 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               0.2                0.2 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             24.69             211.23 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             12.66              27.35 
[1] "0.2 - 24.7 (12.7)"  "0.2 - 211.2 (27.4)"
[1] "hr="     "2.7e+07"
D18V2, continuous
D18V3, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    1  2
  13Q GAIN WILD-TYPE 17 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1    2
  13Q GAIN WILD-TYPE   17   15
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                1                 17
  MALE                  2                 15
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       3                         0     0
  13Q GAIN WILD-TYPE    15                         1    16
D18V4, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    0                 16
[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(19) Variable = 16P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    6  0
  16P GAIN WILD-TYPE 23  5
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 28 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 0                  5 
$`16P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FM-8000 TCGA-GR-A4D4 TCGA-RQ-A68N 
       14.99         0.72         0.82         4.57        36.13        25.91 

$`16P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FF-8041 
        4.34         4.34         0.20         0.20        13.48        35.54 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 
        9.80        10.29        26.01        12.66        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       106.09       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       98.07        42.71        43.86        57.17 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.72               0.20 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             36.13             211.23 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             9.780             29.225 
[1] "0.7 - 36.1 (9.8)"   "0.2 - 211.2 (29.2)"
[1] "hr="     "7.9e+07"
D19V2, continuous
D19V3, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    4  2
  16P GAIN WILD-TYPE 14 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    2
  16P GAIN WILD-TYPE   14   15
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                4                 14
  MALE                  2                 15
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       3                         0     3
  16P GAIN WILD-TYPE    15                         1    13
D19V4, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 13
[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(20) Variable = 16Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    5  1
  16Q GAIN WILD-TYPE 24  4
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 28 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  4 
$`16Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FM-8000 TCGA-G8-6909 TCGA-RQ-A68N 
       14.99         0.72         0.82         4.57       106.09        25.91 

$`16Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FF-8041 
        4.34         4.34         0.20         0.20        13.48        35.54 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 
        9.80        10.29        26.01        12.66        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
       47.38       211.23        19.56       196.60       150.51        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       36.13        42.71        43.86        57.17 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.72               0.20 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            106.09             211.23 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             9.780             29.225 
[1] "0.7 - 106.1 (9.8)"  "0.2 - 211.2 (29.2)"
[1] "hr=" "2.1"
D20V2, continuous
D20V3, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  3
  16Q GAIN WILD-TYPE 15 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    3
  16Q GAIN WILD-TYPE   15   14
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                 15
  MALE                  3                 14
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       3                         0     3
  16Q GAIN WILD-TYPE    15                         1    13
D20V4, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 13
[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(21) Variable = 17Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    3  0
  17Q GAIN WILD-TYPE 26  5
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 31 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 0                  5 
$`17Q GAIN MUTATED`
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 
        0.72         0.82        35.54 

$`17Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        14.99         0.20         0.20        13.48 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        36.13        42.71        43.86        57.17 
TCGA-RQ-A68N 
       25.91 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.72               0.20 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             35.54             211.23 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.82              26.01 
[1] "0.7 - 35.5 (0.8)"   "0.2 - 211.2 (26.0)"
[1] "hr="     "2.6e+07"
D21V2, continuous
D21V3, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    3  0
  17Q GAIN WILD-TYPE 15 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    0
  17Q GAIN WILD-TYPE   15   17
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                3                 15
  MALE                  0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       3                         0     0
  17Q GAIN WILD-TYPE    15                         1    16
D21V4, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    0                 16
[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(22) Variable = 18P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    9  0
  18P GAIN WILD-TYPE 20  5
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                 25 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                  5 
$`18P GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-A7CQ 
        0.20        13.48         0.82        31.10        31.73         9.80 
TCGA-FF-A7CW TCGA-G8-6914 TCGA-GR-A4D6 
       26.01       196.60        43.86 

