[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"        "-oTMESO-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/MESO-TP/10006044/MESO-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/MESO-TP/10013772/transformed.cor.cli.txt"

nPatients in clinical file=21, in cluster file=37, common to both=21
[1] "Reduce the number of clustering variables from 80 to 36."
[1] 36 21
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                5                16 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                5                16 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                17 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                17 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                16 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                16 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                6                15 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                6                15 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                18 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                18 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                5                16 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                5                16 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                5                16 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                5                16 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                3                18 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                3                18 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                4                17 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                4                17 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 5                 16 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 5                 16 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                 16 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                 16 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 16 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 16 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 15 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 15 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                18 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                18 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                18 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                18 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                8                13 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                8                13 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                7                14 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                7                14 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               10                11 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               10                11 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                18 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                18 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                6                15 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                6                15 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                6                15 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                6                15 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                 15 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                 15 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 16 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 16 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 3                 18 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 3                 18 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                13                  8 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                13                  8 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 7                 14 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 7                 14 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 17 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 17 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 4                 17 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 4                 17 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 18 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 18 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 17 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 17 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 17 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 17 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 18 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 18 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                 17 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                 17 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 18 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 18 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                  6 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                  6 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                17 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                17 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "KARNOFSKYPERFORMANCESCORE"             
[13] "RADIATIONS.RADIATION.REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 21 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
          NA           NA           NA           NA          371           NA 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
          NA           NA           NA           NA           NA           NA 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I 
          NA           NA         1316         1575          414            7 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
          NA           NA           NA 
Variable 1:'AGE':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RACE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "PATHOLOGY.M.STAGE"     "GENDER"               
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 21 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=16, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=5, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 3 10  7  1 
[1] "table(vv)"
vv
T1+T2 T3+T4 
   13     8 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 3 10  7  1 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 13

$Class1_nSamples
[1] 8

$Class0_label
[1] "T1+T2"

$Class1_label
[1] "T3+T4"


T1+T2 T3+T4 
   13     8 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
14  4  2 
[1] "table(vv)"
vv
   N0 N1+N2 
   14     6 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
14  4  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 14

$Class1_nSamples
[1] 6

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   14     6 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1Q GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    0  5
  1Q GAIN WILD-TYPE  5 11
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                5                16 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                5                11 
$`1Q GAIN MUTATED`
TCGA-LK-A4NZ TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-SH-A7BC TCGA-SH-A7BH 
        8.02        18.81        23.31        23.90         7.99 

$`1Q GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       17.95         1.87        31.20        12.20        80.84        91.73 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        43.27 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BD 
       51.78        13.61         0.23        15.09 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             7.99              0.23 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            23.90             91.73 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            18.81             16.21 
[1] "8.0 - 23.9 (18.8)" "0.2 - 91.7 (16.2)"
[1] "hr=" "2.1"
D1V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         0        0        2         3        0
  1Q GAIN WILD-TYPE       1        1        4         8        2
D1V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                0                 1
  STAGE II                2                 4
  STAGE III               3                 8
  STAGE IV                0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  1Q GAIN MUTATED       3     2
  1Q GAIN WILD-TYPE    10     6
D1V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1+T2               3                10
  T3+T4               2                 6
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  1Q GAIN MUTATED    3     2
  1Q GAIN WILD-TYPE 11     4
D1V5, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0                  3                11
  N1+N2               2                 4
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1Q GAIN MUTATED    5  0  0
  1Q GAIN WILD-TYPE 10  1  5
D1V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0               5                10
  M1               0                 1
  MX               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    2  3
  1Q GAIN WILD-TYPE  4 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2    3
  1Q GAIN WILD-TYPE    4   12
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               2                 4
  MALE                 3                12
[1] 2 2
[1] FALSE

Clustering(2) Variable = 3P GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    2  2
  3P GAIN WILD-TYPE  3 14
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                17 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                14 
$`3P GAIN MUTATED`
TCGA-LK-A4O5 TCGA-MQ-A6BS TCGA-SH-A7BC TCGA-SH-A7BH 
       12.20        13.61        23.90         7.99 

$`3P GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       17.95         8.02         1.87        31.20        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BD 
       24.89        43.27        51.78         0.23        15.09 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             7.99              0.23 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            23.90             91.73 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           12.905            17.950 
[1] "8.0 - 23.9 (12.9)" "0.2 - 91.7 (17.9)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         0        0        1         3        0
  3P GAIN WILD-TYPE       1        1        5         8        2
D2V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                0                 1
  STAGE II                1                 5
  STAGE III               3                 8
  STAGE IV                0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  3P GAIN MUTATED       1     3
  3P GAIN WILD-TYPE    12     5
D2V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1+T2               1                12
  T3+T4               3                 5
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  3P GAIN MUTATED    3     1
  3P GAIN WILD-TYPE 11     5
D2V5, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0                  3                11
  N1+N2               1                 5
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  3P GAIN MUTATED    3  0  1
  3P GAIN WILD-TYPE 12  1  4
D2V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               3                12
  M1               0                 1
  MX               1                 4
[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"
D2V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    2  2
  3P GAIN WILD-TYPE  4 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2    2
  3P GAIN WILD-TYPE    4   13
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               2                 4
  MALE                 2                13
[1] 2 2
[1] FALSE

Clustering(3) Variable = 3Q GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    2  3
  3Q GAIN WILD-TYPE  3 13
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                16 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                13 
$`3Q GAIN MUTATED`
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A6BS TCGA-SH-A7BC TCGA-SH-A7BH 
        1.87        12.20        13.61        23.90         7.99 

$`3Q GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       17.95         8.02        31.20        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BD 
       43.27        51.78         0.23        15.09 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             1.87              0.23 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            23.90             91.73 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            12.20             18.38 
[1] "1.9 - 23.9 (12.2)" "0.2 - 91.7 (18.4)"
[1] "hr=" "1.7"
D3V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED         0        0        1         4        0
  3Q GAIN WILD-TYPE       1        1        5         7        2
D3V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                0                 1
  STAGE II                1                 5
  STAGE III               4                 7
  STAGE IV                0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  3Q GAIN MUTATED       1     4
  3Q GAIN WILD-TYPE    12     4
D3V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1+T2               1                12
  T3+T4               4                 4
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  3Q GAIN MUTATED    4     1
  3Q GAIN WILD-TYPE 10     5
D3V5, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0                  4                10
  N1+N2               1                 5
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  3Q GAIN MUTATED    4  0  1
  3Q GAIN WILD-TYPE 11  1  4
D3V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0               4                11
  M1               0                 1
  MX               1                 4
[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"
D3V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  2
  3Q GAIN WILD-TYPE  3 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    2
  3Q GAIN WILD-TYPE    3   13
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               3                 3
  MALE                 2                13
[1] 2 2
[1] FALSE

Clustering(4) Variable = 5P GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    2  4
  5P GAIN WILD-TYPE  3 12
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                6                15 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                12 
$`5P GAIN MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-MQ-A4LP TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SH-A7BH 
       17.95         1.87        17.33        51.78        13.61         7.99 

