[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/10005821/DLBC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/10013677/transformed.cor.cli.txt"

nPatients in clinical file=33, in cluster file=28, common to both=25
[1] "Reduce the number of clustering variables from 80 to 20."
[1] 20 25
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                21 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                21 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                21 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                21 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                20 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                20 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                22 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                22 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                8                17 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                8                17 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                7                18 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                7                18 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 22 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 22 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 22 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 22 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                 18 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                 18 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 22 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 22 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 22 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 22 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 22 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 22 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 22 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 22 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                 20 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                 20 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 20 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 20 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 19 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 19 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                22 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                22 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 20 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 20 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 21 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 21 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                22 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                22 
[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 25 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8041 
         132          132          456            6            6         1081 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 
         946          965          126          832          679          139 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
          NA         1581         1441           NA           NA         3227 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
        5980         3872         2254          812          751          911 
TCGA-GR-A4D9 
        1408 
Variable 1:'AGE':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=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=2,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=3,	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 25 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=19, 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 17  4
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                21 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                0                 4 
$`1Q GAIN MUTATED`
TCGA-FM-8000 TCGA-G8-6325 TCGA-GR-7353 TCGA-GR-A4D9 
        4.57        51.98        74.10        46.29 

$`1Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8041 
        4.34         4.34        14.99         0.20         0.20        35.54 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-G8-6324 
       31.10        31.73         4.14        27.35        22.32        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       127.30 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       26.70        24.69        29.95 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             4.57              0.20 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            74.10            211.23 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           49.135            27.350 
[1] "4.6 - 74.1 (49.1)"  "0.2 - 211.2 (27.4)"
[1] "hr="     "3.1e+08"
D1V2, continuous
D1V3, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    2  2
  1Q GAIN WILD-TYPE 12  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2    2
  1Q GAIN WILD-TYPE   12    9
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               2                12
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       0                         0     4
  1Q GAIN WILD-TYPE    10                         1    10
D1V4, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   0                10
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                10
[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 = 3P GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    4  0
  3P GAIN WILD-TYPE 17  4
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                21 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                0                 4 
$`3P GAIN MUTATED`
TCGA-FA-A6HO TCGA-FF-8042 TCGA-G8-6914 TCGA-GR-A4D6 
        0.20        31.10       196.60        29.95 

$`3P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8043 
        4.34         4.34        14.99         0.20        35.54        31.73 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        4.14        27.35        22.32         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       127.30        74.10 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
       26.70        24.69        46.29 

  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 
           30.525            27.350 
[1] "0.2 - 196.6 (30.5)" "0.2 - 211.2 (27.4)"
[1] "hr="     "2.5e+08"
D2V2, continuous
D2V3, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3  1
  3P GAIN WILD-TYPE 11 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    1
  3P GAIN WILD-TYPE   11   10
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               3                11
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       3                         0     1
  3P GAIN WILD-TYPE     7                         1    13
D2V4, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   3                 7
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   1                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(3) Variable = 3Q GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    5  0
  3Q GAIN WILD-TYPE 16  4
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                20 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                0                 4 
$`3Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-FF-8042 TCGA-FF-8047 TCGA-G8-6914 TCGA-GR-A4D6 
        0.20        31.10         4.14       196.60        29.95 

$`3Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8043 
        4.34         4.34        14.99         0.20        35.54        31.73 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       27.35        22.32         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       127.30        74.10        26.70 
TCGA-GR-A4D5 TCGA-GR-A4D9 
       24.69        46.29 

  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 
            29.95             29.54 
[1] "0.2 - 196.6 (29.9)" "0.2 - 211.2 (29.5)"
[1] "hr="     "2.5e+08"
D3V2, continuous
D3V3, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    4  1
  3Q GAIN WILD-TYPE 10 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4    1
  3Q GAIN WILD-TYPE   10   10
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               4                10
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       4                         0     1
  3Q GAIN WILD-TYPE     6                         1    13
D3V4, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   4                 6
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   1                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(4) Variable = 6P GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    3  0
  6P GAIN WILD-TYPE 18  4
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                22 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                0                 4 
$`6P GAIN MUTATED`
TCGA-FA-A6HO TCGA-FF-8042 TCGA-G8-6325 
        0.20        31.10        51.98 

