[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/11541580/MESO-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/MESO-TP/11544696/transformed.cor.cli.txt"

nPatients in clinical file=39, in cluster file=87, common to both=39
[1] "Reduce the number of clustering variables from 80 to 55."
[1] 55 39
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5                34 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5                34 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               12                27 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               12                27 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                29 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                29 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               12                27 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               12                27 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                9                30 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                9                30 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5                34 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5                34 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               10                29 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               10                29 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                9                30 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                9                30 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                32 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                32 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                31 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                31 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 36 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 36 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                 28 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                 28 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                11                 28 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                11                 28 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 35 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 35 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 32 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 32 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                 31 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                 31 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 36 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 36 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                10                 29 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                10                 29 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 36 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 36 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 36 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 36 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 34 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 34 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                 35 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                 35 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 34 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 34 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 6                 33 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 6                 33 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 35 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 35 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                33 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                33 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                36 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                36 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                36 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                36 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3                36 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3                36 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               18                21 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               18                21 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16                23 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16                23 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                36 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                36 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                5                34 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                5                34 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               13                26 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               13                26 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                35 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                35 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               14                25 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               14                25 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               12                27 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               12                27 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                10                 29 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                10                 29 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 9                 30 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 9                 30 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                 36 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                 36 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                 35 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                 35 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                 19 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                 19 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                15                 24 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                15                 24 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 32 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 32 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 34 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 34 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                 33 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                 33 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 30 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 30 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 36 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 36 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 34 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 34 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                 32 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                 32 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 36 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 36 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                 32 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                 32 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 5                 34 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 5                 34 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                31                  8 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                31                  8 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               12                27 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               12                27 
[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 39 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
          NA           NA           NA           NA           NA           NA 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
         371           49          108           NA           NA           NA 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
          NA           NA           NA           NA           NA           NA 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
        1316         1575          414            7           NA          200 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 
          NA           NA           NA          256           NA           NA 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G 
          NA           NA          723          652           NA           NA 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
          NA           NA           NA 
Variable 1:'AGE':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	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=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RACE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=2,	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 39 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=23, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 7 17 13  2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
    7    17    15 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 7 17 13  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
    7    17    15 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
25  6  5 
[1] "table(vv)"
vv
N0 N1 N2 
25  6  5 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
25  6  5 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
25  6  5 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    0  5
  1P GAIN WILD-TYPE 10 24
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5                34 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5                24 
$`1P GAIN MUTATED`
TCGA-LK-A4O0 TCGA-SH-A7BC TCGA-SH-A7BH TCGA-UD-AAC6 TCGA-UD-AAC7 
        6.08        23.90         7.99        14.99        13.35 

$`1P GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        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-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BD 
       51.78        13.61         0.23        28.96         6.58        15.09 
TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E 
        8.42         6.48        23.64        23.77        21.44        14.27 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
        2.50         4.73         4.67         2.76 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             6.08              0.23 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            23.90             91.73 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           13.350            12.905 
[1] "6.1 - 23.9 (13.3)" "0.2 - 91.7 (12.9)"
[1] "hr=" "1.8"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         0        1        0        2         2        0
  1P GAIN WILD-TYPE       3        0        1        9        17        4
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                1                 0
  STAGE IB                0                 1
  STAGE II                2                 9
  STAGE III               2                17
  STAGE IV                0                 4
[1] 6 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 GAIN MUTATED    1  2     2
  1P GAIN WILD-TYPE  6 15    13
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1                  1                 6
  T2                  2                15
  T3+T4               2                13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  1P GAIN MUTATED    4  0  1
  1P GAIN WILD-TYPE 21  6  4
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0               4                21
  N1               0                 6
  N2               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"
                   vv
clus                M0 M1 MX
  1P GAIN MUTATED    5  0  0
  1P GAIN WILD-TYPE 26  2  6
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               5                26
  M1               0                 2
  MX               0                 6
[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
  1P GAIN MUTATED    1  4
  1P GAIN WILD-TYPE  9 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    4
  1P GAIN WILD-TYPE    9   25
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               1                 9
  MALE                 4                25
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    4  8
  1Q GAIN WILD-TYPE  6 21
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               12                27 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                21 
$`1Q GAIN MUTATED`
TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        8.02         6.08         1.61         3.55        18.81        23.31 
TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC7 
        6.58        23.90         7.99         8.42         6.48        13.35 

$`1Q GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         5.52         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-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BD 
       43.27        51.78        13.61         0.23        28.96        15.09 
TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G 
       23.64        14.99        23.77        21.44        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
        4.73         4.67         2.76 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1.61              0.23 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            23.90             91.73 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            8.005            14.990 
[1] "1.6 - 23.9 (8.0)"  "0.2 - 91.7 (15.0)"
[1] "hr=" "1.5"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         0        1        0        5         6        0
  1Q GAIN WILD-TYPE       3        0        1        6        13        4
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                1                 0
  STAGE IB                0                 1
  STAGE II                5                 6
  STAGE III               6                13
  STAGE IV                0                 4
[1] 6 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    1  7     4
  1Q GAIN WILD-TYPE  6 10    11
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1                  1                 6
  T2                  7                10
  T3+T4               4                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  1Q GAIN MUTATED    7  3  2
  1Q GAIN WILD-TYPE 18  3  3
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0               7                18
  N1               3                 3
  N2               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"
                   vv
clus                M0 M1 MX
  1Q GAIN MUTATED   12  0  0
  1Q GAIN WILD-TYPE 19  2  6
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              12                19
  M1               0                 2
  MX               0                 6
[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
  1Q GAIN MUTATED    3  9
  1Q GAIN WILD-TYPE  7 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3    9
  1Q GAIN WILD-TYPE    7   20
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               3                 7
  MALE                 9                20
[1] 2 2
[1] FALSE

Clustering(3) Variable = 3P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    4  6
  3P GAIN WILD-TYPE  6 23
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                29 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                23 
$`3P GAIN MUTATED`
TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A6BS TCGA-SH-A7BC TCGA-SH-A7BH 
        6.08        12.20         1.61        13.61        23.90         7.99 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       14.99        13.35        23.77         2.50 

$`3P GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O7 
       17.95         5.52         8.02         1.87        31.20         3.55 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       80.84        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
        3.52        10.95        24.89        43.27        51.78         0.23 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 
       28.96         6.58        15.09         8.42         6.48        23.64 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       21.44        14.27         4.73         4.67         2.76 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1.61              0.23 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            23.90             91.73 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           12.775            14.270 
[1] "1.6 - 23.9 (12.8)" "0.2 - 91.7 (14.3)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         0        1        0        3         6        0
  3P GAIN WILD-TYPE       3        0        1        8        13        4
D3V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                1                 0
  STAGE IB                0                 1
  STAGE II                3                 8
  STAGE III               6                13
  STAGE IV                0                 4
[1] 6 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     6
  3P GAIN WILD-TYPE  6 14     9
D3V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1                  1                 6
  T2                  3                14
  T3+T4               6                 9
[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"
                   vv
clus                N0 N1 N2
  3P GAIN MUTATED    7  1  2
  3P GAIN WILD-TYPE 18  5  3
D3V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0               7                18
  N1               1                 5
  N2               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"
                   vv
clus                M0 M1 MX
  3P GAIN MUTATED    9  0  1
  3P GAIN WILD-TYPE 22  2  5
D3V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               9                22
  M1               0                 2
  MX               1                 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"
D3V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3  7
  3P GAIN WILD-TYPE  7 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    7
  3P GAIN WILD-TYPE    7   22
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               3                 7
  MALE                 7                22
[1] 2 2
[1] FALSE

Clustering(4) Variable = 3Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    5  7
  3Q GAIN WILD-TYPE  5 22
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               12                27 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                7                22 
$`3Q GAIN MUTATED`
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A6BS TCGA-SH-A7BC 
        6.08         1.87        12.20         1.61        13.61        23.90 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
        7.99         8.42        14.99        13.35        23.77         2.50 

$`3Q GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O7 TCGA-MQ-A4KX 
       17.95         5.52         8.02        31.20         3.55        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-NQ-A57I TCGA-SC-A6LM 
       10.95        24.89        43.27        51.78         0.23        28.96 
TCGA-SC-A6LN TCGA-SH-A7BD TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UT-A88D TCGA-UT-A88E 
        6.58        15.09         6.48        23.64        21.44        14.27 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
        4.73         4.67         2.76 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             1.61              0.23 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            23.90             91.73 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            10.31             15.09 
[1] "1.6 - 23.9 (10.3)" "0.2 - 91.7 (15.1)"
[1] "hr=" "1.3"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED         0        1        0        4         7        0
  3Q GAIN WILD-TYPE       3        0        1        7        12        4
D4V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                1                 0
  STAGE IB                0                 1
  STAGE II                4                 7
  STAGE III               7                12
  STAGE IV                0                 4
[1] 6 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     7
  3Q GAIN WILD-TYPE  6 13     8
D4V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1                  1                 6
  T2                  4                13
  T3+T4               7                 8
[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"
                   vv
clus                N0 N1 N2
  3Q GAIN MUTATED    9  1  2
  3Q GAIN WILD-TYPE 16  5  3
D4V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0               9                16
  N1               1                 5
  N2               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"
                   vv
clus                M0 M1 MX
  3Q GAIN MUTATED   11  0  1
  3Q GAIN WILD-TYPE 20  2  5
D4V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              11                20
  M1               0                 2
  MX               1                 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"
D4V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    4  8
  3Q GAIN WILD-TYPE  6 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4    8
  3Q GAIN WILD-TYPE    6   21
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               4                 6
  MALE                 8                21
[1] 2 2
[1] FALSE

Clustering(5) Variable = 5P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    3  6
  5P GAIN WILD-TYPE  7 23
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                9                30 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                6                23 
$`5P GAIN MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O7 TCGA-MQ-A4LP TCGA-MQ-A6BR 
       17.95         6.08         1.87         3.55        17.33        51.78 
TCGA-MQ-A6BS TCGA-SH-A7BH TCGA-UD-AABZ 
       13.61         7.99         6.48 

$`5P GAIN WILD-TYPE`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX 
        5.52         8.02        31.20        12.20         1.61        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-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC 
       24.89        43.27         0.23        28.96         6.58        23.90 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       15.09         8.42        23.64        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       21.44        14.27         2.50         4.73         4.67         2.76 