$`5P GAIN WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
        8.02        31.20        12.20        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       23.31         5.19         3.52        10.95        24.89        43.27 
TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD 
        0.23        23.90        15.09 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             1.87              0.23 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            51.78             91.73 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            15.47             18.81 
[1] "1.9 - 51.8 (15.5)" "0.2 - 91.7 (18.8)"
[1] "hr=" "1.4"
D4V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  5P GAIN MUTATED         0        0        1         4        1
  5P GAIN WILD-TYPE       1        1        5         7        1
D4V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                0                 1
  STAGE II                1                 5
  STAGE III               4                 7
  STAGE IV                1                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  5P GAIN MUTATED       2     4
  5P GAIN WILD-TYPE    11     4
D4V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1+T2               2                11
  T3+T4               4                 4
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  5P GAIN MUTATED    4     2
  5P GAIN WILD-TYPE 10     4
D4V5, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0                  4                10
  N1+N2               2                 4
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5P GAIN MUTATED    4  0  2
  5P GAIN WILD-TYPE 11  1  3
D4V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               4                11
  M1               0                 1
  MX               2                 3
[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"
D4V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    3  3
  5P GAIN WILD-TYPE  3 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3    3
  5P GAIN WILD-TYPE    3   12
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               3                 3
  MALE                 3                12
[1] 2 2
[1] FALSE

Clustering(5) Variable = 5Q GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    2  1
  5Q GAIN WILD-TYPE  3 15
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                18 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1                15 
$`5Q GAIN MUTATED`
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SH-A7BH 
       51.78        13.61         7.99 

$`5Q GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD 
       10.95        24.89        43.27         0.23        23.90        15.09 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             7.99              0.23 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            51.78             91.73 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            13.61             17.64 
[1] "8.0 - 51.8 (13.6)" "0.2 - 91.7 (17.6)"
[1] "hr=" "2.1"
D5V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED         0        0        1         2        0
  5Q GAIN WILD-TYPE       1        1        5         9        2
D5V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                0                 1
  STAGE II                1                 5
  STAGE III               2                 9
  STAGE IV                0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  5Q GAIN MUTATED       2     1
  5Q GAIN WILD-TYPE    11     7
D5V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1+T2               2                11
  T3+T4               1                 7
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  5Q GAIN MUTATED    2     1
  5Q GAIN WILD-TYPE 12     5
D5V5, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0                  2                12
  N1+N2               1                 5
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5Q GAIN MUTATED    1  0  2
  5Q GAIN WILD-TYPE 14  1  3
D5V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               1                14
  M1               0                 1
  MX               2                 3
[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"
D5V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    2  1
  5Q GAIN WILD-TYPE  4 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    1
  5Q GAIN WILD-TYPE    4   14
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               2                 4
  MALE                 1                14
[1] 2 2
[1] FALSE

Clustering(6) Variable = 7P GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED    1  4
  7P GAIN WILD-TYPE  4 12
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                5                16 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                4                12 
$`7P GAIN MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-MQ-A6BS TCGA-SH-A7BC TCGA-SH-A7BH 
       17.95         1.87        13.61        23.90         7.99 

$`7P GAIN WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
        8.02        31.20        12.20        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BD 
       43.27        51.78         0.23        15.09 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             1.87              0.23 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            23.90             91.73 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            13.61             18.07 
[1] "1.9 - 23.9 (13.6)" "0.2 - 91.7 (18.1)"
[1] "hr=" "2.2"
D6V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  7P GAIN MUTATED         0        0        1         3        1
  7P GAIN WILD-TYPE       1        1        5         8        1
D6V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                0                 1
  STAGE II                1                 5
  STAGE III               3                 8
  STAGE IV                1                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  7P GAIN MUTATED       1     4
  7P GAIN WILD-TYPE    12     4
D6V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1+T2               1                12
  T3+T4               4                 4
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  7P GAIN MUTATED    3     2
  7P GAIN WILD-TYPE 11     4
D6V5, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0                  3                11
  N1+N2               2                 4
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  7P GAIN MUTATED    4  0  1
  7P GAIN WILD-TYPE 11  1  4
D6V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0               4                11
  M1               0                 1
  MX               1                 4
[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"
D6V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    2  3
  7P GAIN WILD-TYPE  4 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2    3
  7P GAIN WILD-TYPE    4   12
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               2                 4
  MALE                 3                12
[1] 2 2
[1] FALSE

Clustering(7) Variable = 7Q GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED    1  4
  7Q GAIN WILD-TYPE  4 12
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                5                16 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                4                12 
$`7Q GAIN MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-MQ-A6BS TCGA-SH-A7BC TCGA-SH-A7BH 
       17.95         1.87        13.61        23.90         7.99 

$`7Q GAIN WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
        8.02        31.20        12.20        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BD 
       43.27        51.78         0.23        15.09 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             1.87              0.23 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            23.90             91.73 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            13.61             18.07 
[1] "1.9 - 23.9 (13.6)" "0.2 - 91.7 (18.1)"
[1] "hr=" "2.2"
D7V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED         0        0        1         3        1
  7Q GAIN WILD-TYPE       1        1        5         8        1
D7V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                0                 1
  STAGE II                1                 5
  STAGE III               3                 8
  STAGE IV                1                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  7Q GAIN MUTATED       1     4
  7Q GAIN WILD-TYPE    12     4
D7V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1+T2               1                12
  T3+T4               4                 4
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  7Q GAIN MUTATED    3     2
  7Q GAIN WILD-TYPE 11     4
D7V5, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0                  3                11
  N1+N2               2                 4
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  7Q GAIN MUTATED    4  0  1
  7Q GAIN WILD-TYPE 11  1  4
D7V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0               4                11
  M1               0                 1
  MX               1                 4
[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"
D7V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    2  3
  7Q GAIN WILD-TYPE  4 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2    3
  7Q GAIN WILD-TYPE    4   12
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               2                 4
  MALE                 3                12
[1] 2 2
[1] FALSE

Clustering(8) Variable = 8P GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    0  3
  8P GAIN WILD-TYPE  5 13
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                3                18 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                3                13 
$`8P GAIN MUTATED`
TCGA-LK-A4NW TCGA-MQ-A4LM TCGA-SH-A7BH 
       17.95         5.19         7.99 

$`8P GAIN WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        8.02         1.87        31.20        12.20        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       18.81        23.31        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD 
       43.27        51.78        13.61         0.23        23.90        15.09 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             5.19              0.23 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            17.95             91.73 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             7.99             18.07 
[1] "5.2 - 17.9 (8.0)"  "0.2 - 91.7 (18.1)"
[1] "hr=" "4.2"
D8V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         0        0        0         2        1
  8P GAIN WILD-TYPE       1        1        6         9        1
D8V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                0                 1
  STAGE II                0                 6
  STAGE III               2                 9
  STAGE IV                1                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  8P GAIN MUTATED       0     3
  8P GAIN WILD-TYPE    13     5
D8V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1+T2               0                13
  T3+T4               3                 5
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  8P GAIN MUTATED    2     1
  8P GAIN WILD-TYPE 12     5
D8V5, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0                  2                12
  N1+N2               1                 5
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8P GAIN MUTATED    3  0  0
  8P GAIN WILD-TYPE 12  1  5
D8V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               3                12
  M1               0                 1
  MX               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    1  2
  8P GAIN WILD-TYPE  5 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1    2
  8P GAIN WILD-TYPE    5   13
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               1                 5
  MALE                 2                13
[1] 2 2
[1] FALSE

Clustering(9) Variable = 8Q GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED    1  3
  8Q GAIN WILD-TYPE  4 13
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                4                17 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                3                13 
$`8Q GAIN MUTATED`
TCGA-LK-A4NW TCGA-MQ-A4LM TCGA-NQ-A57I TCGA-SH-A7BH 
       17.95         5.19         0.23         7.99 