$`6P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8043 
        4.34         4.34        14.99         0.20        35.54        31.73 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 
        4.14        27.35        22.32         4.57        41.16        47.38 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
      211.23        19.56       106.09       196.60       127.30        74.10 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       26.70        24.69        29.95        46.29 

  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 
            31.10             28.65 
[1] "0.2 - 52.0 (31.1)"  "0.2 - 211.2 (28.6)"
[1] "hr="     "7.9e+07"
D4V2, continuous
D4V3, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    2  1
  6P GAIN WILD-TYPE 12 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    1
  6P GAIN WILD-TYPE   12   10
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               2                12
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       2                         0     1
  6P GAIN WILD-TYPE     8                         1    13
D4V4, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   2                 8
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   1                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(5) Variable = 7P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED    8  0
  7P GAIN WILD-TYPE 13  4
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                8                17 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 4 
$`7P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FF-8042 TCGA-FM-8000 TCGA-G8-6914 TCGA-GR-7353 
       14.99         0.20        31.10         4.57       196.60        74.10 
TCGA-GR-A4D4 TCGA-GR-A4D6 
       26.70        29.95 

$`7P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8047 
        4.34         4.34         0.20        35.54        31.73         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       27.35        22.32        41.16        51.98        47.38       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 
       19.56       106.09       127.30        24.69        46.29 

  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 
           28.325            31.730 
[1] "0.2 - 196.6 (28.3)" "0.2 - 211.2 (31.7)"
[1] "hr="     "7.8e+08"
D5V2, continuous
D5V3, binary
                   cls
clus                0 1
  7P GAIN MUTATED   5 3
  7P GAIN WILD-TYPE 9 8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5    3
  7P GAIN WILD-TYPE    9    8
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               5                 9
  MALE                 3                 8
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       4                         0     4
  7P GAIN WILD-TYPE     6                         1    10
D5V4, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   4                 6
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                10
[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 = 7Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED    7  0
  7Q GAIN WILD-TYPE 14  4
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                7                18 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 4 
$`7Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FF-8042 TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D4 
       14.99         0.20        31.10         4.57        74.10        26.70 
TCGA-GR-A4D6 
       29.95 

$`7Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8047 
        4.34         4.34         0.20        35.54        31.73         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       27.35        22.32        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       127.30        24.69        46.29 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              0.2               0.2 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            74.10            211.23 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           26.700            33.635 
[1] "0.2 - 74.1 (26.7)"  "0.2 - 211.2 (33.6)"
[1] "hr="     "2.5e+08"
D6V2, continuous
D6V3, binary
                   cls
clus                0 1
  7Q GAIN MUTATED   5 2
  7Q GAIN WILD-TYPE 9 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5    2
  7Q GAIN WILD-TYPE    9    9
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               5                 9
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       4                         0     3
  7Q GAIN WILD-TYPE     6                         1    11
D6V4, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   4                 6
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                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(7) Variable = 10P GAIN MUTATION ANALYSIS
D7V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    3  0
  10P GAIN WILD-TYPE 18  4
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 22 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  4 
$`10P GAIN MUTATED`
TCGA-FA-A6HO TCGA-FF-8041 TCGA-GR-A4D4 
        0.20        35.54        26.70 

$`10P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8042 TCGA-FF-8043 
        4.34         4.34        14.99         0.20        31.10        31.73 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        4.14        27.35        22.32         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       127.30 
TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       74.10        24.69        29.95        46.29 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               0.2                0.2 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             35.54             211.23 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            26.700             30.525 
[1] "0.2 - 35.5 (26.7)"  "0.2 - 211.2 (30.5)"
[1] "hr="     "7.9e+07"
D7V2, continuous
D7V3, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    3  0
  10P GAIN WILD-TYPE 11 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3    0
  10P GAIN WILD-TYPE   11   11
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                3                 11
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       2                         0     1
  10P GAIN WILD-TYPE     8                         1    13
D7V4, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    2                  8
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 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(8) Variable = 11P GAIN MUTATION ANALYSIS
D8V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    3  0
  11P GAIN WILD-TYPE 18  4
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 22 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                  4 
$`11P GAIN MUTATED`
TCGA-FF-8043 TCGA-GR-A4D5 TCGA-GR-A4D9 
       31.73        24.69        46.29 