$`18P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FF-8041 
        4.34         4.34        14.99         0.20         0.72        35.54 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CX 
       24.69         4.14        27.35        22.32        10.29        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
        4.57        41.16        51.98        47.38       211.23        19.56 
TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
      106.09       150.51        98.07        36.13        42.71        57.17 
TCGA-RQ-A68N 
       25.91 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               0.2                0.2 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            196.60             211.23 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             26.01              25.91 
[1] "0.2 - 196.6 (26.0)" "0.2 - 211.2 (25.9)"
[1] "hr="     "2.7e+08"
D22V2, continuous
D22V3, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    6  3
  18P GAIN WILD-TYPE 12 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6    3
  18P GAIN WILD-TYPE   12   14
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                6                 12
  MALE                  3                 14
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       8                         0     1
  18P GAIN WILD-TYPE    10                         1    15
D22V4, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    8                 10
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 15
[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(23) Variable = 18Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED   10  0
  18Q GAIN WILD-TYPE 19  5
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                 24 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                  5 
$`18Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 
       14.99         0.20        13.48         0.82        31.10        31.73 
TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-G8-6914 TCGA-GR-A4D6 
        9.80        26.01       196.60        43.86 

$`18Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-FF-8046 
        4.34         4.34         0.20         0.72        35.54        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 
        4.14        27.35        22.32        10.29        12.66         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       211.23        19.56       106.09 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-RQ-A68N 
      150.51        98.07        36.13        42.71        57.17        25.91 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               0.2                0.2 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            196.60             211.23 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             20.50              26.63 
[1] "0.2 - 196.6 (20.5)" "0.2 - 211.2 (26.6)"
[1] "hr="     "2.8e+08"
D23V2, continuous
D23V3, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    6  4
  18Q GAIN WILD-TYPE 12 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6    4
  18Q GAIN WILD-TYPE   12   13
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                6                 12
  MALE                  4                 13
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       9                         0     1
  18Q GAIN WILD-TYPE     9                         1    15
D23V4, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    9                  9
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 15
[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(24) Variable = 20P GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    3  0
  20P GAIN WILD-TYPE 26  5
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                 31 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 0                  5 
$`20P GAIN MUTATED`
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8043 
        0.82        35.54        31.73 

$`20P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        14.99         0.20         0.20        13.48 
TCGA-FA-A7Q1 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
        0.72        31.10        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        36.13        42.71        43.86        57.17 
TCGA-RQ-A68N 
       25.91 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.82               0.20 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             35.54             211.23 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             31.73              25.91 
[1] "0.8 - 35.5 (31.7)"  "0.2 - 211.2 (25.9)"
[1] "hr="     "7.6e+07"
D24V2, continuous
D24V3, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    3  0
  20P GAIN WILD-TYPE 15 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3    0
  20P GAIN WILD-TYPE   15   17
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                3                 15
  MALE                  0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       3                         0     0
  20P GAIN WILD-TYPE    15                         1    16
D24V4, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    0                 16
[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(25) Variable = 21Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    6  1
  21Q GAIN WILD-TYPE 23  4
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                 27 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                  4 
$`21Q GAIN MUTATED`
TCGA-FA-A4BB TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8043 TCGA-G8-6909 TCGA-GR-7351 
        4.34         0.82        35.54        31.73       106.09       150.51 
TCGA-GR-7353 
       98.07 

$`21Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        14.99         0.20         0.20        13.48         0.72 
TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.10        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       10.29        26.01        12.66         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-A4D4 TCGA-GR-A4D5 
       47.38       211.23        19.56       196.60        36.13        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
       43.86        57.17        25.91 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.82               0.20 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            150.51             211.23 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             35.54              24.69 
[1] "0.8 - 150.5 (35.5)" "0.2 - 211.2 (24.7)"
[1] "hr=" "1.3"
D25V2, continuous
D25V3, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    4  3
  21Q GAIN WILD-TYPE 14 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4    3
  21Q GAIN WILD-TYPE   14   14
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                4                 14
  MALE                  3                 14
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       3                         0     4
  21Q GAIN WILD-TYPE    15                         1    12
D25V4, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 12
[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(26) Variable = XQ GAIN MUTATION ANALYSIS
D26V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    4  0
  XQ GAIN WILD-TYPE 25  5
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                30 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                 5 
$`XQ GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-A7CW TCGA-RQ-A68N 
       14.99        35.54        26.01        25.91 