$`8Q GAIN WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        8.02         1.87        31.20        12.20        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       18.81        23.31        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SH-A7BC TCGA-SH-A7BD 
       43.27        51.78        13.61        23.90        15.09 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.23              1.87 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            17.95             91.73 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             6.59             18.81 
[1] "0.2 - 17.9 (6.6)"  "1.9 - 91.7 (18.8)"
[1] "hr=" "4.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         0        1        0         2        1
  8Q GAIN WILD-TYPE       1        0        6         9        1
D9V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                1                 0
  STAGE II                0                 6
  STAGE III               2                 9
  STAGE IV                1                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  8Q GAIN MUTATED       1     3
  8Q GAIN WILD-TYPE    12     5
D9V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1+T2               1                12
  T3+T4               3                 5
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  8Q GAIN MUTATED    2     1
  8Q GAIN WILD-TYPE 12     5
D9V5, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0                  2                12
  N1+N2               1                 5
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED    3  0  1
  8Q GAIN WILD-TYPE 12  1  4
D9V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0               3                12
  M1               0                 1
  MX               1                 4
[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"
D9V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    1  3
  8Q GAIN WILD-TYPE  5 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1    3
  8Q GAIN WILD-TYPE    5   12
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               1                 5
  MALE                 3                12
[1] 2 2
[1] FALSE

Clustering(10) Variable = 12P GAIN MUTATION ANALYSIS
D10V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    2  3
  12P GAIN WILD-TYPE  3 13
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 5                 16 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 13 
$`12P GAIN MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A6BS TCGA-SH-A7BC 
       17.95        12.20        80.84        13.61        23.90 

$`12P GAIN WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        8.02         1.87        31.20        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        43.27 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BD TCGA-SH-A7BH 
       51.78         0.23        15.09         7.99 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             12.20               0.23 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             80.84              91.73 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             17.95              16.21 
[1] "12.2 - 80.8 (17.9)" "0.2 - 91.7 (16.2)" 
[1] "hr=" "1.6"
D10V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  12P GAIN MUTATED         1        0        1         2        1
  12P GAIN WILD-TYPE       0        1        5         9        1
D10V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  1                  0
  STAGE IB                 0                  1
  STAGE II                 1                  5
  STAGE III                2                  9
  STAGE IV                 1                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  12P GAIN MUTATED       2     3
  12P GAIN WILD-TYPE    11     5
D10V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1+T2                2                 11
  T3+T4                3                  5
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  12P GAIN MUTATED    3     2
  12P GAIN WILD-TYPE 11     4
D10V5, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                   3                 11
  N1+N2                2                  4
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12P GAIN MUTATED    4  0  1
  12P GAIN WILD-TYPE 11  1  4
D10V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                4                 11
  M1                0                  1
  MX                1                  4
[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"
D10V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1  4
  12P GAIN WILD-TYPE  5 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    4
  12P GAIN WILD-TYPE    5   11
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                1                  5
  MALE                  4                 11
[1] 2 2
[1] FALSE

Clustering(11) Variable = 12Q GAIN MUTATION ANALYSIS
D11V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    2  3
  12Q GAIN WILD-TYPE  3 13
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                 16 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 13 
$`12Q GAIN MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A6BS TCGA-SH-A7BC 
       17.95        12.20        80.84        13.61        23.90 

$`12Q GAIN WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        8.02         1.87        31.20        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        43.27 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BD TCGA-SH-A7BH 
       51.78         0.23        15.09         7.99 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             12.20               0.23 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             80.84              91.73 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             17.95              16.21 
[1] "12.2 - 80.8 (17.9)" "0.2 - 91.7 (16.2)" 
[1] "hr=" "1.6"
D11V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED         1        0        1         2        1
  12Q GAIN WILD-TYPE       0        1        5         9        1
D11V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  1                  0
  STAGE IB                 0                  1
  STAGE II                 1                  5
  STAGE III                2                  9
  STAGE IV                 1                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  12Q GAIN MUTATED       2     3
  12Q GAIN WILD-TYPE    11     5
D11V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1+T2                2                 11
  T3+T4                3                  5
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  12Q GAIN MUTATED    3     2
  12Q GAIN WILD-TYPE 11     4
D11V5, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                   3                 11
  N1+N2                2                  4
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12Q GAIN MUTATED    4  0  1
  12Q GAIN WILD-TYPE 11  1  4
D11V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                4                 11
  M1                0                  1
  MX                1                  4
[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"
D11V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1  4
  12Q GAIN WILD-TYPE  5 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    4
  12Q GAIN WILD-TYPE    5   11
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                1                  5
  MALE                  4                 11
[1] 2 2
[1] FALSE

Clustering(12) Variable = 16P GAIN MUTATION ANALYSIS
D12V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    1  4
  16P GAIN WILD-TYPE  4 12
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 16 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 12 
$`16P GAIN MUTATED`
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BH 
       18.81        23.31         0.23        23.90         7.99 

$`16P GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       91.73         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SH-A7BD 
       43.27        51.78        13.61        15.09 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.23               1.87 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             23.90              91.73 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             18.81              16.21 
[1] "0.2 - 23.9 (18.8)" "1.9 - 91.7 (16.2)"
[1] "hr=" "1.7"
D12V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  16P GAIN MUTATED         0        1        1         3        0
  16P GAIN WILD-TYPE       1        0        5         8        2
D12V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 1                  0
  STAGE II                 1                  5
  STAGE III                3                  8
  STAGE IV                 0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  16P GAIN MUTATED       3     2
  16P GAIN WILD-TYPE    10     6
D12V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1+T2                3                 10
  T3+T4                2                  6
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  16P GAIN MUTATED    2     2
  16P GAIN WILD-TYPE 12     4
D12V5, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                   2                 12
  N1+N2                2                  4
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16P GAIN MUTATED    4  0  1
  16P GAIN WILD-TYPE 11  1  4
D12V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                4                 11
  M1                0                  1
  MX                1                  4
[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"
D12V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    2  3
  16P GAIN WILD-TYPE  4 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2    3
  16P GAIN WILD-TYPE    4   12
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                2                  4
  MALE                  3                 12
[1] 2 2
[1] FALSE

Clustering(13) Variable = 16Q GAIN MUTATION ANALYSIS
D13V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    1  5
  16Q GAIN WILD-TYPE  4 11
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 15 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 11 
$`16Q GAIN MUTATED`
TCGA-LK-A4O2 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BH 
        1.87        18.81        23.31         0.23        23.90         7.99 

$`16Q GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       17.95         8.02        31.20        12.20        80.84        91.73 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        43.27 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SH-A7BD 
       51.78        13.61        15.09 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.23               3.52 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             23.90              91.73 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             13.40              17.33 
[1] "0.2 - 23.9 (13.4)" "3.5 - 91.7 (17.3)"
[1] "hr=" "2.3"
D13V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED         0        1        1         4        0
  16Q GAIN WILD-TYPE       1        0        5         7        2
D13V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 1                  0
  STAGE II                 1                  5
  STAGE III                4                  7
  STAGE IV                 0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  16Q GAIN MUTATED       3     3
  16Q GAIN WILD-TYPE    10     5
D13V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1+T2                3                 10
  T3+T4                3                  5
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  16Q GAIN MUTATED    3     2
  16Q GAIN WILD-TYPE 11     4
D13V5, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                   3                 11
  N1+N2                2                  4
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16Q GAIN MUTATED    5  0  1
  16Q GAIN WILD-TYPE 10  1  4
D13V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                5                 10
  M1                0                  1
  MX                1                  4
[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"
D13V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  3
  16Q GAIN WILD-TYPE  3 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    3
  16Q GAIN WILD-TYPE    3   12
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                  3
  MALE                  3                 12
[1] 2 2
[1] FALSE

Clustering(14) Variable = 1P LOSS MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    1  2
  1P LOSS WILD-TYPE  4 14
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                18 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                14 
$`1P LOSS MUTATED`
TCGA-MQ-A4LI TCGA-MQ-A6BL TCGA-MQ-A6BS 
       18.81        10.95        13.61 