  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 
             7.99             13.81 
[1] "1.9 - 51.8 (8.0)"  "0.2 - 91.7 (13.8)"
[1] "hr=" "1.2"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  5P GAIN MUTATED         0        1        0        2         5        1
  5P GAIN WILD-TYPE       3        0        1        9        14        3
D5V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                1                 0
  STAGE IB                0                 1
  STAGE II                2                 9
  STAGE III               5                14
  STAGE IV                1                 3
[1] 6 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  2     5
  5P GAIN WILD-TYPE  5 15    10
D5V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1                  2                 5
  T2                  2                15
  T3+T4               5                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  5P GAIN MUTATED    6  2  1
  5P GAIN WILD-TYPE 19  4  4
D5V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0               6                19
  N1               2                 4
  N2               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"
                   vv
clus                M0 M1 MX
  5P GAIN MUTATED    7  0  2
  5P GAIN WILD-TYPE 24  2  4
D5V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               7                24
  M1               0                 2
  MX               2                 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"
D5V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    3  6
  5P GAIN WILD-TYPE  7 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3    6
  5P GAIN WILD-TYPE    7   23
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               3                 7
  MALE                 6                23
[1] 2 2
[1] FALSE

Clustering(6) Variable = 5Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    2  3
  5Q GAIN WILD-TYPE  8 26
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5                34 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                26 
$`5Q GAIN MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SH-A7BH TCGA-UD-AABZ 
        6.08        51.78        13.61         7.99         6.48 

$`5Q GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        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-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT 
        0.23        28.96         6.58        23.90        15.09         8.42 
TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E 
       23.64        14.99        13.35        23.77        21.44        14.27 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
        2.50         4.73         4.67         2.76 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             6.08              0.23 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            51.78             91.73 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             7.99             13.81 
[1] "6.1 - 51.8 (8.0)"  "0.2 - 91.7 (13.8)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED         0        1        0        2         2        0
  5Q GAIN WILD-TYPE       3        0        1        9        17        4
D6V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                1                 0
  STAGE IB                0                 1
  STAGE II                2                 9
  STAGE III               2                17
  STAGE IV                0                 4
[1] 6 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  2     1
  5Q GAIN WILD-TYPE  5 15    14
D6V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1                  2                 5
  T2                  2                15
  T3+T4               1                14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  5Q GAIN MUTATED    4  1  0
  5Q GAIN WILD-TYPE 21  5  5
D6V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               4                21
  N1               1                 5
  N2               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"
                   vv
clus                M0 M1 MX
  5Q GAIN MUTATED    3  0  2
  5Q GAIN WILD-TYPE 28  2  4
D6V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               3                28
  M1               0                 2
  MX               2                 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
  5Q GAIN MUTATED    2  3
  5Q GAIN WILD-TYPE  8 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    3
  5Q GAIN WILD-TYPE    8   26
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               2                 8
  MALE                 3                26
[1] 2 2
[1] FALSE

Clustering(7) Variable = 7P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED    2  8
  7P GAIN WILD-TYPE  8 21
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               10                29 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                8                21 
$`7P GAIN MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-MQ-A6BS TCGA-SH-A7BC TCGA-SH-A7BH 
       17.95         6.08         1.87        13.61        23.90         7.99 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       14.99        13.35        23.77         2.50 

$`7P GAIN WILD-TYPE`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
        5.52         8.02        31.20        12.20         1.61         3.55 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       80.84        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
        3.52        10.95        24.89        43.27        51.78         0.23 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 
       28.96         6.58        15.09         8.42         6.48        23.64 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       21.44        14.27         4.73         4.67         2.76 

  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 
            13.48             12.20 
[1] "1.9 - 23.9 (13.5)" "0.2 - 91.7 (12.2)"
[1] "hr=" "1.6"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  7P GAIN MUTATED         0        1        0        3         5        1
  7P GAIN WILD-TYPE       3        0        1        8        14        3
D7V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                1                 0
  STAGE IB                0                 1
  STAGE II                3                 8
  STAGE III               5                14
  STAGE IV                1                 3
[1] 6 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  3     6
  7P GAIN WILD-TYPE  6 14     9
D7V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1                  1                 6
  T2                  3                14
  T3+T4               6                 9
[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"
                   vv
clus                N0 N1 N2
  7P GAIN MUTATED    7  0  3
  7P GAIN WILD-TYPE 18  6  2
D7V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0               7                18
  N1               0                 6
  N2               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"
                   vv
clus                M0 M1 MX
  7P GAIN MUTATED    9  0  1
  7P GAIN WILD-TYPE 22  2  5
D7V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0               9                22
  M1               0                 2
  MX               1                 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"
D7V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    2  8
  7P GAIN WILD-TYPE  8 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2    8
  7P GAIN WILD-TYPE    8   21
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               2                 8
  MALE                 8                21
[1] 2 2
[1] FALSE

Clustering(8) Variable = 7Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED    2  7
  7Q GAIN WILD-TYPE  8 22
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                9                30 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                7                22 
$`7Q GAIN MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-MQ-A6BS TCGA-SH-A7BC TCGA-SH-A7BH TCGA-UD-AAC6 
       17.95         1.87        13.61        23.90         7.99        14.99 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       13.35        23.77         2.50 

$`7Q GAIN WILD-TYPE`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08        31.20        12.20         1.61 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
        3.55        80.84        91.73        18.81        23.31         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-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ 
        0.23        28.96         6.58        15.09         8.42         6.48 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       23.64        21.44        14.27         4.73         4.67         2.76 

  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 
           13.610            11.575 
[1] "1.9 - 23.9 (13.6)" "0.2 - 91.7 (11.6)"
[1] "hr=" "1.4"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED         0        0        0        3         5        1
  7Q GAIN WILD-TYPE       3        1        1        8        14        3
D8V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                0                 1
  STAGE IB                0                 1
  STAGE II                3                 8
  STAGE III               5                14
  STAGE IV                1                 3
[1] 6 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    0  3     6
  7Q GAIN WILD-TYPE  7 14     9
D8V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1                  0                 7
  T2                  3                14
  T3+T4               6                 9
[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"
                   vv
clus                N0 N1 N2
  7Q GAIN MUTATED    6  0  3
  7Q GAIN WILD-TYPE 19  6  2
D8V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0               6                19
  N1               0                 6
  N2               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"
                   vv
clus                M0 M1 MX
  7Q GAIN MUTATED    8  0  1
  7Q GAIN WILD-TYPE 23  2  5
D8V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0               8                23
  M1               0                 2
  MX               1                 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
  7Q GAIN MUTATED    2  7
  7Q GAIN WILD-TYPE  8 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2    7
  7Q GAIN WILD-TYPE    8   22
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               2                 8
  MALE                 7                22
[1] 2 2
[1] FALSE

Clustering(9) Variable = 8P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    1  6
  8P GAIN WILD-TYPE  9 23
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                32 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6                23 
$`8P GAIN MUTATED`
TCGA-LK-A4NW TCGA-MQ-A4LM TCGA-SH-A7BH TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       17.95         5.19         7.99        13.35        23.77         2.50 
TCGA-XT-AASU 
        4.67 

$`8P GAIN WILD-TYPE`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
        5.52         8.02         6.08         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        91.73        18.81        23.31 
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-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD 
       13.61         0.23        28.96         6.58        23.90        15.09 
TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A88E 
        8.42         6.48        23.64        14.99        21.44        14.27 
TCGA-UT-A97Y TCGA-YS-AA4M 
        4.73         2.76 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             2.50              0.23 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            23.77             91.73 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             7.99             13.94 
[1] "2.5 - 23.8 (8.0)"  "0.2 - 91.7 (13.9)"
[1] "hr=" "2.1"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         0        0        0        1         5        1
  8P GAIN WILD-TYPE       3        1        1       10        14        3
D9V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                0                 1
  STAGE IB                0                 1
  STAGE II                1                10
  STAGE III               5                14
  STAGE IV                1                 3
[1] 6 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  1     6
  8P GAIN WILD-TYPE  7 16     9
D9V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1                  0                 7
  T2                  1                16
  T3+T4               6                 9
[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"
                   vv
clus                N0 N1 N2
  8P GAIN MUTATED    4  0  2
  8P GAIN WILD-TYPE 21  6  3
D9V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0               4                21
  N1               0                 6
  N2               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"
                   vv
clus                M0 M1 MX
  8P GAIN MUTATED    6  0  1
  8P GAIN WILD-TYPE 25  2  5
D9V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               6                25
  M1               0                 2
  MX               1                 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"
D9V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    1  6
  8P GAIN WILD-TYPE  9 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1    6
  8P GAIN WILD-TYPE    9   23
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               1                 9
  MALE                 6                23
[1] 2 2
[1] FALSE

Clustering(10) Variable = 8Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED    1  7
  8Q GAIN WILD-TYPE  9 22
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                31 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7                22 
$`8Q GAIN MUTATED`
TCGA-LK-A4NW TCGA-MQ-A4LM TCGA-NQ-A57I TCGA-SH-A7BH TCGA-UD-AAC7 TCGA-UT-A88C 
       17.95         5.19         0.23         7.99        13.35        23.77 
TCGA-UT-A88G TCGA-XT-AASU 
        2.50         4.67 

$`8Q GAIN WILD-TYPE`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
        5.52         8.02         6.08         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        91.73        18.81        23.31 
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-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT 
       13.61        28.96         6.58        23.90        15.09         8.42 
TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y 
        6.48        23.64        14.99        21.44        14.27         4.73 
TCGA-YS-AA4M 
        2.76 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.23              1.61 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            23.77             91.73 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             6.59             14.27 
[1] "0.2 - 23.8 (6.6)"  "1.6 - 91.7 (14.3)"
[1] "hr=" "2.6"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         0        0        1        1         5        1
  8Q GAIN WILD-TYPE       3        1        0       10        14        3
D10V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                0                 1
  STAGE IB                1                 0
  STAGE II                1                10
  STAGE III               5                14
  STAGE IV                1                 3
[1] 6 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  1     6
  8Q GAIN WILD-TYPE  6 16     9
D10V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1                  1                 6
  T2                  1                16
  T3+T4               6                 9
[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"
                   vv
clus                N0 N1 N2
  8Q GAIN MUTATED    4  0  2
  8Q GAIN WILD-TYPE 21  6  3
D10V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0               4                21
  N1               0                 6
  N2               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"
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED    6  0  2
  8Q GAIN WILD-TYPE 25  2  4
D10V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0               6                25
  M1               0                 2
  MX               2                 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
  8Q GAIN MUTATED    1  7
  8Q GAIN WILD-TYPE  9 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1    7
  8Q GAIN WILD-TYPE    9   22
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               1                 9
  MALE                 7                22
[1] 2 2
[1] FALSE

Clustering(11) Variable = 11Q GAIN MUTATION ANALYSIS
D11V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    2  1
  11Q GAIN WILD-TYPE  8 28
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 36 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 28 
$`11Q GAIN MUTATED`
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-UD-AAC7 
       51.78        13.61        13.35 