$`XQ GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         0.20         0.20        13.48         0.72 
TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
        0.82        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
       22.32         9.80        10.29        12.66         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        36.13        42.71        43.86        57.17 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            14.99              0.20 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            35.54            211.23 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            25.96             26.02 
[1] "15.0 - 35.5 (26.0)" "0.2 - 211.2 (26.0)"
[1] "hr="     "8.6e+07"
D26V2, continuous
D26V3, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    1  3
  XQ GAIN WILD-TYPE 17 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1    3
  XQ GAIN WILD-TYPE   17   14
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               1                17
  MALE                 3                14
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       3                         0     1
  XQ GAIN WILD-TYPE    15                         1    15
D26V4, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   1                15
[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(27) Variable = 1P LOSS MUTATION ANALYSIS
D27V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    3  0
  1P LOSS WILD-TYPE 26  5
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                31 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                0                 5 
$`1P LOSS MUTATED`
TCGA-FA-A6HO TCGA-G8-6325 TCGA-RQ-A68N 
        0.20        51.98        25.91 

$`1P LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
        0.82        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
        4.57        41.16        47.38       211.23        19.56       106.09 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        36.13        42.71        43.86 
TCGA-GR-A4D9 
       57.17 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              0.2               0.2 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            51.98            211.23 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            25.91             26.01 
[1] "0.2 - 52.0 (25.9)"  "0.2 - 211.2 (26.0)"
[1] "hr="     "7.6e+07"
D27V2, continuous
D27V3, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  2
  1P LOSS WILD-TYPE 17 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    2
  1P LOSS WILD-TYPE   17   15
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               1                17
  MALE                 2                15
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         0     2
  1P LOSS WILD-TYPE    17                         1    14
D27V4, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   2                14
[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(28) Variable = 4Q LOSS MUTATION ANALYSIS
D28V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    2  0
  4Q LOSS WILD-TYPE 27  5
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                32 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                0                 5 
$`4Q LOSS MUTATED`
TCGA-FF-8043 TCGA-FF-8047 
       31.73         4.14 

$`4Q LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        14.99         0.20         0.20        13.48 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 
        0.72         0.82        35.54        31.10        24.69        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       211.23        19.56       106.09 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        36.13        42.71        43.86 
TCGA-GR-A4D9 TCGA-RQ-A68N 
       57.17        25.91 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             4.14              0.20 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            31.73            211.23 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           17.935            25.960 
[1] "4.1 - 31.7 (17.9)"  "0.2 - 211.2 (26.0)"
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
D28V2, continuous
D28V3, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    3  0
  4Q LOSS WILD-TYPE 15 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3    0
  4Q LOSS WILD-TYPE   15   17
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               3                15
  MALE                 0                17
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       2                         0     1
  4Q LOSS WILD-TYPE    16                         1    15
D28V4, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   2                16
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   1                15
[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(29) Variable = 6Q LOSS MUTATION ANALYSIS
D29V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    3  1
  6Q LOSS WILD-TYPE 26  4
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                4                30 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                1                 4 
$`6Q LOSS MUTATED`
TCGA-FF-A7CX TCGA-G8-6906 TCGA-GR-A4D5 TCGA-RQ-A68N 
       12.66       211.23        42.71        25.91 

$`6Q LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        14.99         0.20         0.20        13.48 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        0.72         0.82        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6909 
        4.57        41.16        51.98        47.38        19.56       106.09 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60       150.51        98.07        36.13        43.86        57.17 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            12.66              0.20 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           211.23            196.60 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            34.31             25.35 
[1] "12.7 - 211.2 (34.3)" "0.2 - 196.6 (25.4)" 
[1] "hr="     "2.5e+08"
D29V2, continuous
D29V3, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    1  3
  6Q LOSS WILD-TYPE 17 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1    3
  6Q LOSS WILD-TYPE   17   14
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               1                17
  MALE                 3                14
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       1                         0     3
  6Q LOSS WILD-TYPE    17                         1    13
D29V4, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                13
[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(30) Variable = 8P LOSS MUTATION ANALYSIS
D30V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    5  0
  8P LOSS WILD-TYPE 24  5
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                5                29 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                 5 
$`8P LOSS MUTATED`
TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FF-8047 TCGA-GR-A4D6 TCGA-RQ-A68N 
        0.20         0.72         4.14        43.86        25.91 