$`1P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN 
       91.73        23.31         5.19        17.33         3.52        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       43.27        51.78         0.23        23.90        15.09         7.99 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            10.95              0.23 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            18.81             91.73 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            13.61             17.64 
[1] "10.9 - 18.8 (13.6)" "0.2 - 91.7 (17.6)" 
[1] "hr=" "1.5"
D14V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  1P LOSS MUTATED         0        0        3         0        0
  1P LOSS WILD-TYPE       1        1        3        11        2
D14V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                0                 1
  STAGE II                3                 3
  STAGE III               0                11
  STAGE IV                0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  1P LOSS MUTATED       3     0
  1P LOSS WILD-TYPE    10     8
D14V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1+T2               3                10
  T3+T4               0                 8
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  1P LOSS MUTATED    3     0
  1P LOSS WILD-TYPE 11     6
D14V5, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0                  3                11
  N1+N2               0                 6
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1P LOSS MUTATED    2  0  1
  1P LOSS WILD-TYPE 13  1  4
D14V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               2                13
  M1               0                 1
  MX               1                 4
[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"
D14V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  2
  1P LOSS WILD-TYPE  5 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    2
  1P LOSS WILD-TYPE    5   13
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               1                 5
  MALE                 2                13
[1] 2 2
[1] FALSE

Clustering(15) Variable = 2Q LOSS MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    0  3
  2Q LOSS WILD-TYPE  5 13
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                18 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                13 
$`2Q LOSS MUTATED`
TCGA-LK-A4O2 TCGA-MQ-A4LI TCGA-SH-A7BH 
        1.87        18.81         7.99 

$`2Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       17.95         8.02        31.20        12.20        80.84        91.73 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD 
       43.27        51.78        13.61         0.23        23.90        15.09 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             1.87              0.23 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            18.81             91.73 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             7.99             17.64 
[1] "1.9 - 18.8 (8.0)"  "0.2 - 91.7 (17.6)"
[1] "hr=" "3.9"
D15V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED         0        0        1         2        0
  2Q LOSS WILD-TYPE       1        1        5         9        2
D15V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                0                 1
  STAGE II                1                 5
  STAGE III               2                 9
  STAGE IV                0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  2Q LOSS MUTATED       1     2
  2Q LOSS WILD-TYPE    12     6
D15V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1+T2               1                12
  T3+T4               2                 6
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  2Q LOSS MUTATED    3     0
  2Q LOSS WILD-TYPE 11     6
D15V5, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0                  3                11
  N1+N2               0                 6
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  2Q LOSS MUTATED    3  0  0
  2Q LOSS WILD-TYPE 12  1  5
D15V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               3                12
  M1               0                 1
  MX               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    3  0
  2Q LOSS WILD-TYPE  3 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3    0
  2Q LOSS WILD-TYPE    3   15
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               3                 3
  MALE                 0                15
[1] 2 2
[1] FALSE

Clustering(16) Variable = 4P LOSS MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    3  5
  4P LOSS WILD-TYPE  2 11
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                8                13 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5                11 
$`4P LOSS MUTATED`
TCGA-LK-A4O5 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BR 
       12.20        18.81         5.19        17.33        10.95        51.78 
TCGA-MQ-A6BS TCGA-SH-A7BH 
       13.61         7.99 

$`4P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       17.95         8.02         1.87        31.20        80.84        91.73 
TCGA-MQ-A4LJ TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SH-A7BC 
       23.31         3.52        24.89        43.27         0.23        23.90 
TCGA-SH-A7BD 
       15.09 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             5.19              0.23 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            51.78             91.73 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           12.905            23.310 
[1] "5.2 - 51.8 (12.9)" "0.2 - 91.7 (23.3)"
[1] "hr=" "1.4"
D16V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         0        0        3         5        0
  4P LOSS WILD-TYPE       1        1        3         6        2
D16V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                0                 1
  STAGE II                3                 3
  STAGE III               5                 6
  STAGE IV                0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  4P LOSS MUTATED       4     4
  4P LOSS WILD-TYPE     9     4
D16V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1+T2               4                 9
  T3+T4               4                 4
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  4P LOSS MUTATED    7     1
  4P LOSS WILD-TYPE  7     5
D16V5, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0                  7                 7
  N1+N2               1                 5
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4P LOSS MUTATED    6  0  2
  4P LOSS WILD-TYPE  9  1  3
D16V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               6                 9
  M1               0                 1
  MX               2                 3
[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"
D16V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    4  4
  4P LOSS WILD-TYPE  2 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      4    4
  4P LOSS WILD-TYPE    2   11
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               4                 2
  MALE                 4                11
[1] 2 2
[1] FALSE

Clustering(17) Variable = 4Q LOSS MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    2  5
  4Q LOSS WILD-TYPE  3 11
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                7                14 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                5                11 
$`4Q LOSS MUTATED`
TCGA-LK-A4O5 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BR 
       12.20        18.81         5.19        17.33        10.95        51.78 
TCGA-SH-A7BH 
        7.99 

$`4Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       17.95         8.02         1.87        31.20        80.84        91.73 
TCGA-MQ-A4LJ TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I 
       23.31         3.52        24.89        43.27        13.61         0.23 
TCGA-SH-A7BC TCGA-SH-A7BD 
       23.90        15.09 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             5.19              0.23 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            51.78             91.73 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            12.20             20.63 
[1] "5.2 - 51.8 (12.2)" "0.2 - 91.7 (20.6)"
[1] "hr=" "1.6"
D17V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         0        0        2         5        0
  4Q LOSS WILD-TYPE       1        1        4         6        2
D17V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                0                 1
  STAGE II                2                 4
  STAGE III               5                 6
  STAGE IV                0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  4Q LOSS MUTATED       3     4
  4Q LOSS WILD-TYPE    10     4
D17V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1+T2               3                10
  T3+T4               4                 4
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  4Q LOSS MUTATED    6     1
  4Q LOSS WILD-TYPE  8     5
D17V5, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0                  6                 8
  N1+N2               1                 5
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4Q LOSS MUTATED    6  0  1
  4Q LOSS WILD-TYPE  9  1  4
D17V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               6                 9
  M1               0                 1
  MX               1                 4
[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"
D17V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    4  3
  4Q LOSS WILD-TYPE  2 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4    3
  4Q LOSS WILD-TYPE    2   12
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               4                 2
  MALE                 3                12
[1] 2 2
[1] FALSE

Clustering(18) Variable = 6Q LOSS MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2               0 1
  6Q LOSS MUTATED   2 8
  6Q LOSS WILD-TYPE 3 8
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               10                11 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                8                 8 
$`6Q LOSS MUTATED`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LM 
        8.02         1.87        80.84        91.73        18.81         5.19 
TCGA-MQ-A6BL TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SH-A7BC 
       10.95        43.27         0.23        23.90 

$`6Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV 
       17.95        31.20        12.20        23.31        17.33         3.52 
TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SH-A7BD TCGA-SH-A7BH 
       24.89        51.78        13.61        15.09         7.99 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.23              3.52 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            91.73             51.78 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            14.88             17.33 
[1] "0.2 - 91.7 (14.9)" "3.5 - 51.8 (17.3)"
[1] "hr=" "1.2"
D18V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED         1        1        5         3        0
  6Q LOSS WILD-TYPE       0        0        1         8        2
D18V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IB                1                 0
  STAGE II                5                 1
  STAGE III               3                 8
  STAGE IV                0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  6Q LOSS MUTATED       7     3
  6Q LOSS WILD-TYPE     6     5
D18V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1+T2               7                 6
  T3+T4               3                 5
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  6Q LOSS MUTATED    8     1
  6Q LOSS WILD-TYPE  6     5
D18V5, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0                  8                 6
  N1+N2               1                 5
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  6Q LOSS MUTATED    8  0  2
  6Q LOSS WILD-TYPE  7  1  3
D18V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0               8                 7
  M1               0                 1
  MX               2                 3
[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"
D18V7, binary
                   cls
clus                0 1
  6Q LOSS MUTATED   2 8
  6Q LOSS WILD-TYPE 4 7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2    8
  6Q LOSS WILD-TYPE    4    7
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               2                 4
  MALE                 8                 7
[1] 2 2
[1] FALSE