$`11Q GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.20         1.61         3.55        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-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD 
       43.27         0.23        28.96         6.58        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C 
        7.99         8.42         6.48        23.64        14.99        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       21.44        14.27         2.50         4.73         4.67         2.76 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             13.35               0.23 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             51.78              91.73 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            13.610             11.575 
[1] "13.3 - 51.8 (13.6)" "0.2 - 91.7 (11.6)" 
[1] "hr=" "3"  
D11V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         0        0        0        2         1        0
  11Q GAIN WILD-TYPE       3        1        1        9        18        4
D11V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 0                  1
  STAGE IB                 0                  1
  STAGE II                 2                  9
  STAGE III                1                 18
  STAGE IV                 0                  4
[1] 6 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 GAIN MUTATED    1  2     0
  11Q GAIN WILD-TYPE  6 15    15
D11V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                   1                  6
  T2                   2                 15
  T3+T4                0                 15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  11Q GAIN MUTATED    2  1  0
  11Q GAIN WILD-TYPE 23  5  5
D11V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                2                 23
  N1                1                  5
  N2                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"
                    vv
clus                 M0 M1 MX
  11Q GAIN MUTATED    1  0  2
  11Q GAIN WILD-TYPE 30  2  4
D11V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                1                 30
  M1                0                  2
  MX                2                  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
  11Q GAIN MUTATED    1  2
  11Q GAIN WILD-TYPE  9 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    2
  11Q GAIN WILD-TYPE    9   27
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                1                  9
  MALE                  2                 27
[1] 2 2
[1] FALSE

Clustering(12) Variable = 12P GAIN MUTATION ANALYSIS
D12V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    3  8
  12P GAIN WILD-TYPE  7 21
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                 28 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 8                 21 
$`12P GAIN MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A6BS TCGA-NQ-A57I 
       17.95         6.08        12.20        80.84        13.61         0.23 
TCGA-SH-A7BC TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       23.90        14.99        13.35        23.77         2.50 

$`12P GAIN WILD-TYPE`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-LK-A4O7 
        5.52         8.02         1.87        31.20         1.61         3.55 
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-SC-A6LM TCGA-SC-A6LN 
       10.95        24.89        43.27        51.78        28.96         6.58 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UT-A88D 
       15.09         7.99         8.42         6.48        23.64        21.44 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       14.27         4.73         4.67         2.76 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.23               1.61 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             80.84              91.73 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            13.610              9.685 
[1] "0.2 - 80.8 (13.6)" "1.6 - 91.7 (9.7)" 
[1] "hr=" "1"  
D12V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  12P GAIN MUTATED         1        1        1        3         4        1
  12P GAIN WILD-TYPE       2        0        0        8        15        3
D12V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  1                  2
  STAGE IA                 1                  0
  STAGE IB                 1                  0
  STAGE II                 3                  8
  STAGE III                4                 15
  STAGE IV                 1                  3
[1] 6 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    3  3     5
  12P GAIN WILD-TYPE  4 14    10
D12V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                   3                  4
  T2                   3                 14
  T3+T4                5                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  12P GAIN MUTATED    7  0  3
  12P GAIN WILD-TYPE 18  6  2
D12V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                7                 18
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  12P GAIN MUTATED    9  0  2
  12P GAIN WILD-TYPE 22  2  4
D12V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                9                 22
  M1                0                  2
  MX                2                  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
  12P GAIN MUTATED    1 10
  12P GAIN WILD-TYPE  9 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   10
  12P GAIN WILD-TYPE    9   19
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                1                  9
  MALE                 10                 19
[1] 2 2
[1] FALSE

Clustering(13) Variable = 12Q GAIN MUTATION ANALYSIS
D13V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    3  8
  12Q GAIN WILD-TYPE  7 21
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                11                 28 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 8                 21 
$`12Q GAIN MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A6BS TCGA-NQ-A57I 
       17.95         6.08        12.20        80.84        13.61         0.23 
TCGA-SH-A7BC TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       23.90        14.99        13.35        23.77         2.50 

$`12Q GAIN WILD-TYPE`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-LK-A4O7 
        5.52         8.02         1.87        31.20         1.61         3.55 
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-SC-A6LM TCGA-SC-A6LN 
       10.95        24.89        43.27        51.78        28.96         6.58 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UT-A88D 
       15.09         7.99         8.42         6.48        23.64        21.44 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       14.27         4.73         4.67         2.76 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.23               1.61 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             80.84              91.73 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            13.610              9.685 
[1] "0.2 - 80.8 (13.6)" "1.6 - 91.7 (9.7)" 
[1] "hr=" "1"  
D13V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED         1        1        1        3         4        1
  12Q GAIN WILD-TYPE       2        0        0        8        15        3
D13V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  1                  2
  STAGE IA                 1                  0
  STAGE IB                 1                  0
  STAGE II                 3                  8
  STAGE III                4                 15
  STAGE IV                 1                  3
[1] 6 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    3  3     5
  12Q GAIN WILD-TYPE  4 14    10
D13V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                   3                  4
  T2                   3                 14
  T3+T4                5                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  12Q GAIN MUTATED    7  0  3
  12Q GAIN WILD-TYPE 18  6  2
D13V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                7                 18
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  12Q GAIN MUTATED    9  0  2
  12Q GAIN WILD-TYPE 22  2  4
D13V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                9                 22
  M1                0                  2
  MX                2                  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
  12Q GAIN MUTATED    1 10
  12Q GAIN WILD-TYPE  9 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   10
  12Q GAIN WILD-TYPE    9   19
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                1                  9
  MALE                 10                 19
[1] 2 2
[1] FALSE

Clustering(14) Variable = 15Q GAIN MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    1  3
  15Q GAIN WILD-TYPE  9 26
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 35 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 26 
$`15Q GAIN MUTATED`
TCGA-LK-A4NY TCGA-SC-A6LN TCGA-UT-A88E TCGA-UT-A88G 
        5.52         6.58        14.27         2.50 

$`15Q GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         8.02         6.08         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        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-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BC TCGA-SH-A7BD 
       51.78        13.61         0.23        28.96        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 
        7.99         8.42         6.48        23.64        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       23.77        21.44         4.73         4.67         2.76 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              2.50               0.23 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             14.27              91.73 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              6.05              13.61 
[1] "2.5 - 14.3 (6.0)"  "0.2 - 91.7 (13.6)"
[1] "hr=" "2.7"
D14V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED         1        0        0        0         3        0
  15Q GAIN WILD-TYPE       2        1        1       11        16        4
D14V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  1                  2
  STAGE IA                 0                  1
  STAGE IB                 0                  1
  STAGE II                 0                 11
  STAGE III                3                 16
  STAGE IV                 0                  4
[1] 6 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 GAIN MUTATED    1  1     2
  15Q GAIN WILD-TYPE  6 16    13
D14V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                   1                  6
  T2                   1                 16
  T3+T4                2                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  15Q GAIN MUTATED    3  0  1
  15Q GAIN WILD-TYPE 22  6  4
D14V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                3                 22
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  15Q GAIN MUTATED    4  0  0
  15Q GAIN WILD-TYPE 27  2  6
D14V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                4                 27
  M1                0                  2
  MX                0                  6
[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
  15Q GAIN MUTATED    1  3
  15Q GAIN WILD-TYPE  9 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    3
  15Q GAIN WILD-TYPE    9   26
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                1                  9
  MALE                  3                 26
[1] 2 2
[1] FALSE

Clustering(15) Variable = 16P GAIN MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    1  6
  16P GAIN WILD-TYPE  9 23
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 32 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 23 
$`16P GAIN MUTATED`
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BH TCGA-UD-AAC7 
       18.81        23.31         0.23        23.90         7.99        13.35 
TCGA-UT-A88C 
       23.77 

$`16P GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM 
       12.20         1.61         3.55        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-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ 
       13.61        28.96         6.58        15.09         8.42         6.48 
TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       23.64        14.99        21.44        14.27         2.50         4.73 
TCGA-XT-AASU TCGA-YS-AA4M 
        4.67         2.76 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.23               1.61 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             23.90              91.73 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            18.810             11.575 
[1] "0.2 - 23.9 (18.8)" "1.6 - 91.7 (11.6)"
[1] "hr=" "1.2"
D15V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  16P GAIN MUTATED         0        0        1        2         4        0
  16P GAIN WILD-TYPE       3        1        0        9        15        4
D15V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 0                  1
  STAGE IB                 1                  0
  STAGE II                 2                  9
  STAGE III                4                 15
  STAGE IV                 0                  4
[1] 6 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    1  3     3
  16P GAIN WILD-TYPE  6 14    12
D15V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                   1                  6
  T2                   3                 14
  T3+T4                3                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  16P GAIN MUTATED    3  1  2
  16P GAIN WILD-TYPE 22  5  3
D15V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                3                 22
  N1                1                  5
  N2                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"
                    vv
clus                 M0 M1 MX
  16P GAIN MUTATED    6  0  1
  16P GAIN WILD-TYPE 25  2  5
D15V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                6                 25
  M1                0                  2
  MX                1                  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
  16P GAIN MUTATED    2  5
  16P GAIN WILD-TYPE  8 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2    5
  16P GAIN WILD-TYPE    8   24
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                2                  8
  MALE                  5                 24
[1] 2 2
[1] FALSE

Clustering(16) Variable = 16Q GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    1  7
  16Q GAIN WILD-TYPE  9 22
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                 31 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                 22 
$`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 
TCGA-UD-AAC7 TCGA-UT-A88C 
       13.35        23.77 

$`16Q GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         6.08        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM TCGA-MQ-A4LP 
        1.61         3.55        80.84        91.73         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
        3.52        10.95        24.89        43.27        51.78        13.61 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 
       28.96         6.58        15.09         8.42         6.48        23.64 
TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       14.99        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-AA4M 
        2.76 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.23               1.61 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             23.90              91.73 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             16.08              12.20 
[1] "0.2 - 23.9 (16.1)" "1.6 - 91.7 (12.2)"
[1] "hr=" "1.5"
D16V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED         0        0        1        2         5        0
  16Q GAIN WILD-TYPE       3        1        0        9        14        4
D16V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 0                  1
  STAGE IB                 1                  0
  STAGE II                 2                  9
  STAGE III                5                 14
  STAGE IV                 0                  4
[1] 6 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    1  3     4
  16Q GAIN WILD-TYPE  6 14    11
D16V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                   1                  6
  T2                   3                 14
  T3+T4                4                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  16Q GAIN MUTATED    4  1  2
  16Q GAIN WILD-TYPE 21  5  3
D16V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                4                 21
  N1                1                  5
  N2                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"
                    vv
clus                 M0 M1 MX
  16Q GAIN MUTATED    7  0  1
  16Q GAIN WILD-TYPE 24  2  5
D16V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                7                 24
  M1                0                  2
  MX                1                  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"
D16V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  5
  16Q GAIN WILD-TYPE  7 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    5
  16Q GAIN WILD-TYPE    7   24
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                  7
  MALE                  5                 24
[1] 2 2
[1] FALSE