$`11P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8041 
        4.34         4.34        14.99         0.20         0.20        35.54 
TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 
       31.10         4.14        27.35        22.32         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 
      127.30        74.10        26.70        29.95 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             24.69               0.20 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             46.29             211.23 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             31.73              28.65 
[1] "24.7 - 46.3 (31.7)" "0.2 - 211.2 (28.6)"
[1] "hr="     "2.3e+08"
D8V2, continuous
D8V3, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  0
  11P GAIN WILD-TYPE 11 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    0
  11P GAIN WILD-TYPE   11   11
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                3                 11
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       1                         0     2
  11P GAIN WILD-TYPE     9                         1    12
D8V4, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    1                  9
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 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(9) Variable = 11Q GAIN MUTATION ANALYSIS
D9V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    7  0
  11Q GAIN WILD-TYPE 14  4
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                 18 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                  4 
$`11Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8043 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 
       14.99        35.54        31.73       127.30        74.10        24.69 
TCGA-GR-A4D9 
       46.29 

$`11Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8042 TCGA-FF-8047 
        4.34         4.34         0.20         0.20        31.10         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       27.35        22.32         4.57        41.16        51.98        47.38 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-A4D4 TCGA-GR-A4D6 
      211.23        19.56       106.09       196.60        26.70        29.95 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             14.99               0.20 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            127.30             211.23 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            35.540             27.025 
[1] "15.0 - 127.3 (35.5)" "0.2 - 211.2 (27.0)" 
[1] "hr="   "9e+08"
D9V2, continuous
D9V3, binary
                    cls
clus                 0 1
  11Q GAIN MUTATED   5 2
  11Q GAIN WILD-TYPE 9 9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    2
  11Q GAIN WILD-TYPE    9    9
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                5                  9
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       3                         0     4
  11Q GAIN WILD-TYPE     7                         1    10
D9V4, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    3                  7
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 10
[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 = 12P GAIN MUTATION ANALYSIS
D10V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    3  0
  12P GAIN WILD-TYPE 18  4
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 22 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  4 
$`12P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-GR-A4D5 
       14.99        35.54        24.69 

$`12P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8042 TCGA-FF-8043 
        4.34         4.34         0.20         0.20        31.10        31.73 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        4.14        27.35        22.32         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       127.30 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 
       74.10        26.70        29.95        46.29 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             14.99               0.20 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             35.54             211.23 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            24.690             30.525 
[1] "15.0 - 35.5 (24.7)" "0.2 - 211.2 (30.5)"
[1] "hr="     "7.9e+07"
D10V2, continuous
D10V3, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    2  1
  12P GAIN WILD-TYPE 12 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    1
  12P GAIN WILD-TYPE   12   10
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                2                 12
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       2                         0     1
  12P GAIN WILD-TYPE     8                         1    13
D10V4, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    2                  8
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 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 = 12Q GAIN MUTATION ANALYSIS
D11V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    3  0
  12Q GAIN WILD-TYPE 18  4
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 22 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                  4 
$`12Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-GR-A4D5 
       14.99        35.54        24.69 

$`12Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8042 TCGA-FF-8043 
        4.34         4.34         0.20         0.20        31.10        31.73 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        4.14        27.35        22.32         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       127.30 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 
       74.10        26.70        29.95        46.29 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             14.99               0.20 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             35.54             211.23 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            24.690             30.525 
[1] "15.0 - 35.5 (24.7)" "0.2 - 211.2 (30.5)"
[1] "hr="     "7.9e+07"
D11V2, continuous
D11V3, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    2  1
  12Q GAIN WILD-TYPE 12 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2    1
  12Q GAIN WILD-TYPE   12   10
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                2                 12
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       2                         0     1
  12Q GAIN WILD-TYPE     8                         1    13
D11V4, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    2                  8
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 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(12) Variable = 16P GAIN MUTATION ANALYSIS
D12V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    3  0
  16P GAIN WILD-TYPE 18  4
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 22 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 0                  4 
$`16P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FM-8000 TCGA-GR-A4D4 
       14.99         4.57        26.70 

$`16P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8041 TCGA-FF-8042 
        4.34         4.34         0.20         0.20        35.54        31.10 
TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-G8-6324 TCGA-G8-6325 
       31.73         4.14        27.35        22.32        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       127.30 
TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       74.10        24.69        29.95        46.29 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              4.57               0.20 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             26.70             211.23 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            14.990             31.415 
[1] "4.6 - 26.7 (15.0)"  "0.2 - 211.2 (31.4)"
[1] "hr="     "2.6e+07"
D12V2, continuous
D12V3, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    2  1
  16P GAIN WILD-TYPE 12 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2    1
  16P GAIN WILD-TYPE   12   10
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                2                 12
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         0     2
  16P GAIN WILD-TYPE     9                         1    12
D12V4, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  9
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 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(13) Variable = 16Q GAIN MUTATION ANALYSIS
D13V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    2  1
  16Q GAIN WILD-TYPE 19  3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 22 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  3 
$`16Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FM-8000 TCGA-G8-6909 
       14.99         4.57       106.09 