Clustering(19) Variable = 8P LOSS MUTATION ANALYSIS
D19V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    1  2
  8P LOSS WILD-TYPE  4 14
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                18 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                14 
$`8P LOSS MUTATED`
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A6BQ 
       91.73        18.81        43.27 

$`8P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       51.78        13.61         0.23        23.90        15.09         7.99 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            18.81              0.23 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            91.73             80.84 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            43.27             14.35 
[1] "18.8 - 91.7 (43.3)" "0.2 - 80.8 (14.3)" 
[1] "hr=" "5.3"
D19V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         0        0        3         0        0
  8P LOSS WILD-TYPE       1        1        3        11        2
D19V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                0                 1
  STAGE II                3                 3
  STAGE III               0                11
  STAGE IV                0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  8P LOSS MUTATED       3     0
  8P LOSS WILD-TYPE    10     8
D19V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1+T2               3                10
  T3+T4               0                 8
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  8P LOSS MUTATED    3     0
  8P LOSS WILD-TYPE 11     6
D19V5, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0                  3                11
  N1+N2               0                 6
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8P LOSS MUTATED    2  0  1
  8P LOSS WILD-TYPE 13  1  4
D19V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               2                13
  M1               0                 1
  MX               1                 4
[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"
D19V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    1  2
  8P LOSS WILD-TYPE  5 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    2
  8P LOSS WILD-TYPE    5   13
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               1                 5
  MALE                 2                13
[1] 2 2
[1] FALSE

Clustering(20) Variable = 9P LOSS MUTATION ANALYSIS
D20V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED    2  4
  9P LOSS WILD-TYPE  3 12
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                6                15 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4                12 
$`9P LOSS MUTATED`
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC 
        5.19        17.33         3.52        13.61         0.23        23.90 

$`9P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       91.73        18.81        23.31        10.95        24.89        43.27 
TCGA-MQ-A6BR TCGA-SH-A7BD TCGA-SH-A7BH 
       51.78        15.09         7.99 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.23              1.87 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            23.90             91.73 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             9.40             18.81 
[1] "0.2 - 23.9 (9.4)"  "1.9 - 91.7 (18.8)"
[1] "hr=" "2.4"
D20V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         0        1        1         4        0
  9P LOSS WILD-TYPE       1        0        5         7        2
D20V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                1                 0
  STAGE II                1                 5
  STAGE III               4                 7
  STAGE IV                0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  9P LOSS MUTATED       2     4
  9P LOSS WILD-TYPE    11     4
D20V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1+T2               2                11
  T3+T4               4                 4
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  9P LOSS MUTATED    4     1
  9P LOSS WILD-TYPE 10     5
D20V5, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0                  4                10
  N1+N2               1                 5
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9P LOSS MUTATED    4  0  2
  9P LOSS WILD-TYPE 11  1  3
D20V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0               4                11
  M1               0                 1
  MX               2                 3
[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"
D20V7, binary
                   cls
clus                0 1
  9P LOSS MUTATED   0 6
  9P LOSS WILD-TYPE 6 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0    6
  9P LOSS WILD-TYPE    6    9
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               0                 6
  MALE                 6                 9
[1] 2 2
[1] FALSE

Clustering(21) Variable = 9Q LOSS MUTATION ANALYSIS
D21V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    2  4
  9Q LOSS WILD-TYPE  3 12
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                6                15 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                4                12 
$`9Q LOSS MUTATED`
TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC 
       18.81         5.19         3.52        13.61         0.23        23.90 

$`9Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       91.73        23.31        17.33        10.95        24.89        43.27 
TCGA-MQ-A6BR TCGA-SH-A7BD TCGA-SH-A7BH 
       51.78        15.09         7.99 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.23              1.87 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            23.90             91.73 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             9.40             17.95 
[1] "0.2 - 23.9 (9.4)"  "1.9 - 91.7 (17.9)"
[1] "hr=" "2.1"
D21V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         0        1        2         3        0
  9Q LOSS WILD-TYPE       1        0        4         8        2
D21V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                1                 0
  STAGE II                2                 4
  STAGE III               3                 8
  STAGE IV                0                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  9Q LOSS MUTATED       3     3
  9Q LOSS WILD-TYPE    10     5
D21V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1+T2               3                10
  T3+T4               3                 5
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  9Q LOSS MUTATED    4     1
  9Q LOSS WILD-TYPE 10     5
D21V5, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0                  4                10
  N1+N2               1                 5
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9Q LOSS MUTATED    4  0  2
  9Q LOSS WILD-TYPE 11  1  3
D21V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0               4                11
  M1               0                 1
  MX               2                 3
[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"
D21V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    1  5
  9Q LOSS WILD-TYPE  5 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1    5
  9Q LOSS WILD-TYPE    5   10
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               1                 5
  MALE                 5                10
[1] 2 2
[1] FALSE

Clustering(22) Variable = 10P LOSS MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    2  4
  10P LOSS WILD-TYPE  3 12
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                 15 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 4                 12 
$`10P LOSS MUTATED`
TCGA-MQ-A4LP TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       17.33        13.61         0.23        23.90        15.09         7.99 

$`10P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL 
       91.73        18.81        23.31         5.19         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       24.89        43.27        51.78 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.23               1.87 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             23.90              91.73 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             14.35              18.81 
[1] "0.2 - 23.9 (14.3)" "1.9 - 91.7 (18.8)"
[1] "hr=" "1.9"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         0        1        1         3        1
  10P LOSS WILD-TYPE       1        0        5         8        1
D22V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 1                  0
  STAGE II                 1                  5
  STAGE III                3                  8
  STAGE IV                 1                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  10P LOSS MUTATED       3     3
  10P LOSS WILD-TYPE    10     5
D22V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1+T2                3                 10
  T3+T4                3                  5
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  10P LOSS MUTATED    4     1
  10P LOSS WILD-TYPE 10     5
D22V5, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                   4                 10
  N1+N2                1                  5
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10P LOSS MUTATED    3  1  2
  10P LOSS WILD-TYPE 12  0  3
D22V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                3                 12
  M1                1                  0
  MX                2                  3
[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"
D22V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    1  5
  10P LOSS WILD-TYPE  5 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    5
  10P LOSS WILD-TYPE    5   10
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                1                  5
  MALE                  5                 10
[1] 2 2
[1] FALSE

Clustering(23) Variable = 10Q LOSS MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    2  3
  10Q LOSS WILD-TYPE  3 13
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 16 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 3                 13 
$`10Q LOSS MUTATED`
TCGA-MQ-A4LP TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BD TCGA-SH-A7BH 
       17.33        13.61         0.23        15.09         7.99 

$`10Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL 
       91.73        18.81        23.31         5.19         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SH-A7BC 
       24.89        43.27        51.78        23.90 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.23               1.87 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             17.33              91.73 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             13.61              21.06 
[1] "0.2 - 17.3 (13.6)" "1.9 - 91.7 (21.1)"
[1] "hr=" "2.6"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         0        1        1         2        1
  10Q LOSS WILD-TYPE       1        0        5         9        1
D23V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 1                  0
  STAGE II                 1                  5
  STAGE III                2                  9
  STAGE IV                 1                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  10Q LOSS MUTATED       3     2
  10Q LOSS WILD-TYPE    10     6
D23V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1+T2                3                 10
  T3+T4                2                  6
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  10Q LOSS MUTATED    4     0
  10Q LOSS WILD-TYPE 10     6
D23V5, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                   4                 10
  N1+N2                0                  6
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10Q LOSS MUTATED    2  1  2
  10Q LOSS WILD-TYPE 13  0  3
D23V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                2                 13
  M1                1                  0
  MX                2                  3
[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"
D23V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    1  4
  10Q LOSS WILD-TYPE  5 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1    4
  10Q LOSS WILD-TYPE    5   11
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                1                  5
  MALE                  4                 11
[1] 2 2
[1] FALSE