Clustering(17) Variable = 17P GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    0  3
  17P GAIN WILD-TYPE 10 26
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 36 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 26 
$`17P GAIN MUTATED`
TCGA-LK-A4O0 TCGA-SH-A7BC TCGA-UT-A88E 
        6.08        23.90        14.27 

$`17P GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        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-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BD 
       51.78        13.61         0.23        28.96         6.58        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 
        7.99         8.42         6.48        23.64        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       23.77        21.44         2.50         4.73         4.67         2.76 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              6.08               0.23 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             23.90              91.73 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            14.270             12.775 
[1] "6.1 - 23.9 (14.3)" "0.2 - 91.7 (12.8)"
[1] "hr=" "1.5"
D17V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  17P GAIN MUTATED         1        1        0        0         1        0
  17P GAIN WILD-TYPE       2        0        1       11        18        4
D17V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  1                  2
  STAGE IA                 1                  0
  STAGE IB                 0                  1
  STAGE II                 0                 11
  STAGE III                1                 18
  STAGE IV                 0                  4
[1] 6 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 GAIN MUTATED    2  0     1
  17P GAIN WILD-TYPE  5 17    14
D17V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                   2                  5
  T2                   0                 17
  T3+T4                1                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  17P GAIN MUTATED    2  0  1
  17P GAIN WILD-TYPE 23  6  4
D17V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                2                 23
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  17P GAIN MUTATED    3  0  0
  17P GAIN WILD-TYPE 28  2  6
D17V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                3                 28
  M1                0                  2
  MX                0                  6
[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
  17P GAIN MUTATED    0  3
  17P GAIN WILD-TYPE 10 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    3
  17P GAIN WILD-TYPE   10   26
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                0                 10
  MALE                  3                 26
[1] 2 2
[1] FALSE

Clustering(18) Variable = 17Q GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    2  8
  17Q GAIN WILD-TYPE  8 21
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                10                 29 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 8                 21 
$`17Q GAIN MUTATED`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-MQ-A6BS TCGA-SH-A7BC TCGA-UD-AAC4 
       17.95         5.52         6.08        13.61        23.90        23.64 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E 
       14.99        13.35        23.77        14.27 

$`17Q GAIN WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
        8.02         1.87        31.20        12.20         1.61         3.55 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       80.84        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
        3.52        10.95        24.89        43.27        51.78         0.23 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ 
       28.96         6.58        15.09         7.99         8.42         6.48 
TCGA-UT-A88D TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       21.44         2.50         4.73         4.67         2.76 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              5.52               0.23 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             23.90              91.73 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             14.63               8.42 
[1] "5.5 - 23.9 (14.6)" "0.2 - 91.7 (8.4)" 
[1] "hr=" "1.2"
D18V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED         1        1        0        3         4        1
  17Q GAIN WILD-TYPE       2        0        1        8        15        3
D18V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  1                  2
  STAGE IA                 1                  0
  STAGE IB                 0                  1
  STAGE II                 3                  8
  STAGE III                4                 15
  STAGE IV                 1                  3
[1] 6 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 GAIN MUTATED    2  4     4
  17Q GAIN WILD-TYPE  5 13    11
D18V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                   2                  5
  T2                   4                 13
  T3+T4                4                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  17Q GAIN MUTATED    6  0  4
  17Q GAIN WILD-TYPE 19  6  1
D18V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                6                 19
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  17Q GAIN MUTATED    9  0  1
  17Q GAIN WILD-TYPE 22  2  5
D18V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0                9                 22
  M1                0                  2
  MX                1                  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"
D18V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    1  9
  17Q GAIN WILD-TYPE  9 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1    9
  17Q GAIN WILD-TYPE    9   20
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                1                  9
  MALE                  9                 20
[1] 2 2
[1] FALSE

Clustering(19) Variable = 18P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    0  3
  18P GAIN WILD-TYPE 10 26
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 36 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 26 
$`18P GAIN MUTATED`
TCGA-LK-A4O0 TCGA-SH-A7BH TCGA-UD-AAC7 
        6.08         7.99        13.35 

$`18P GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        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-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC 
       51.78        13.61         0.23        28.96         6.58        23.90 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C 
       15.09         8.42         6.48        23.64        14.99        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       21.44        14.27         2.50         4.73         4.67         2.76 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              6.08               0.23 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             13.35              91.73 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              7.99              13.94 
[1] "6.1 - 13.3 (8.0)"  "0.2 - 91.7 (13.9)"
[1] "hr=" "2.9"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         0        1        0        1         1        0
  18P GAIN WILD-TYPE       3        0        1       10        18        4
D19V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 1                  0
  STAGE IB                 0                  1
  STAGE II                 1                 10
  STAGE III                1                 18
  STAGE IV                 0                  4
[1] 6 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 GAIN MUTATED    1  1     1
  18P GAIN WILD-TYPE  6 16    14
D19V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                   1                  6
  T2                   1                 16
  T3+T4                1                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  18P GAIN MUTATED    3  0  0
  18P GAIN WILD-TYPE 22  6  5
D19V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                3                 22
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  18P GAIN MUTATED    3  0  0
  18P GAIN WILD-TYPE 28  2  6
D19V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                3                 28
  M1                0                  2
  MX                0                  6
[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
  18P GAIN MUTATED    1  2
  18P GAIN WILD-TYPE  9 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    2
  18P GAIN WILD-TYPE    9   27
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                1                  9
  MALE                  2                 27
[1] 2 2
[1] FALSE

Clustering(20) Variable = 18Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    0  3
  18Q GAIN WILD-TYPE 10 26
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 36 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 26 
$`18Q GAIN MUTATED`
TCGA-LK-A4O0 TCGA-SH-A7BH TCGA-UD-AAC7 
        6.08         7.99        13.35 

$`18Q GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        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-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC 
       51.78        13.61         0.23        28.96         6.58        23.90 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C 
       15.09         8.42         6.48        23.64        14.99        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       21.44        14.27         2.50         4.73         4.67         2.76 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              6.08               0.23 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             13.35              91.73 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              7.99              13.94 
[1] "6.1 - 13.3 (8.0)"  "0.2 - 91.7 (13.9)"
[1] "hr=" "2.9"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED         0        1        0        1         1        0
  18Q GAIN WILD-TYPE       3        0        1       10        18        4
D20V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 1                  0
  STAGE IB                 0                  1
  STAGE II                 1                 10
  STAGE III                1                 18
  STAGE IV                 0                  4
[1] 6 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 GAIN MUTATED    1  1     1
  18Q GAIN WILD-TYPE  6 16    14
D20V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                   1                  6
  T2                   1                 16
  T3+T4                1                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  18Q GAIN MUTATED    3  0  0
  18Q GAIN WILD-TYPE 22  6  5
D20V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                3                 22
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  18Q GAIN MUTATED    3  0  0
  18Q GAIN WILD-TYPE 28  2  6
D20V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                3                 28
  M1                0                  2
  MX                0                  6
[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
  18Q GAIN MUTATED    1  2
  18Q GAIN WILD-TYPE  9 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    2
  18Q GAIN WILD-TYPE    9   27
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                  9
  MALE                  2                 27
[1] 2 2
[1] FALSE

Clustering(21) Variable = 19P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    0  5
  19P GAIN WILD-TYPE 10 24
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 34 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 24 
$`19P GAIN MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A4LP TCGA-SH-A7BH TCGA-UD-AAC4 TCGA-UD-AAC7 
        6.08        17.33         7.99        23.64        13.35 

$`19P GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
        5.19         3.52        10.95        24.89        43.27        51.78 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD 
       13.61         0.23        28.96         6.58        23.90        15.09 
TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E 
        8.42         6.48        14.99        23.77        21.44        14.27 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
        2.50         4.73         4.67         2.76 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              6.08               0.23 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             23.64              91.73 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            13.350             12.905 
[1] "6.1 - 23.6 (13.3)" "0.2 - 91.7 (12.9)"
[1] "hr=" "1.8"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  19P GAIN MUTATED         0        1        0        1         3        0
  19P GAIN WILD-TYPE       3        0        1       10        16        4
D21V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 1                  0
  STAGE IB                 0                  1
  STAGE II                 1                 10
  STAGE III                3                 16
  STAGE IV                 0                  4
[1] 6 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
  19P GAIN MUTATED    1  2     2
  19P GAIN WILD-TYPE  6 15    13
D21V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                   1                  6
  T2                   2                 15
  T3+T4                2                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  19P GAIN MUTATED    4  0  1
  19P GAIN WILD-TYPE 21  6  4
D21V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                4                 21
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  19P GAIN MUTATED    5  0  0
  19P GAIN WILD-TYPE 26  2  6
D21V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                5                 26
  M1                0                  2
  MX                0                  6
[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
  19P GAIN MUTATED    1  4
  19P GAIN WILD-TYPE  9 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    4
  19P GAIN WILD-TYPE    9   25
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                1                  9
  MALE                  4                 25
[1] 2 2
[1] FALSE

Clustering(22) Variable = 19Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    0  4
  19Q GAIN WILD-TYPE 10 25
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                 35 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                 25 
$`19Q GAIN MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A4LP TCGA-SH-A7BH TCGA-UD-AAC7 
        6.08        17.33         7.99        13.35 

$`19Q GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
        5.19         3.52        10.95        24.89        43.27        51.78 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD 
       13.61         0.23        28.96         6.58        23.90        15.09 
TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D 
        8.42         6.48        23.64        14.99        23.77        21.44 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       14.27         2.50         4.73         4.67         2.76 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              6.08               0.23 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             17.33              91.73 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             10.67              13.61 
[1] "6.1 - 17.3 (10.7)" "0.2 - 91.7 (13.6)"
[1] "hr=" "2.3"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED         0        1        0        1         2        0
  19Q GAIN WILD-TYPE       3        0        1       10        17        4
D22V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 1                  0
  STAGE IB                 0                  1
  STAGE II                 1                 10
  STAGE III                2                 17
  STAGE IV                 0                  4
[1] 6 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 GAIN MUTATED    1  1     2
  19Q GAIN WILD-TYPE  6 16    13
D22V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                   1                  6
  T2                   1                 16
  T3+T4                2                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  19Q GAIN MUTATED    4  0  0
  19Q GAIN WILD-TYPE 21  6  5
D22V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                4                 21
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  19Q GAIN MUTATED    4  0  0
  19Q GAIN WILD-TYPE 27  2  6
D22V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                4                 27
  M1                0                  2
  MX                0                  6
[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
  19Q GAIN MUTATED    1  3
  19Q GAIN WILD-TYPE  9 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    3
  19Q GAIN WILD-TYPE    9   26
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                1                  9
  MALE                  3                 26
[1] 2 2
[1] FALSE