$`8P LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A82F 
        4.34         4.34        14.99         0.20        13.48         0.82 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        31.73        24.69        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
      150.51        98.07        36.13        42.71        57.17 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              0.2               0.2 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            43.86            211.23 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             4.14             27.35 
[1] "0.2 - 43.9 (4.1)"   "0.2 - 211.2 (27.4)"
[1] "hr="     "7.6e+07"
D30V2, continuous
D30V3, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    5  1
  8P LOSS WILD-TYPE 13 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5    1
  8P LOSS WILD-TYPE   13   16
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               5                13
  MALE                 1                16
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       4                         0     2
  8P LOSS WILD-TYPE    14                         1    14
D30V4, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   4                14
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   2                14
[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(31) Variable = 8Q LOSS MUTATION ANALYSIS
D31V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    2  0
  8Q LOSS WILD-TYPE 27  5
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                32 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                 5 
$`8Q LOSS MUTATED`
TCGA-FA-A6HO TCGA-RQ-A68N 
        0.20        25.91 

$`8Q LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
        0.82        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
        4.57        41.16        51.98        47.38       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
      106.09       196.60       150.51        98.07        36.13        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 
       43.86        57.17 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
              0.2               0.2 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            25.91            211.23 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           13.055            26.680 
[1] "0.2 - 25.9 (13.1)"  "0.2 - 211.2 (26.7)"
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
D31V2, continuous
D31V3, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  1
  8Q LOSS WILD-TYPE 16 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    1
  8Q LOSS WILD-TYPE   16   16
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               2                16
  MALE                 1                16
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       1                         0     2
  8Q LOSS WILD-TYPE    17                         1    14
D31V4, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   2                14
[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(32) Variable = 15Q LOSS MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    5  0
  15Q LOSS WILD-TYPE 24  5
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 29 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 0                  5 
$`15Q LOSS MUTATED`
TCGA-FA-A6HO TCGA-FF-8043 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
        0.20        31.73        98.07        36.13        43.86 

$`15Q LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
        0.82        35.54        31.10        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       211.23        19.56       106.09 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-RQ-A68N 
      196.60       150.51        42.71        57.17        25.91 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               0.2                0.2 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             98.07             211.23 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             36.13              24.69 
[1] "0.2 - 98.1 (36.1)"  "0.2 - 211.2 (24.7)"
[1] "hr="     "2.4e+08"
D32V2, continuous
D32V3, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    5  1
  15Q LOSS WILD-TYPE 13 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5    1
  15Q LOSS WILD-TYPE   13   16
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                5                 13
  MALE                  1                 16
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       3                         0     3
  15Q LOSS WILD-TYPE    15                         1    13
D32V4, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 13
[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(33) Variable = 16Q LOSS MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    4  0
  16Q LOSS WILD-TYPE 25  5
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 30 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 0                  5 
$`16Q LOSS MUTATED`
TCGA-FA-A6HO TCGA-FF-8043 TCGA-FF-8047 TCGA-GR-A4D4 
        0.20        31.73         4.14        36.13 

$`16Q LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 
        0.82        35.54        31.10        24.69        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
      150.51        98.07        42.71        43.86        57.17        25.91 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               0.2                0.2 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             36.13             211.23 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            17.935             25.960 
[1] "0.2 - 36.1 (17.9)"  "0.2 - 211.2 (26.0)"
[1] "hr="     "7.6e+07"
D33V2, continuous
D33V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    4  0
  16Q LOSS WILD-TYPE 14 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4    0
  16Q LOSS WILD-TYPE   14   17
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                4                 14
  MALE                  0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       3                         0     1
  16Q LOSS WILD-TYPE    15                         1    15
D33V4, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 15
[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(34) Variable = 17P LOSS MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED    4  0
  17P LOSS WILD-TYPE 25  5
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 4                 30 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 0                  5 
$`17P LOSS MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-GR-A4D4 TCGA-RQ-A68N 
        0.20         0.82        36.13        25.91 