Clustering(24) Variable = 11Q LOSS MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    1  2
  11Q LOSS WILD-TYPE  4 14
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 3                 18 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                 14 
$`11Q LOSS MUTATED`
TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-NQ-A57I 
        5.19         3.52         0.23 

$`11Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN 
       91.73        18.81        23.31        17.33        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       43.27        51.78        13.61        23.90        15.09         7.99 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.23               1.87 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              5.19              91.73 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              3.52              18.38 
[1] "0.2 - 5.2 (3.5)"   "1.9 - 91.7 (18.4)"
[1] "hr=" "22" 
D24V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         0        1        0         2        0
  11Q LOSS WILD-TYPE       1        0        6         9        2
D24V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 1                  0
  STAGE II                 0                  6
  STAGE III                2                  9
  STAGE IV                 0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  11Q LOSS MUTATED       1     2
  11Q LOSS WILD-TYPE    12     6
D24V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1+T2                1                 12
  T3+T4                2                  6
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  11Q LOSS MUTATED    2     0
  11Q LOSS WILD-TYPE 12     6
D24V5, multiclass
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                 18 
        TCGA-LK-A4NW         TCGA-LK-A4NZ         TCGA-LK-A4O2 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-LK-A4O4         TCGA-LK-A4O5         TCGA-MQ-A4KX 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LC         TCGA-MQ-A4LI         TCGA-MQ-A4LJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LP         TCGA-MQ-A6BL         TCGA-MQ-A6BN 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-MQ-A6BQ         TCGA-MQ-A6BR         TCGA-MQ-A6BS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-SH-A7BC         TCGA-SH-A7BD         TCGA-SH-A7BH 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  11Q LOSS MUTATED    2  0  1
  11Q LOSS WILD-TYPE 13  1  4
D24V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                2                 13
  M1                0                  1
  MX                1                  4
[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"
D24V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    0  3
  11Q LOSS WILD-TYPE  6 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    3
  11Q LOSS WILD-TYPE    6   12
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                0                  6
  MALE                  3                 12
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q LOSS MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    2 11
  13Q LOSS WILD-TYPE  3  5
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                13                  8 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                11                  5 
$`13Q LOSS MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       17.95         1.87        12.20        80.84        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-SH-A7BC TCGA-SH-A7BD 
        5.19         3.52        10.95        13.61        23.90        15.09 
TCGA-SH-A7BH 
        7.99 

$`13Q LOSS WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-MQ-A4LC TCGA-MQ-A4LP TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        8.02        31.20        91.73        17.33        24.89        43.27 
TCGA-MQ-A6BR TCGA-NQ-A57I 
       51.78         0.23 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              1.87               0.23 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             80.84              91.73 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            13.610             28.045 
[1] "1.9 - 80.8 (13.6)" "0.2 - 91.7 (28.0)"
[1] "hr=" "3.5"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         1        0        3         7        2
  13Q LOSS WILD-TYPE       0        1        3         4        0
D25V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IB                 0                  1
  STAGE II                 3                  3
  STAGE III                7                  4
  STAGE IV                 2                  0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  13Q LOSS MUTATED       6     7
  13Q LOSS WILD-TYPE     7     1
D25V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1+T2                6                  7
  T3+T4                7                  1
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  13Q LOSS MUTATED   10     3
  13Q LOSS WILD-TYPE  4     3
D25V5, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                  10                  4
  N1+N2                3                  3
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  13Q LOSS MUTATED   11  1  1
  13Q LOSS WILD-TYPE  4  0  4
D25V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               11                  4
  M1                1                  0
  MX                1                  4
[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"
D25V7, binary
                    cls
clus                 0 1
  13Q LOSS MUTATED   4 9
  13Q LOSS WILD-TYPE 2 6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    9
  13Q LOSS WILD-TYPE    2    6
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                4                  2
  MALE                  9                  6
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q LOSS MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    2  5
  14Q LOSS WILD-TYPE  3 11
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 7                 14 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 5                 11 
$`14Q LOSS MUTATED`
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BS TCGA-SH-A7BC 
        1.87        12.20        18.81        23.31        13.61        23.90 
TCGA-SH-A7BH 
        7.99 

$`14Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM 
       17.95         8.02        31.20        80.84        91.73         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        43.27        51.78 
TCGA-NQ-A57I TCGA-SH-A7BD 
        0.23        15.09 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              1.87               0.23 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             23.90              91.73 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             13.61              17.64 
[1] "1.9 - 23.9 (13.6)" "0.2 - 91.7 (17.6)"
[1] "hr=" "1.7"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED         0        0        2         5        0
  14Q LOSS WILD-TYPE       1        1        4         6        2
D26V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 0                  1
  STAGE II                 2                  4
  STAGE III                5                  6
  STAGE IV                 0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  14Q LOSS MUTATED       3     4
  14Q LOSS WILD-TYPE    10     4
D26V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1+T2                3                 10
  T3+T4                4                  4
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  14Q LOSS MUTATED    5     2
  14Q LOSS WILD-TYPE  9     4
D26V5, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                   5                  9
  N1+N2                2                  4
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  14Q LOSS MUTATED    6  0  1
  14Q LOSS WILD-TYPE  9  1  4
D26V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0                6                  9
  M1                0                  1
  MX                1                  4
[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"
D26V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    4  3
  14Q LOSS WILD-TYPE  2 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4    3
  14Q LOSS WILD-TYPE    2   12
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                4                  2
  MALE                  3                 12
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q LOSS MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    2  2
  15Q LOSS WILD-TYPE  3 14
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 17 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 14 
$`15Q LOSS MUTATED`
TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BH 
        3.52        13.61         0.23         7.99 

$`15Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL 
       91.73        18.81        23.31         5.19        17.33        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SH-A7BC TCGA-SH-A7BD 
       24.89        43.27        51.78        23.90        15.09 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.23               1.87 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             13.61              91.73 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             5.755             18.810 
[1] "0.2 - 13.6 (5.8)"  "1.9 - 91.7 (18.8)"
[1] "hr=" "4.1"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         0        1        1         2        0
  15Q LOSS WILD-TYPE       1        0        5         9        2
D27V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 1                  0
  STAGE II                 1                  5
  STAGE III                2                  9
  STAGE IV                 0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  15Q LOSS MUTATED       2     2
  15Q LOSS WILD-TYPE    11     6
D27V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1+T2                2                 11
  T3+T4                2                  6
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  15Q LOSS MUTATED    3     0
  15Q LOSS WILD-TYPE 11     6
D27V5, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                   3                 11
  N1+N2                0                  6
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  15Q LOSS MUTATED    2  0  2
  15Q LOSS WILD-TYPE 13  1  3
D27V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                2                 13
  M1                0                  1
  MX                2                  3
[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"
D27V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  3
  15Q LOSS WILD-TYPE  5 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    3
  15Q LOSS WILD-TYPE    5   12
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                1                  5
  MALE                  3                 12
[1] 2 2
[1] FALSE

Clustering(28) Variable = 17P LOSS MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED    2  2
  17P LOSS WILD-TYPE  3 14
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 4                 17 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 14 
$`17P LOSS MUTATED`
TCGA-LK-A4NW TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BH 
       17.95        13.61         0.23         7.99 