Clustering(23) Variable = 20P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    0  5
  20P GAIN WILD-TYPE 10 24
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 34 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 24 
$`20P GAIN MUTATED`
TCGA-LK-A4NY TCGA-MQ-A6BL TCGA-NQ-A57I TCGA-UD-AAC7 TCGA-UT-A88G 
        5.52        10.95         0.23        13.35         2.50 

$`20P GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         8.02         6.08         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
        5.19        17.33         3.52        24.89        43.27        51.78 
TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       13.61        28.96         6.58        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D 
        8.42         6.48        23.64        14.99        23.77        21.44 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       14.27         4.73         4.67         2.76 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.23               1.61 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             13.35              91.73 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              5.52              14.63 
[1] "0.2 - 13.3 (5.5)"  "1.6 - 91.7 (14.6)"
[1] "hr=" "5.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  20P GAIN MUTATED         0        0        1        2         2        0
  20P GAIN WILD-TYPE       3        1        0        9        17        4
D23V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 0                  1
  STAGE IB                 1                  0
  STAGE II                 2                  9
  STAGE III                2                 17
  STAGE IV                 0                  4
[1] 6 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 GAIN MUTATED    1  2     2
  20P GAIN WILD-TYPE  6 15    13
D23V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                   1                  6
  T2                   2                 15
  T3+T4                2                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  20P GAIN MUTATED    4  0  0
  20P GAIN WILD-TYPE 21  6  5
D23V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                4                 21
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  20P GAIN MUTATED    4  0  1
  20P GAIN WILD-TYPE 27  2  5
D23V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0                4                 27
  M1                0                  2
  MX                1                  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"
D23V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    1  4
  20P GAIN WILD-TYPE  9 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1    4
  20P GAIN WILD-TYPE    9   25
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                1                  9
  MALE                  4                 25
[1] 2 2
[1] FALSE

Clustering(24) Variable = 20Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED    2  4
  20Q GAIN WILD-TYPE  8 25
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 6                 33 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 4                 25 
$`20Q GAIN MUTATED`
TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       10.95        13.61         0.23        13.35        23.77         2.50 

$`20Q GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.20         1.61         3.55        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       23.31         5.19        17.33         3.52        24.89        43.27 
TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       51.78        28.96         6.58        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A88E 
        8.42         6.48        23.64        14.99        21.44        14.27 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
        4.73         4.67         2.76 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.23               1.61 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             23.77              91.73 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             12.15              14.27 
[1] "0.2 - 23.8 (12.1)" "1.6 - 91.7 (14.3)"
[1] "hr=" "1.6"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED         0        0        1        3         2        0
  20Q GAIN WILD-TYPE       3        1        0        8        17        4
D24V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 0                  1
  STAGE IB                 1                  0
  STAGE II                 3                  8
  STAGE III                2                 17
  STAGE IV                 0                  4
[1] 6 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
  20Q GAIN MUTATED    1  3     2
  20Q GAIN WILD-TYPE  6 14    13
D24V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                   1                  6
  T2                   3                 14
  T3+T4                2                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  20Q GAIN MUTATED    4  0  1
  20Q GAIN WILD-TYPE 21  6  4
D24V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                4                 21
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED    4  0  2
  20Q GAIN WILD-TYPE 27  2  4
D24V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0                4                 27
  M1                0                  2
  MX                2                  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
  20Q GAIN MUTATED    0  6
  20Q GAIN WILD-TYPE 10 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0    6
  20Q GAIN WILD-TYPE   10   23
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                0                 10
  MALE                  6                 23
[1] 2 2
[1] FALSE

Clustering(25) Variable = 21Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    0  4
  21Q GAIN WILD-TYPE 10 25
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 35 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 25 
$`21Q GAIN MUTATED`
TCGA-SH-A7BH TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88G 
        7.99         6.48        13.35         2.50 

$`21Q GAIN WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.20         1.61         3.55        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-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       43.27        51.78        13.61         0.23        28.96         6.58 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C 
       23.90        15.09         8.42        23.64        14.99        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       21.44        14.27         4.73         4.67         2.76 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              2.50               0.23 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             13.35              91.73 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             7.235             14.270 
[1] "2.5 - 13.3 (7.2)"  "0.2 - 91.7 (14.3)"
[1] "hr=" "3.8"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED         0        0        0        2         2        0
  21Q GAIN WILD-TYPE       3        1        1        9        17        4
D25V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 0                  1
  STAGE IB                 0                  1
  STAGE II                 2                  9
  STAGE III                2                 17
  STAGE IV                 0                  4
[1] 6 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 GAIN MUTATED    0  2     2
  21Q GAIN WILD-TYPE  7 15    13
D25V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                   0                  7
  T2                   2                 15
  T3+T4                2                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  21Q GAIN MUTATED    4  0  0
  21Q GAIN WILD-TYPE 21  6  5
D25V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                4                 21
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  21Q GAIN MUTATED    4  0  0
  21Q GAIN WILD-TYPE 27  2  6
D25V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                4                 27
  M1                0                  2
  MX                0                  6
[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
  21Q GAIN MUTATED    1  3
  21Q GAIN WILD-TYPE  9 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    3
  21Q GAIN WILD-TYPE    9   26
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                1                  9
  MALE                  3                 26
[1] 2 2
[1] FALSE

Clustering(26) Variable = 1P LOSS MUTATION ANALYSIS
D26V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    4  2
  1P LOSS WILD-TYPE  6 27
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                33 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                27 
$`1P LOSS MUTATED`
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-SC-A6LN 
        1.61         3.55        18.81        10.95        13.61         6.58 

$`1P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       12.20        80.84        91.73        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM 
        3.52        24.89        43.27        51.78         0.23        28.96 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 
       23.90        15.09         7.99         8.42         6.48        23.64 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G 
       14.99        13.35        23.77        21.44        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
        4.73         4.67         2.76 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             1.61              0.23 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            18.81             91.73 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            8.765            14.270 
[1] "1.6 - 18.8 (8.8)"  "0.2 - 91.7 (14.3)"
[1] "hr=" "1.2"
D26V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  1P LOSS MUTATED         0        0        0        3         3        0
  1P LOSS WILD-TYPE       3        1        1        8        16        4
D26V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                0                 1
  STAGE IB                0                 1
  STAGE II                3                 8
  STAGE III               3                16
  STAGE IV                0                 4
[1] 6 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    0  4     2
  1P LOSS WILD-TYPE  7 13    13
D26V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1                  0                 7
  T2                  4                13
  T3+T4               2                13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  1P LOSS MUTATED    3  2  1
  1P LOSS WILD-TYPE 22  4  4
D26V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0               3                22
  N1               2                 4
  N2               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"
                   vv
clus                M0 M1 MX
  1P LOSS MUTATED    5  0  1
  1P LOSS WILD-TYPE 26  2  5
D26V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               5                26
  M1               0                 2
  MX               1                 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"
D26V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    2  4
  1P LOSS WILD-TYPE  8 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    4
  1P LOSS WILD-TYPE    8   25
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               2                 8
  MALE                 4                25
[1] 2 2
[1] FALSE

Clustering(27) Variable = 2P LOSS MUTATION ANALYSIS
D27V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    0  3
  2P LOSS WILD-TYPE 10 26
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                36 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                26 
$`2P LOSS MUTATED`
TCGA-MQ-A4LI TCGA-SH-A7BH TCGA-UT-A88G 
       18.81         7.99         2.50 

$`2P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ 
       12.20         1.61         3.55        80.84        91.73        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-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC 
       51.78        13.61         0.23        28.96         6.58        23.90 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 
       15.09         8.42         6.48        23.64        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       23.77        21.44        14.27         4.73         4.67         2.76 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.50              0.23 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            18.81             91.73 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             7.99             13.48 
[1] "2.5 - 18.8 (8.0)"  "0.2 - 91.7 (13.5)"
[1] "hr=" "2.4"
D27V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  2P LOSS MUTATED         0        0        0        1         2        0
  2P LOSS WILD-TYPE       3        1        1       10        17        4
D27V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                0                 1
  STAGE IB                0                 1
  STAGE II                1                10
  STAGE III               2                17
  STAGE IV                0                 4
[1] 6 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
  2P LOSS MUTATED    0  1     2
  2P LOSS WILD-TYPE  7 16    13
D27V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1                  0                 7
  T2                  1                16
  T3+T4               2                13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  2P LOSS MUTATED    3  0  0
  2P LOSS WILD-TYPE 22  6  5
D27V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               3                22
  N1               0                 6
  N2               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"
                   vv
clus                M0 M1 MX
  2P LOSS MUTATED    3  0  0
  2P LOSS WILD-TYPE 28  2  6
D27V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               3                28
  M1               0                 2
  MX               0                 6
[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
  2P LOSS MUTATED    2  1
  2P LOSS WILD-TYPE  8 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    1
  2P LOSS WILD-TYPE    8   28
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               2                 8
  MALE                 1                28
[1] 2 2
[1] FALSE

Clustering(28) Variable = 2Q LOSS MUTATION ANALYSIS
D28V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    0  3
  2Q LOSS WILD-TYPE 10 26
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                36 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                26 
$`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-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         6.08        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM 
        1.61         3.55        80.84        91.73        23.31         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-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD 
       13.61         0.23        28.96         6.58        23.90        15.09 
TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        8.42         6.48        23.64        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       21.44        14.27         2.50         4.73         4.67         2.76 

  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             13.48 
[1] "1.9 - 18.8 (8.0)"  "0.2 - 91.7 (13.5)"
[1] "hr=" "2.4"
D28V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED         0        0        0        1         2        0
  2Q LOSS WILD-TYPE       3        1        1       10        17        4
D28V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                0                 1
  STAGE IB                0                 1
  STAGE II                1                10
  STAGE III               2                17
  STAGE IV                0                 4
[1] 6 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    0  1     2
  2Q LOSS WILD-TYPE  7 16    13
D28V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1                  0                 7
  T2                  1                16
  T3+T4               2                13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  2Q LOSS MUTATED    3  0  0
  2Q LOSS WILD-TYPE 22  6  5
D28V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0               3                22
  N1               0                 6
  N2               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"
                   vv
clus                M0 M1 MX
  2Q LOSS MUTATED    3  0  0
  2Q LOSS WILD-TYPE 28  2  6
D28V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               3                28
  M1               0                 2
  MX               0                 6
[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
  2Q LOSS MUTATED    3  0
  2Q LOSS WILD-TYPE  7 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3    0
  2Q LOSS WILD-TYPE    7   29
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               3                 7
  MALE                 0                29
[1] 2 2
[1] FALSE

Clustering(29) Variable = 3P LOSS MUTATION ANALYSIS
D29V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    1  2
  3P LOSS WILD-TYPE  9 27
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3                36 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                27 
$`3P LOSS MUTATED`
TCGA-LK-A4O7 TCGA-NQ-A57I TCGA-UD-AABZ 
        3.55         0.23         6.48 