$`17P LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       35.54        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       211.23        19.56       106.09 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60       150.51        98.07        42.71        43.86        57.17 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               0.2                0.2 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             36.13             211.23 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            13.365             26.680 
[1] "0.2 - 36.1 (13.4)"  "0.2 - 211.2 (26.7)"
[1] "hr="     "7.6e+07"
D34V2, continuous
D34V3, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    3  1
  17P LOSS WILD-TYPE 15 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3    1
  17P LOSS WILD-TYPE   15   16
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                3                 15
  MALE                  1                 16
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       2                         0     2
  17P LOSS WILD-TYPE    16                         1    14
D34V4, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 14
[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(35) Variable = 18P LOSS MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    3  0
  18P LOSS WILD-TYPE 26  5
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 3                 31 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 0                  5 
$`18P LOSS MUTATED`
TCGA-FA-A4XK TCGA-FF-A7CX TCGA-G8-6325 
       14.99        12.66        51.98 

$`18P LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         0.20         0.20        13.48         0.72 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
        0.82        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FM-8000 
       27.35        22.32         9.80        10.29        26.01         4.57 
TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       41.16        47.38       211.23        19.56       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        36.13        42.71        43.86        57.17 
TCGA-RQ-A68N 
       25.91 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             12.66               0.20 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             51.98             211.23 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             14.99              26.01 
[1] "12.7 - 52.0 (15.0)" "0.2 - 211.2 (26.0)"
[1] "hr="     "7.7e+07"
D35V2, continuous
D35V3, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    0  3
  18P LOSS WILD-TYPE 18 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0    3
  18P LOSS WILD-TYPE   18   14
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                0                 18
  MALE                  3                 14
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       2                         0     1
  18P LOSS WILD-TYPE    16                         1    15
D35V4, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 15
[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(36) Variable = 22Q LOSS MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    3  0
  22Q LOSS WILD-TYPE 26  5
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 31 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 0                  5 
$`22Q LOSS MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8043 
        0.20         0.82        31.73 

$`22Q LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        36.13        42.71        43.86        57.17 
TCGA-RQ-A68N 
       25.91 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               0.2                0.2 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             31.73             211.23 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.82              26.01 
[1] "0.2 - 31.7 (0.8)"   "0.2 - 211.2 (26.0)"
[1] "hr="     "2.6e+07"
D36V2, continuous
D36V3, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    3  0
  22Q LOSS WILD-TYPE 15 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3    0
  22Q LOSS WILD-TYPE   15   17
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                3                 15
  MALE                  0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       3                         0     0
  22Q LOSS WILD-TYPE    15                         1    16
D36V4, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    0                 16
[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(37) Variable = XQ LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    3  1
  XQ LOSS WILD-TYPE 26  4
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                30 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                 4 
$`XQ LOSS MUTATED`
TCGA-FA-A7Q1 TCGA-FF-8043 TCGA-FF-8047 TCGA-G8-6907 
        0.72        31.73         4.14        19.56 

$`XQ LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        14.99         0.20         0.20        13.48 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 
        0.82        35.54        31.10        24.69        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       51.98        47.38       211.23       106.09       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
       98.07        36.13        42.71        43.86        57.17        25.91 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.72              0.20 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            31.73            211.23 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            11.85             26.68 
[1] "0.7 - 31.7 (11.8)"  "0.2 - 211.2 (26.7)"
[1] "hr=" "10" 
D37V2, continuous
D37V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    4  0
  XQ LOSS WILD-TYPE 14 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4    0
  XQ LOSS WILD-TYPE   14   17
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               4                14
  MALE                 0                17
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       3                         0     1
  XQ LOSS WILD-TYPE    15                         1    15
D37V4, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   1                15
[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"