$`17P LOSS WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        8.02         1.87        31.20        12.20        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SH-A7BC TCGA-SH-A7BD 
       24.89        43.27        51.78        23.90        15.09 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.23               1.87 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             17.95              91.73 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             10.80              18.81 
[1] "0.2 - 17.9 (10.8)" "1.9 - 91.7 (18.8)"
[1] "hr=" "1.9"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         0        1        1         1        1
  17P LOSS WILD-TYPE       1        0        5        10        1
D28V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 1                  0
  STAGE II                 1                  5
  STAGE III                1                 10
  STAGE IV                 1                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  17P LOSS MUTATED       2     2
  17P LOSS WILD-TYPE    11     6
D28V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1+T2                2                 11
  T3+T4                2                  6
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  17P LOSS MUTATED    2     1
  17P LOSS WILD-TYPE 12     5
D28V5, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                   2                 12
  N1+N2                1                  5
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  17P LOSS MUTATED    2  0  2
  17P LOSS WILD-TYPE 13  1  3
D28V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0                2                 13
  M1                0                  1
  MX                2                  3
[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"
D28V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    1  3
  17P LOSS WILD-TYPE  5 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1    3
  17P LOSS WILD-TYPE    5   12
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                1                  5
  MALE                  3                 12
[1] 2 2
[1] FALSE

Clustering(29) Variable = 17Q LOSS MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    2  1
  17Q LOSS WILD-TYPE  3 15
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 18 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 15 
$`17Q LOSS MUTATED`
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BH 
       13.61         0.23         7.99 

$`17Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SH-A7BC TCGA-SH-A7BD 
       10.95        24.89        43.27        51.78        23.90        15.09 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.23               1.87 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             13.61              91.73 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              7.99              18.38 
[1] "0.2 - 13.6 (8.0)"  "1.9 - 91.7 (18.4)"
[1] "hr=" "1.9"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED         0        1        1         1        0
  17Q LOSS WILD-TYPE       1        0        5        10        2
D29V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 1                  0
  STAGE II                 1                  5
  STAGE III                1                 10
  STAGE IV                 0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  17Q LOSS MUTATED       2     1
  17Q LOSS WILD-TYPE    11     7
D29V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1+T2                2                 11
  T3+T4                1                  7
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  17Q LOSS MUTATED    2     0
  17Q LOSS WILD-TYPE 12     6
D29V5, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 18 
        TCGA-LK-A4NW         TCGA-LK-A4NZ         TCGA-LK-A4O2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-LK-A4O4         TCGA-LK-A4O5         TCGA-MQ-A4KX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LC         TCGA-MQ-A4LI         TCGA-MQ-A4LJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LM         TCGA-MQ-A4LP         TCGA-MQ-A4LV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MQ-A6BL         TCGA-MQ-A6BN         TCGA-MQ-A6BQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MQ-A6BR         TCGA-SH-A7BC         TCGA-SH-A7BD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  17Q LOSS MUTATED    1  0  2
  17Q LOSS WILD-TYPE 14  1  3
D29V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                1                 14
  M1                0                  1
  MX                2                  3
[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"
D29V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    1  2
  17Q LOSS WILD-TYPE  5 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    2
  17Q LOSS WILD-TYPE    5   13
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                1                  5
  MALE                  2                 13
[1] 2 2
[1] FALSE

Clustering(30) Variable = 18P LOSS MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    1  3
  18P LOSS WILD-TYPE  4 13
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 17 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 3                 13 
$`18P LOSS MUTATED`
TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BS 
       18.81         5.19        10.95        13.61 

$`18P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       91.73        23.31        17.33         3.52        24.89        43.27 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       51.78         0.23        23.90        15.09         7.99 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              5.19               0.23 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             18.81              91.73 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             12.28              17.95 
[1] "5.2 - 18.8 (12.3)" "0.2 - 91.7 (17.9)"
[1] "hr=" "2.3"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  18P LOSS MUTATED         0        0        3         1        0
  18P LOSS WILD-TYPE       1        1        3        10        2
D30V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 0                  1
  STAGE II                 3                  3
  STAGE III                1                 10
  STAGE IV                 0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  18P LOSS MUTATED       3     1
  18P LOSS WILD-TYPE    10     7
D30V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1+T2                3                 10
  T3+T4                1                  7
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  18P LOSS MUTATED    4     0
  18P LOSS WILD-TYPE 10     6
D30V5, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                   4                 10
  N1+N2                0                  6
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18P LOSS MUTATED    3  0  1
  18P LOSS WILD-TYPE 12  1  4
D30V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                3                 12
  M1                0                  1
  MX                1                  4
[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"
D30V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    1  3
  18P LOSS WILD-TYPE  5 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    3
  18P LOSS WILD-TYPE    5   12
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                1                  5
  MALE                  3                 12
[1] 2 2
[1] FALSE

Clustering(31) Variable = 18Q LOSS MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    1  3
  18Q LOSS WILD-TYPE  4 13
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 17 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 3                 13 
$`18Q LOSS MUTATED`
TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BS 
       18.81         5.19        10.95        13.61 

$`18Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       91.73        23.31        17.33         3.52        24.89        43.27 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       51.78         0.23        23.90        15.09         7.99 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              5.19               0.23 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             18.81              91.73 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             12.28              17.95 
[1] "5.2 - 18.8 (12.3)" "0.2 - 91.7 (17.9)"
[1] "hr=" "2.3"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED         0        0        3         1        0
  18Q LOSS WILD-TYPE       1        1        3        10        2
D31V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 0                  1
  STAGE II                 3                  3
  STAGE III                1                 10
  STAGE IV                 0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  18Q LOSS MUTATED       3     1
  18Q LOSS WILD-TYPE    10     7
D31V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1+T2                3                 10
  T3+T4                1                  7
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  18Q LOSS MUTATED    4     0
  18Q LOSS WILD-TYPE 10     6
D31V5, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                   4                 10
  N1+N2                0                  6
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18Q LOSS MUTATED    3  0  1
  18Q LOSS WILD-TYPE 12  1  4
D31V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0                3                 12
  M1                0                  1
  MX                1                  4
[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"
D31V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    1  3
  18Q LOSS WILD-TYPE  5 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    3
  18Q LOSS WILD-TYPE    5   12
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                1                  5
  MALE                  3                 12
[1] 2 2
[1] FALSE

Clustering(32) Variable = 19Q LOSS MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    3  0
  19Q LOSS WILD-TYPE  2 16
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 18 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 0                 16 
$`19Q LOSS MUTATED`
TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I 
       43.27        13.61         0.23 

$`19Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       10.95        24.89        51.78        23.90        15.09         7.99 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.23               1.87 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             43.27              91.73 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             13.61              17.64 
[1] "0.2 - 43.3 (13.6)" "1.9 - 91.7 (17.6)"
[1] "hr="     "2.2e+08"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         0        1        2         0        0
  19Q LOSS WILD-TYPE       1        0        4        11        2
D32V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 1                  0
  STAGE II                 2                  4
  STAGE III                0                 11
  STAGE IV                 0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  19Q LOSS MUTATED       3     0
  19Q LOSS WILD-TYPE    10     8
D32V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1+T2                3                 10
  T3+T4                0                  8
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  19Q LOSS MUTATED    2     0
  19Q LOSS WILD-TYPE 12     6
D32V5, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 18 
        TCGA-LK-A4NW         TCGA-LK-A4NZ         TCGA-LK-A4O2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-LK-A4O4         TCGA-LK-A4O5         TCGA-MQ-A4KX 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LC         TCGA-MQ-A4LI         TCGA-MQ-A4LJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LM         TCGA-MQ-A4LP         TCGA-MQ-A4LV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MQ-A6BL         TCGA-MQ-A6BN         TCGA-MQ-A6BR 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-SH-A7BC         TCGA-SH-A7BD         TCGA-SH-A7BH 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  19Q LOSS MUTATED    0  0  3
  19Q LOSS WILD-TYPE 15  1  2
D32V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                0                 15
  M1                0                  1
  MX                3                  2
[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"
D32V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    0  3
  19Q LOSS WILD-TYPE  6 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    3
  19Q LOSS WILD-TYPE    6   12
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                0                  6
  MALE                  3                 12
[1] 2 2
[1] FALSE