$`3P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       12.20         1.61        80.84        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-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD 
       51.78        13.61        28.96         6.58        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        7.99         8.42        23.64        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       21.44        14.27         2.50         4.73         4.67         2.76 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.23              1.61 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             6.48             91.73 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             3.55             13.94 
[1] "0.2 - 6.5 (3.5)"   "1.6 - 91.7 (13.9)"
[1] "hr=" "4.7"
D29V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         0        0        1        1         1        0
  3P LOSS WILD-TYPE       3        1        0       10        18        4
D29V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                0                 1
  STAGE IB                1                 0
  STAGE II                1                10
  STAGE III               1                18
  STAGE IV                0                 4
[1] 6 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 LOSS MUTATED    1  1     1
  3P LOSS WILD-TYPE  6 16    14
D29V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1                  1                 6
  T2                  1                16
  T3+T4               1                14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  3P LOSS MUTATED    1  1  0
  3P LOSS WILD-TYPE 24  5  5
D29V5, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                34 
       TCGA-LK-A4NW        TCGA-LK-A4NY        TCGA-LK-A4NZ        TCGA-LK-A4O0 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-LK-A4O2        TCGA-LK-A4O4        TCGA-LK-A4O5        TCGA-LK-A4O6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-MQ-A4KX        TCGA-MQ-A4LC        TCGA-MQ-A4LI        TCGA-MQ-A4LJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-MQ-A4LM        TCGA-MQ-A4LP        TCGA-MQ-A4LV        TCGA-MQ-A6BL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-MQ-A6BN        TCGA-MQ-A6BQ        TCGA-MQ-A6BR        TCGA-MQ-A6BS 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SH-A7BC        TCGA-SH-A7BD        TCGA-SH-A7BH 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-SH-A9CT        TCGA-UD-AAC4        TCGA-UD-AAC6        TCGA-UD-AAC7 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-UT-A88C        TCGA-UT-A88D        TCGA-UT-A88E        TCGA-UT-A88G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-UT-A97Y        TCGA-YS-AA4M 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
                   vv
clus                M0 M1 MX
  3P LOSS MUTATED    2  0  1
  3P LOSS WILD-TYPE 29  2  5
D29V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               2                29
  M1               0                 2
  MX               1                 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"
D29V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    0  3
  3P LOSS WILD-TYPE 10 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    3
  3P LOSS WILD-TYPE   10   26
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               0                10
  MALE                 3                26
[1] 2 2
[1] FALSE

Clustering(30) Variable = 4P LOSS MUTATION ANALYSIS
D30V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    6 12
  4P LOSS WILD-TYPE  4 17
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               18                21 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               12                17 
$`4P LOSS MUTATED`
TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LM 
        6.08        12.20         1.61         3.55        18.81         5.19 
TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BH 
       17.33        10.95        51.78        13.61         6.58         7.99 
TCGA-UD-AABZ TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
        6.48        14.99        13.35        14.27         2.50         4.73 

$`4P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4KX 
       17.95         5.52         8.02         1.87        31.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I 
       91.73        23.31         3.52        24.89        43.27         0.23 
TCGA-SC-A6LM TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AAC4 TCGA-UT-A88C 
       28.96        23.90        15.09         8.42        23.64        23.77 
TCGA-UT-A88D TCGA-XT-AASU TCGA-YS-AA4M 
       21.44         4.67         2.76 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             1.61              0.23 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            51.78             91.73 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             9.47             21.44 
[1] "1.6 - 51.8 (9.5)"  "0.2 - 91.7 (21.4)"
[1] "hr=" "1.8"
D30V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         2        1        0        6         9        0
  4P LOSS WILD-TYPE       1        0        1        5        10        4
D30V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 2                 1
  STAGE IA                1                 0
  STAGE IB                0                 1
  STAGE II                6                 5
  STAGE III               9                10
  STAGE IV                0                 4
[1] 6 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  7     7
  4P LOSS WILD-TYPE  3 10     8
D30V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1                  4                 3
  T2                  7                10
  T3+T4               7                 8
[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"
                   vv
clus                N0 N1 N2
  4P LOSS MUTATED   14  3  1
  4P LOSS WILD-TYPE 11  3  4
D30V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              14                11
  N1               3                 3
  N2               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"
                   vv
clus                M0 M1 MX
  4P LOSS MUTATED   16  0  2
  4P LOSS WILD-TYPE 15  2  4
D30V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              16                15
  M1               0                 2
  MX               2                 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
  4P LOSS MUTATED    6 12
  4P LOSS WILD-TYPE  4 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6   12
  4P LOSS WILD-TYPE    4   17
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               6                 4
  MALE                12                17
[1] 2 2
[1] FALSE

Clustering(31) Variable = 4Q LOSS MUTATION ANALYSIS
D31V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    6 10
  4Q LOSS WILD-TYPE  4 19
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16                23 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10                19 
$`4Q LOSS MUTATED`
TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LM 
        6.08        12.20         1.61         3.55        18.81         5.19 
TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-SC-A6LN TCGA-SH-A7BH TCGA-SH-A9CT 
       17.33        10.95        51.78         6.58         7.99         8.42 
TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88G TCGA-UT-A97Y 
        6.48        13.35         2.50         4.73 

$`4Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4KX 
       17.95         5.52         8.02         1.87        31.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS 
       91.73        23.31         3.52        24.89        43.27        13.61 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BC TCGA-SH-A7BD TCGA-UD-AAC4 TCGA-UD-AAC6 
        0.23        28.96        23.90        15.09        23.64        14.99 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-AA4M 
       23.77        21.44        14.27         4.67         2.76 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             1.61              0.23 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            51.78             91.73 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            7.285            17.950 
[1] "1.6 - 51.8 (7.3)"  "0.2 - 91.7 (17.9)"
[1] "hr=" "1.6"
D31V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         1        1        0        5         9        0
  4Q LOSS WILD-TYPE       2        0        1        6        10        4
D31V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 1                 2
  STAGE IA                1                 0
  STAGE IB                0                 1
  STAGE II                5                 6
  STAGE III               9                10
  STAGE IV                0                 4
[1] 6 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  6     7
  4Q LOSS WILD-TYPE  4 11     8
D31V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1                  3                 4
  T2                  6                11
  T3+T4               7                 8
[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"
                   vv
clus                N0 N1 N2
  4Q LOSS MUTATED   12  3  1
  4Q LOSS WILD-TYPE 13  3  4
D31V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              12                13
  N1               3                 3
  N2               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"
                   vv
clus                M0 M1 MX
  4Q LOSS MUTATED   15  0  1
  4Q LOSS WILD-TYPE 16  2  5
D31V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              15                16
  M1               0                 2
  MX               1                 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"
D31V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    6 10
  4Q LOSS WILD-TYPE  4 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      6   10
  4Q LOSS WILD-TYPE    4   19
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               6                 4
  MALE                10                19
[1] 2 2
[1] FALSE

Clustering(32) Variable = 5Q LOSS MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    1  2
  5Q LOSS WILD-TYPE  9 27
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                36 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                27 
$`5Q LOSS MUTATED`
TCGA-MQ-A4LV TCGA-SC-A6LN TCGA-UD-AAC7 
        3.52         6.58        13.35 

$`5Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.20         1.61         3.55        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       23.31         5.19        17.33        10.95        24.89        43.27 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BC TCGA-SH-A7BD 
       51.78        13.61         0.23        28.96        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C 
        7.99         8.42         6.48        23.64        14.99        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       21.44        14.27         2.50         4.73         4.67         2.76 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             3.52              0.23 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            13.35             91.73 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             6.58             13.94 
[1] "3.5 - 13.3 (6.6)"  "0.2 - 91.7 (13.9)"
[1] "hr=" "2.2"
D32V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         0        0        0        1         2        0
  5Q LOSS WILD-TYPE       3        1        1       10        17        4
D32V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                0                 1
  STAGE IB                0                 1
  STAGE II                1                10
  STAGE III               2                17
  STAGE IV                0                 4
[1] 6 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 LOSS MUTATED    0  2     1
  5Q LOSS WILD-TYPE  7 15    14
D32V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1                  0                 7
  T2                  2                15
  T3+T4               1                14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  5Q LOSS MUTATED    2  0  1
  5Q LOSS WILD-TYPE 23  6  4
D32V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0               2                23
  N1               0                 6
  N2               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"
                   vv
clus                M0 M1 MX
  5Q LOSS MUTATED    3  0  0
  5Q LOSS WILD-TYPE 28  2  6
D32V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               3                28
  M1               0                 2
  MX               0                 6
[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
  5Q LOSS MUTATED    0  3
  5Q LOSS WILD-TYPE 10 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    3
  5Q LOSS WILD-TYPE   10   26
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               0                10
  MALE                 3                26
[1] 2 2
[1] FALSE

Clustering(33) Variable = 6P LOSS MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    1  4
  6P LOSS WILD-TYPE  9 25
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                5                34 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4                25 
$`6P LOSS MUTATED`
TCGA-LK-A4O0 TCGA-LK-A4O7 TCGA-MQ-A6BL TCGA-NQ-A57I TCGA-UT-A88G 
        6.08         3.55        10.95         0.23         2.50 

$`6P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
        1.61        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
       17.33         3.52        24.89        43.27        51.78        13.61 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
       28.96         6.58        23.90        15.09         7.99         8.42 
TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D 
        6.48        23.64        14.99        13.35        23.77        21.44 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       14.27         4.73         4.67         2.76 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.23              1.61 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            10.95             91.73 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             3.55             14.63 
[1] "0.2 - 10.9 (3.5)"  "1.6 - 91.7 (14.6)"
[1] "hr=" "5.3"
D33V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  6P LOSS MUTATED         0        1        1        1         2        0
  6P LOSS WILD-TYPE       3        0        0       10        17        4
D33V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                1                 0
  STAGE IB                1                 0
  STAGE II                1                10
  STAGE III               2                17
  STAGE IV                0                 4
[1] 6 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
  6P LOSS MUTATED    2  1     2
  6P LOSS WILD-TYPE  5 16    13
D33V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1                  2                 5
  T2                  1                16
  T3+T4               2                13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  6P LOSS MUTATED    3  1  0
  6P LOSS WILD-TYPE 22  5  5
D33V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0               3                22
  N1               1                 5
  N2               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"
                   vv
clus                M0 M1 MX
  6P LOSS MUTATED    4  0  1
  6P LOSS WILD-TYPE 27  2  5
D33V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               4                27
  M1               0                 2
  MX               1                 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"
D33V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    0  5
  6P LOSS WILD-TYPE 10 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    5
  6P LOSS WILD-TYPE   10   24
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               0                10
  MALE                 5                24
[1] 2 2
[1] FALSE