$`16Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8041 TCGA-FF-8042 
        4.34         4.34         0.20         0.20        35.54        31.10 
TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-G8-6324 TCGA-G8-6325 
       31.73         4.14        27.35        22.32        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       127.30        74.10 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       26.70        24.69        29.95        46.29 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              4.57               0.20 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            106.09             211.23 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            14.990             30.525 
[1] "4.6 - 106.1 (15.0)" "0.2 - 211.2 (30.5)"
[1] "hr=" "3.4"
D13V2, continuous
D13V3, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    1  2
  16Q GAIN WILD-TYPE 13  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    2
  16Q GAIN WILD-TYPE   13    9
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                1                 13
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       1                         0     2
  16Q GAIN WILD-TYPE     9                         1    12
D13V4, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    1                  9
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 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(14) Variable = 18P GAIN MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    5  0
  18P GAIN WILD-TYPE 16  4
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                 20 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                  4 
$`18P GAIN MUTATED`
TCGA-FA-A6HO TCGA-FF-8042 TCGA-FF-8043 TCGA-G8-6914 TCGA-GR-A4D6 
        0.20        31.10        31.73       196.60        29.95 

$`18P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8047 
        4.34         4.34        14.99         0.20        35.54         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       27.35        22.32         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       127.30        74.10        26.70 
TCGA-GR-A4D5 TCGA-GR-A4D9 
       24.69        46.29 

  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 
            31.100             27.025 
[1] "0.2 - 196.6 (31.1)" "0.2 - 211.2 (27.0)"
[1] "hr="     "2.6e+08"
D14V2, continuous
D14V3, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    4  1
  18P GAIN WILD-TYPE 10 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    1
  18P GAIN WILD-TYPE   10   10
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                4                 10
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       4                         0     1
  18P GAIN WILD-TYPE     6                         1    13
D14V4, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    4                  6
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 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 = 18Q GAIN MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    5  0
  18Q GAIN WILD-TYPE 16  4
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 20 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                  4 
$`18Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-FF-8042 TCGA-FF-8043 TCGA-G8-6914 TCGA-GR-A4D6 
        0.20        31.10        31.73       196.60        29.95 

$`18Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8047 
        4.34         4.34        14.99         0.20        35.54         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       27.35        22.32         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       127.30        74.10        26.70 
TCGA-GR-A4D5 TCGA-GR-A4D9 
       24.69        46.29 

  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 
            31.100             27.025 
[1] "0.2 - 196.6 (31.1)" "0.2 - 211.2 (27.0)"
[1] "hr="     "2.6e+08"
D15V2, continuous
D15V3, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4  1
  18Q GAIN WILD-TYPE 10 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    1
  18Q GAIN WILD-TYPE   10   10
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                 10
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       4                         0     1
  18Q GAIN WILD-TYPE     6                         1    13
D15V4, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    4                  6
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 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(16) Variable = 21Q GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    5  1
  21Q GAIN WILD-TYPE 16  3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 19 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                  3 
$`21Q GAIN MUTATED`
TCGA-FA-A4BB TCGA-FF-8041 TCGA-FF-8043 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 
        4.34        35.54        31.73       106.09       127.30        74.10 

$`21Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8042 TCGA-FF-8047 
        4.34        14.99         0.20         0.20        31.10         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       27.35        22.32         4.57        41.16        51.98        47.38 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      211.23        19.56       196.60        26.70        24.69        29.95 
TCGA-GR-A4D9 
       46.29 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              4.34               0.20 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            127.30             211.23 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             54.82              26.70 
[1] "4.3 - 127.3 (54.8)" "0.2 - 211.2 (26.7)"
[1] "hr=" "1.2"
D16V2, continuous
D16V3, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    3  3
  21Q GAIN WILD-TYPE 11  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    3
  21Q GAIN WILD-TYPE   11    8
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                3                 11
  MALE                  3                  8
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       2                         0     4
  21Q GAIN WILD-TYPE     8                         1    10
D16V4, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    2                  8
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 10
[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 = 8P LOSS MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    3  0
  8P LOSS WILD-TYPE 18  4
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                22 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                 4 
$`8P LOSS MUTATED`
TCGA-FA-A6HO TCGA-FF-8047 TCGA-GR-A4D6 
        0.20         4.14        29.95 