Clustering(33) Variable = 20P LOSS MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    3  1
  20P LOSS WILD-TYPE  2 15
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                 17 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 15 
$`20P LOSS MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O5 TCGA-MQ-A6BQ TCGA-MQ-A6BS 
       17.95        12.20        43.27        13.61 

$`20P LOSS WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
        8.02         1.87        31.20        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       51.78         0.23        23.90        15.09         7.99 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             12.20               0.23 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             43.27              91.73 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             15.78              17.33 
[1] "12.2 - 43.3 (15.8)" "0.2 - 91.7 (17.3)" 
[1] "hr=" "3.1"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         0        0        2         1        1
  20P LOSS WILD-TYPE       1        1        4        10        1
D33V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 0                  1
  STAGE II                 2                  4
  STAGE III                1                 10
  STAGE IV                 1                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  20P LOSS MUTATED       2     2
  20P LOSS WILD-TYPE    11     6
D33V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1+T2                2                 11
  T3+T4                2                  6
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  20P LOSS MUTATED    3     1
  20P LOSS WILD-TYPE 11     5
D33V5, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                   3                 11
  N1+N2                1                  5
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20P LOSS MUTATED    2  0  2
  20P LOSS WILD-TYPE 13  1  3
D33V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                2                 13
  M1                0                  1
  MX                2                  3
[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"
D33V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    1  3
  20P LOSS WILD-TYPE  5 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    3
  20P LOSS WILD-TYPE    5   12
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                1                  5
  MALE                  3                 12
[1] 2 2
[1] FALSE

Clustering(34) Variable = 21Q LOSS MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    2  1
  21Q LOSS WILD-TYPE  3 15
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 18 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 1                 15 
$`21Q LOSS MUTATED`
TCGA-LK-A4O2 TCGA-MQ-A6BS TCGA-NQ-A57I 
        1.87        13.61         0.23 

$`21Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       17.95         8.02        31.20        12.20        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       24.89        43.27        51.78        23.90        15.09         7.99 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.23               3.52 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             13.61              91.73 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              1.87              18.38 
[1] "0.2 - 13.6 (1.9)"  "3.5 - 91.7 (18.4)"
[1] "hr=" "2.8"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED         0        1        1         1        0
  21Q LOSS WILD-TYPE       1        0        5        10        2
D34V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 1                  0
  STAGE II                 1                  5
  STAGE III                1                 10
  STAGE IV                 0                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  21Q LOSS MUTATED       2     1
  21Q LOSS WILD-TYPE    11     7
D34V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1+T2                2                 11
  T3+T4                1                  7
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  21Q LOSS MUTATED    2     0
  21Q LOSS WILD-TYPE 12     6
D34V5, multiclass
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                 18 
        TCGA-LK-A4NW         TCGA-LK-A4NZ         TCGA-LK-A4O4 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-MQ-A4KX         TCGA-MQ-A4LC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LJ         TCGA-MQ-A4LM 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LP         TCGA-MQ-A4LV         TCGA-MQ-A6BL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-MQ-A6BN         TCGA-MQ-A6BQ         TCGA-MQ-A6BR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-SH-A7BC         TCGA-SH-A7BD         TCGA-SH-A7BH 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  21Q LOSS MUTATED    1  0  2
  21Q LOSS WILD-TYPE 14  1  3
D34V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0                1                 14
  M1                0                  1
  MX                2                  3
[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"
D34V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    1  2
  21Q LOSS WILD-TYPE  5 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1    2
  21Q LOSS WILD-TYPE    5   13
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                1                  5
  MALE                  2                 13
[1] 2 2
[1] FALSE

Clustering(35) Variable = 22Q LOSS MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    4 11
  22Q LOSS WILD-TYPE  1  5
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                  6 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                11                  5 
$`22Q LOSS MUTATED`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        8.02         1.87        12.20        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS 
        5.19        17.33         3.52        24.89        43.27        13.61 
TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD 
        0.23        23.90        15.09 

$`22Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-SH-A7BH 
       17.95        31.20        80.84        10.95        51.78         7.99 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.23               7.99 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             91.73              80.84 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            15.090             24.575 
[1] "0.2 - 91.7 (15.1)" "8.0 - 80.8 (24.6)"
[1] "hr=" "1.3"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IB STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED         0        1        5         8        1
  22Q LOSS WILD-TYPE       1        0        1         3        1
D35V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IB                 1                  0
  STAGE II                 5                  1
  STAGE III                8                  3
  STAGE IV                 1                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  22Q LOSS MUTATED       9     6
  22Q LOSS WILD-TYPE     4     2
D35V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1+T2                9                  4
  T3+T4                6                  2
[1] 2 2
[1] FALSE
                    vv
clus                 N0 N1+N2
  22Q LOSS MUTATED   11     3
  22Q LOSS WILD-TYPE  3     3
D35V5, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                  11                  3
  N1+N2                3                  3
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  22Q LOSS MUTATED   10  1  4
  22Q LOSS WILD-TYPE  5  0  1
D35V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               10                  5
  M1                1                  0
  MX                4                  1
[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"
D35V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    4 11
  22Q LOSS WILD-TYPE  2  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4   11
  22Q LOSS WILD-TYPE    2    4
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                4                  2
  MALE                 11                  4
[1] 2 2
[1] FALSE

Clustering(36) Variable = XQ LOSS MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    1  3
  XQ LOSS WILD-TYPE  4 13
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                17 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                13 
$`XQ LOSS MUTATED`
TCGA-MQ-A4LI TCGA-MQ-A4LP TCGA-MQ-A6BS TCGA-SH-A7BD 
       18.81        17.33        13.61        15.09 

$`XQ LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       91.73        23.31         5.19         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BH 
       43.27        51.78         0.23        23.90         7.99 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            13.61              0.23 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            18.81             91.73 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            16.21             17.95 
[1] "13.6 - 18.8 (16.2)" "0.2 - 91.7 (17.9)" 
[1] "hr=" "1.7"
D36V2, continuous
                   vv
clus                STAGE I STAGE IB STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         0        0        2         1        1
  XQ LOSS WILD-TYPE       1        1        4        10        1
D36V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IB                0                 1
  STAGE II                2                 4
  STAGE III               1                10
  STAGE IV                1                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  XQ LOSS MUTATED       3     1
  XQ LOSS WILD-TYPE    10     7
D36V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1+T2               3                10
  T3+T4               1                 7
[1] 2 2
[1] FALSE
                   vv
clus                N0 N1+N2
  XQ LOSS MUTATED    4     0
  XQ LOSS WILD-TYPE 10     6
D36V5, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0                  4                10
  N1+N2               0                 6
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  XQ LOSS MUTATED    2  1  1
  XQ LOSS WILD-TYPE 13  0  4
D36V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               2                13
  M1               1                 0
  MX               1                 4
[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"
D36V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    1  3
  XQ LOSS WILD-TYPE  5 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    3
  XQ LOSS WILD-TYPE    5   12
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               1                 5
  MALE                 3                12
[1] 2 2
[1] FALSE