Clustering(34) Variable = 6Q LOSS MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    1 12
  6Q LOSS WILD-TYPE  9 17
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               13                26 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               12                17 
$`6Q LOSS MUTATED`
TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
        8.02         6.08         1.87        80.84        91.73        18.81 
TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SH-A7BC TCGA-UD-AAC7 
        5.19        10.95        43.27         0.23        23.90        13.35 
TCGA-UT-A88G 
        2.50 

$`6Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
       17.95         5.52        31.20        12.20         1.61         3.55 
TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-MQ-A6BS 
       23.31        17.33         3.52        24.89        51.78        13.61 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ 
       28.96         6.58        15.09         7.99         8.42         6.48 
TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y 
       23.64        14.99        23.77        21.44        14.27         4.73 
TCGA-XT-AASU TCGA-YS-AA4M 
        4.67         2.76 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.23              1.61 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            91.73             51.78 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            10.95             13.94 
[1] "0.2 - 91.7 (10.9)" "1.6 - 51.8 (13.9)"
[1] "hr=" "1.1"
D34V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED         1        1        1        6         4        0
  6Q LOSS WILD-TYPE       2        0        0        5        15        4
D34V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 1                 2
  STAGE IA                1                 0
  STAGE IB                1                 0
  STAGE II                6                 5
  STAGE III               4                15
  STAGE IV                0                 4
[1] 6 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    3  6     4
  6Q LOSS WILD-TYPE  4 11    11
D34V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1                  3                 4
  T2                  6                11
  T3+T4               4                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  6Q LOSS MUTATED   11  0  1
  6Q LOSS WILD-TYPE 14  6  4
D34V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              11                14
  N1               0                 6
  N2               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"
                   vv
clus                M0 M1 MX
  6Q LOSS MUTATED   11  0  2
  6Q LOSS WILD-TYPE 20  2  4
D34V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              11                20
  M1               0                 2
  MX               2                 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"
D34V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    2 11
  6Q LOSS WILD-TYPE  8 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   11
  6Q LOSS WILD-TYPE    8   18
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               2                 8
  MALE                11                18
[1] 2 2
[1] FALSE

Clustering(35) Variable = 8P LOSS MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    1  3
  8P LOSS WILD-TYPE  9 26
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                35 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                26 
$`8P LOSS MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A6BQ 
        6.08        91.73        18.81        43.27 

$`8P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
        1.61         3.55        80.84        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I 
        3.52        10.95        24.89        51.78        13.61         0.23 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
       28.96         6.58        23.90        15.09         7.99         8.42 
TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D 
        6.48        23.64        14.99        13.35        23.77        21.44 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       14.27         2.50         4.73         4.67         2.76 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             6.08              0.23 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            91.73             80.84 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            31.04             12.20 
[1] "6.1 - 91.7 (31.0)" "0.2 - 80.8 (12.2)"
[1] "hr=" "3.1"
D35V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         0        1        0        3         0        0
  8P LOSS WILD-TYPE       3        0        1        8        19        4
D35V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 0                 3
  STAGE IA                1                 0
  STAGE IB                0                 1
  STAGE II                3                 8
  STAGE III               0                19
  STAGE IV                0                 4
[1] 6 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    1  3     0
  8P LOSS WILD-TYPE  6 14    15
D35V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1                  1                 6
  T2                  3                14
  T3+T4               0                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  8P LOSS MUTATED    4  0  0
  8P LOSS WILD-TYPE 21  6  5
D35V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0               4                21
  N1               0                 6
  N2               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"
                   vv
clus                M0 M1 MX
  8P LOSS MUTATED    3  0  1
  8P LOSS WILD-TYPE 28  2  5
D35V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               3                28
  M1               0                 2
  MX               1                 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"
D35V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    1  3
  8P LOSS WILD-TYPE  9 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    3
  8P LOSS WILD-TYPE    9   26
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               1                 9
  MALE                 3                26
[1] 2 2
[1] FALSE

Clustering(36) Variable = 9P LOSS MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED    3 11
  9P LOSS WILD-TYPE  7 18
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               14                25 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               11                18 
$`9P LOSS MUTATED`
TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O7 TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
        5.52         6.08         3.55         5.19        17.33         3.52 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-UD-AAC7 
       13.61         0.23        28.96         6.58        23.90        13.35 
TCGA-UT-A88E TCGA-UT-A88G 
       14.27         2.50 

$`9P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 
       17.95         8.02         1.87        31.20        12.20         1.61 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BL TCGA-MQ-A6BN 
       80.84        91.73        18.81        23.31        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ 
       43.27        51.78        15.09         7.99         8.42         6.48 
TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A97Y TCGA-XT-AASU 
       23.64        14.99        23.77        21.44         4.73         4.67 
TCGA-YS-AA4M 
        2.76 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.23              1.61 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            28.96             91.73 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             6.33             15.09 
[1] "0.2 - 29.0 (6.3)"  "1.6 - 91.7 (15.1)"
[1] "hr=" "2.2"
D36V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         1        1        1        2         8        1
  9P LOSS WILD-TYPE       2        0        0        9        11        3
D36V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 1                 2
  STAGE IA                1                 0
  STAGE IB                1                 0
  STAGE II                2                 9
  STAGE III               8                11
  STAGE IV                1                 3
[1] 6 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    3  3     8
  9P LOSS WILD-TYPE  4 14     7
D36V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1                  3                 4
  T2                  3                14
  T3+T4               8                 7
[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"
                   vv
clus                N0 N1 N2
  9P LOSS MUTATED    9  1  2
  9P LOSS WILD-TYPE 16  5  3
D36V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0               9                16
  N1               1                 5
  N2               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"
                   vv
clus                M0 M1 MX
  9P LOSS MUTATED   12  0  2
  9P LOSS WILD-TYPE 19  2  4
D36V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              12                19
  M1               0                 2
  MX               2                 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
  9P LOSS MUTATED    2 12
  9P LOSS WILD-TYPE  8 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2   12
  9P LOSS WILD-TYPE    8   17
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               2                 8
  MALE                12                17
[1] 2 2
[1] FALSE

Clustering(37) Variable = 9Q LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    2 10
  9Q LOSS WILD-TYPE  8 19
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               12                27 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               10                19 
$`9Q LOSS MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I 
        6.08        18.81         5.19         3.52        13.61         0.23 
TCGA-SC-A6LM TCGA-SH-A7BC TCGA-SH-A9CT TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G 
       28.96        23.90         8.42        13.35        14.27         2.50 

$`9Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LP 
        1.61         3.55        80.84        91.73        23.31        17.33 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LN TCGA-SH-A7BD 
       10.95        24.89        43.27        51.78         6.58        15.09 
TCGA-SH-A7BH TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D 
        7.99         6.48        23.64        14.99        23.77        21.44 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
        4.73         4.67         2.76 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.23              1.61 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            28.96             91.73 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           10.885            14.990 
[1] "0.2 - 29.0 (10.9)" "1.6 - 91.7 (15.0)"
[1] "hr=" "1.9"
D37V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         1        1        1        4         4        1
  9Q LOSS WILD-TYPE       2        0        0        7        15        3
D37V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 1                 2
  STAGE IA                1                 0
  STAGE IB                1                 0
  STAGE II                4                 7
  STAGE III               4                15
  STAGE IV                1                 3
[1] 6 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  4     5
  9Q LOSS WILD-TYPE  4 13    10
D37V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1                  3                 4
  T2                  4                13
  T3+T4               5                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  9Q LOSS MUTATED    9  0  1
  9Q LOSS WILD-TYPE 16  6  4
D37V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0               9                16
  N1               0                 6
  N2               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"
                   vv
clus                M0 M1 MX
  9Q LOSS MUTATED   10  0  2
  9Q LOSS WILD-TYPE 21  2  4
D37V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              10                21
  M1               0                 2
  MX               2                 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"
D37V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    2 10
  9Q LOSS WILD-TYPE  8 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2   10
  9Q LOSS WILD-TYPE    8   19
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               2                 8
  MALE                10                19
[1] 2 2
[1] FALSE

Clustering(38) Variable = 10P LOSS MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    2  8
  10P LOSS WILD-TYPE  8 21
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                10                 29 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                 21 
$`10P LOSS MUTATED`
TCGA-LK-A4O7 TCGA-MQ-A4LP TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD 
        3.55        17.33        13.61         0.23        23.90        15.09 
TCGA-SH-A7BH TCGA-UD-AAC7 TCGA-UT-A88G TCGA-XT-AASU 
        7.99        13.35         2.50         4.67 

$`10P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       12.20         1.61        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
        5.19         3.52        10.95        24.89        43.27        51.78 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 
       28.96         6.58         8.42         6.48        23.64        14.99 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-YS-AA4M 
       23.77        21.44        14.27         4.73         2.76 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.23               1.61 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             23.90              91.73 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             10.67              14.27 
[1] "0.2 - 23.9 (10.7)" "1.6 - 91.7 (14.3)"
[1] "hr=" "2.2"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         0        0        1        2         6        1
  10P LOSS WILD-TYPE       3        1        0        9        13        3
D38V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 0                  1
  STAGE IB                 1                  0
  STAGE II                 2                  9
  STAGE III                6                 13
  STAGE IV                 1                  3
[1] 6 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    1  3     6
  10P LOSS WILD-TYPE  6 14     9
D38V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                   1                  6
  T2                   3                 14
  T3+T4                6                  9
[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"
                    vv
clus                 N0 N1 N2
  10P LOSS MUTATED    6  1  1
  10P LOSS WILD-TYPE 19  5  4
D38V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                6                 19
  N1                1                  5
  N2                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"
                    vv
clus                 M0 M1 MX
  10P LOSS MUTATED    6  1  3
  10P LOSS WILD-TYPE 25  1  3
D38V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                6                 25
  M1                1                  1
  MX                3                  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"
D38V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    1  9
  10P LOSS WILD-TYPE  9 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    9
  10P LOSS WILD-TYPE    9   20
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                1                  9
  MALE                  9                 20
[1] 2 2
[1] FALSE

Clustering(39) Variable = 10Q LOSS MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    2  7
  10Q LOSS WILD-TYPE  8 22
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 9                 30 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 7                 22 
$`10Q LOSS MUTATED`
TCGA-LK-A4O7 TCGA-MQ-A4LP TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BD TCGA-SH-A7BH 
        3.55        17.33        13.61         0.23        15.09         7.99 
TCGA-UD-AAC7 TCGA-UT-A88G TCGA-UT-A97Y 
       13.35         2.50         4.73 