$`8P LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8042 
        4.34         4.34        14.99         0.20        35.54        31.10 
TCGA-FF-8043 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       31.73        27.35        22.32         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       127.30 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
       74.10        26.70        24.69        46.29 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              0.2               0.2 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            29.95            211.23 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            4.140            31.415 
[1] "0.2 - 29.9 (4.1)"   "0.2 - 211.2 (31.4)"
[1] "hr="     "2.6e+07"
D17V2, continuous
D17V3, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    3  0
  8P LOSS WILD-TYPE 11 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    0
  8P LOSS WILD-TYPE   11   11
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               3                11
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       3                         0     0
  8P LOSS WILD-TYPE     7                         1    14
D17V4, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   3                 7
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   0                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 = 15Q LOSS MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    5  0
  15Q LOSS WILD-TYPE 16  4
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 20 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 0                  4 
$`15Q LOSS MUTATED`
TCGA-FA-A6HO TCGA-FF-8043 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
        0.20        31.73        74.10        26.70        29.95 

$`15Q LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8042 
        4.34         4.34        14.99         0.20        35.54        31.10 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        4.14        27.35        22.32         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       127.30 
TCGA-GR-A4D5 TCGA-GR-A4D9 
       24.69        46.29 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               0.2                0.2 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             74.10             211.23 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            29.950             29.225 
[1] "0.2 - 74.1 (29.9)"  "0.2 - 211.2 (29.2)"
[1] "hr="     "2.5e+08"
D18V2, continuous
D18V3, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    4  1
  15Q LOSS WILD-TYPE 10 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4    1
  15Q LOSS WILD-TYPE   10   10
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                4                 10
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       3                         0     2
  15Q LOSS WILD-TYPE     7                         1    12
D18V4, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    3                  7
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 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(19) Variable = 16Q LOSS MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    4  0
  16Q LOSS WILD-TYPE 17  4
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 21 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 0                  4 
$`16Q LOSS MUTATED`
TCGA-FA-A6HO TCGA-FF-8043 TCGA-FF-8047 TCGA-GR-A4D4 
        0.20        31.73         4.14        26.70 

$`16Q LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8042 
        4.34         4.34        14.99         0.20        35.54        31.10 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       27.35        22.32         4.57        41.16        51.98        47.38 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
      211.23        19.56       106.09       196.60       127.30        74.10 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       24.69        29.95        46.29 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               0.2                0.2 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             31.73             211.23 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             15.42              31.10 
[1] "0.2 - 31.7 (15.4)"  "0.2 - 211.2 (31.1)"
[1] "hr="     "7.9e+07"
D19V2, continuous
D19V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    4  0
  16Q LOSS WILD-TYPE 10 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4    0
  16Q LOSS WILD-TYPE   10   11
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                4                 10
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       3                         0     1
  16Q LOSS WILD-TYPE     7                         1    13
D19V4, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    3                  7
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 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 = XQ LOSS MUTATION ANALYSIS
D20V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    2  1
  XQ LOSS WILD-TYPE 19  3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                22 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                 3 
$`XQ LOSS MUTATED`
TCGA-FF-8043 TCGA-FF-8047 TCGA-G8-6907 
       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-FF-8041 
        4.34         4.34        14.99         0.20         0.20        35.54 
TCGA-FF-8042 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       31.10        27.35        22.32         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
       47.38       211.23       106.09       196.60       127.30        74.10 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       26.70        24.69        29.95        46.29 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             4.14              0.20 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            31.73            211.23 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           19.560            30.525 
[1] "4.1 - 31.7 (19.6)"  "0.2 - 211.2 (30.5)"
[1] "hr="     "3.6e+09"
D20V2, continuous
D20V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    3  0
  XQ LOSS WILD-TYPE 11 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    0
  XQ LOSS WILD-TYPE   11   11
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               3                11
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       2                         0     1
  XQ LOSS WILD-TYPE     8                         1    13
D20V4, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   2                 8
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   1                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"