$`10Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       12.20         1.61        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
        5.19         3.52        10.95        24.89        43.27        51.78 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 
       28.96         6.58        23.90         8.42         6.48        23.64 
TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-AA4M 
       14.99        23.77        21.44        14.27         4.67         2.76 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.23               1.61 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             17.33              91.73 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              7.99              14.63 
[1] "0.2 - 17.3 (8.0)"  "1.6 - 91.7 (14.6)"
[1] "hr=" "2.8"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         1        0        1        2         4        1
  10Q LOSS WILD-TYPE       2        1        0        9        15        3
D39V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  1                  2
  STAGE IA                 0                  1
  STAGE IB                 1                  0
  STAGE II                 2                  9
  STAGE III                4                 15
  STAGE IV                 1                  3
[1] 6 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    2  3     4
  10Q LOSS WILD-TYPE  5 14    11
D39V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                   2                  5
  T2                   3                 14
  T3+T4                4                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  10Q LOSS MUTATED    7  1  0
  10Q LOSS WILD-TYPE 18  5  5
D39V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                7                 18
  N1                1                  5
  N2                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"
                    vv
clus                 M0 M1 MX
  10Q LOSS MUTATED    6  1  2
  10Q LOSS WILD-TYPE 25  1  4
D39V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                6                 25
  M1                1                  1
  MX                2                  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"
D39V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    2  7
  10Q LOSS WILD-TYPE  8 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2    7
  10Q LOSS WILD-TYPE    8   22
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                2                  8
  MALE                  7                 22
[1] 2 2
[1] FALSE

Clustering(40) Variable = 11P LOSS MUTATION ANALYSIS
D40V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    1  2
  11P LOSS WILD-TYPE  9 27
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                 36 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 27 
$`11P LOSS MUTATED`
TCGA-LK-A4O0 TCGA-NQ-A57I TCGA-SC-A6LN 
        6.08         0.23         6.58 

$`11P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        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-MQ-A6BS TCGA-SC-A6LM TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       51.78        13.61        28.96        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        8.42         6.48        23.64        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       21.44        14.27         2.50         4.73         4.67         2.76 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.23               1.61 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              6.58              91.73 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              6.08              13.94 
[1] "0.2 - 6.6 (6.1)"   "1.6 - 91.7 (13.9)"
[1] "hr=" "3.4"
D40V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         0        1        1        0         1        0
  11P LOSS WILD-TYPE       3        0        0       11        18        4
D40V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 1                  0
  STAGE IB                 1                  0
  STAGE II                 0                 11
  STAGE III                1                 18
  STAGE IV                 0                  4
[1] 6 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
  11P LOSS MUTATED    2  1     0
  11P LOSS WILD-TYPE  5 16    15
D40V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                   2                  5
  T2                   1                 16
  T3+T4                0                 15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  11P LOSS MUTATED    1  0  1
  11P LOSS WILD-TYPE 24  6  4
D40V5, multiclass
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 34 
        TCGA-LK-A4NW         TCGA-LK-A4NY         TCGA-LK-A4NZ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-LK-A4O2         TCGA-LK-A4O4         TCGA-LK-A4O5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-LK-A4O6         TCGA-LK-A4O7         TCGA-MQ-A4KX 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-MQ-A4LC         TCGA-MQ-A4LI         TCGA-MQ-A4LJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-MQ-A4LM         TCGA-MQ-A4LP         TCGA-MQ-A4LV 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-MQ-A6BL         TCGA-MQ-A6BN         TCGA-MQ-A6BQ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-MQ-A6BR         TCGA-MQ-A6BS         TCGA-SH-A7BC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-SH-A7BD         TCGA-SH-A7BH         TCGA-SH-A9CT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-UD-AABZ         TCGA-UD-AAC4         TCGA-UD-AAC6 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-UD-AAC7         TCGA-UT-A88C         TCGA-UT-A88D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-UT-A88E         TCGA-UT-A88G         TCGA-UT-A97Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-YS-AA4M 
"11P LOSS WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  11P LOSS MUTATED    2  0  1
  11P LOSS WILD-TYPE 29  2  5
D40V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                2                 29
  M1                0                  2
  MX                1                  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"
D40V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    0  3
  11P LOSS WILD-TYPE 10 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0    3
  11P LOSS WILD-TYPE   10   26
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                0                 10
  MALE                  3                 26
[1] 2 2
[1] FALSE

Clustering(41) Variable = 11Q LOSS MUTATION ANALYSIS
D41V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    0  4
  11Q LOSS WILD-TYPE 10 25
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                 35 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                 25 
$`11Q LOSS MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-NQ-A57I 
        6.08         5.19         3.52         0.23 

$`11Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
       17.33        10.95        24.89        43.27        51.78        13.61 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
       28.96         6.58        23.90        15.09         7.99         8.42 
TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D 
        6.48        23.64        14.99        13.35        23.77        21.44 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       14.27         2.50         4.73         4.67         2.76 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.23               1.61 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              6.08              91.73 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             4.355             14.270 
[1] "0.2 - 6.1 (4.4)"   "1.6 - 91.7 (14.3)"
[1] "hr=" "9.1"
D41V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         0        1        1        0         2        0
  11Q LOSS WILD-TYPE       3        0        0       11        17        4
D41V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 1                  0
  STAGE IB                 1                  0
  STAGE II                 0                 11
  STAGE III                2                 17
  STAGE IV                 0                  4
[1] 6 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    2  0     2
  11Q LOSS WILD-TYPE  5 17    13
D41V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                   2                  5
  T2                   0                 17
  T3+T4                2                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  11Q LOSS MUTATED    3  0  0
  11Q LOSS WILD-TYPE 22  6  5
D41V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                3                 22
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  11Q LOSS MUTATED    3  0  1
  11Q LOSS WILD-TYPE 28  2  5
D41V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                3                 28
  M1                0                  2
  MX                1                  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"
D41V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    0  4
  11Q LOSS WILD-TYPE 10 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    4
  11Q LOSS WILD-TYPE   10   25
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                0                 10
  MALE                  4                 25
[1] 2 2
[1] FALSE

Clustering(42) Variable = 13Q LOSS MUTATION ANALYSIS
D42V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    4 16
  13Q LOSS WILD-TYPE  6 13
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                 19 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                16                 13 
$`13Q LOSS MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LI 
       17.95         6.08         1.87        12.20        80.84        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-SC-A6LN 
       23.31         5.19         3.52        10.95        13.61         6.58 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88C 
       23.90        15.09         7.99         6.48        13.35        23.77 
TCGA-UT-A88G TCGA-YS-AA4M 
        2.50         2.76 

$`13Q LOSS WILD-TYPE`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LC 
        5.52         8.02        31.20         1.61         3.55        91.73 
TCGA-MQ-A4LP TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM 
       17.33        24.89        43.27        51.78         0.23        28.96 
TCGA-SH-A9CT TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y 
        8.42        23.64        14.99        21.44        14.27         4.73 
TCGA-XT-AASU 
        4.67 

  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 
            11.575             14.990 
[1] "1.9 - 80.8 (11.6)" "0.2 - 91.7 (15.0)"
[1] "hr=" "1.9"
D42V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         1        1        0        5        10        3
  13Q LOSS WILD-TYPE       2        0        1        6         9        1
D42V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  1                  2
  STAGE IA                 1                  0
  STAGE IB                 0                  1
  STAGE II                 5                  6
  STAGE III               10                  9
  STAGE IV                 3                  1
[1] 6 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    3  8     9
  13Q LOSS WILD-TYPE  4  9     6
D42V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                   3                  4
  T2                   8                  9
  T3+T4                9                  6
[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"
                    vv
clus                 N0 N1 N2
  13Q LOSS MUTATED   15  1  4
  13Q LOSS WILD-TYPE 10  5  1
D42V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               15                 10
  N1                1                  5
  N2                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"
                    vv
clus                 M0 M1 MX
  13Q LOSS MUTATED   17  2  1
  13Q LOSS WILD-TYPE 14  0  5
D42V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               17                 14
  M1                2                  0
  MX                1                  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"
D42V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    4 16
  13Q LOSS WILD-TYPE  6 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4   16
  13Q LOSS WILD-TYPE    6   13
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                4                  6
  MALE                 16                 13
[1] 2 2
[1] FALSE

Clustering(43) Variable = 14Q LOSS MUTATION ANALYSIS
D43V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    6  9
  14Q LOSS WILD-TYPE  4 20
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                15                 24 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 9                 20 
$`14Q LOSS MUTATED`
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.87        12.20         1.61         3.55        18.81        23.31 
TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ 
       13.61         6.58        23.90         7.99         8.42         6.48 
TCGA-UD-AAC7 TCGA-UT-A88G TCGA-UT-A97Y 
       13.35         2.50         4.73 

$`14Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O4 TCGA-MQ-A4KX 
       17.95         5.52         8.02         6.08        31.20        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-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BD TCGA-UD-AAC4 
       43.27        51.78         0.23        28.96        15.09        23.64 
TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-AA4M 
       14.99        23.77        21.44        14.27         4.67         2.76 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              1.61               0.23 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             23.90              91.73 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              7.99              16.21 
[1] "1.6 - 23.9 (8.0)"  "0.2 - 91.7 (16.2)"
[1] "hr=" "1.6"
D43V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED         1        0        0        5         9        0
  14Q LOSS WILD-TYPE       2        1        1        6        10        4
D43V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  1                  2
  STAGE IA                 0                  1
  STAGE IB                 0                  1
  STAGE II                 5                  6
  STAGE III                9                 10
  STAGE IV                 0                  4
[1] 6 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    1  7     7
  14Q LOSS WILD-TYPE  6 10     8
D43V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                   1                  6
  T2                   7                 10
  T3+T4                7                  8
[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"
                    vv
clus                 N0 N1 N2
  14Q LOSS MUTATED   10  3  2
  14Q LOSS WILD-TYPE 15  3  3
D43V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               10                 15
  N1                3                  3
  N2                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"
                    vv
clus                 M0 M1 MX
  14Q LOSS MUTATED   14  0  1
  14Q LOSS WILD-TYPE 17  2  5
D43V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               14                 17
  M1                0                  2
  MX                1                  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"
D43V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    6  9
  14Q LOSS WILD-TYPE  4 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      6    9
  14Q LOSS WILD-TYPE    4   20
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                6                  4
  MALE                  9                 20
[1] 2 2
[1] FALSE

Clustering(44) Variable = 15Q LOSS MUTATION ANALYSIS
D44V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    1  6
  15Q LOSS WILD-TYPE  9 23
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 32 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 23 
$`15Q LOSS MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BH 
        6.08         3.52        13.61         0.23        23.90         7.99 
TCGA-UD-AABZ 
        6.48 

$`15Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
        5.19        17.33        10.95        24.89        43.27        51.78 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AAC4 TCGA-UD-AAC6 
       28.96         6.58        15.09         8.42        23.64        14.99 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       13.35        23.77        21.44        14.27         2.50         4.73 
TCGA-XT-AASU TCGA-YS-AA4M 
        4.67         2.76 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.23               1.61 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             23.90              91.73 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              6.48              14.63 
[1] "0.2 - 23.9 (6.5)"  "1.6 - 91.7 (14.6)"
[1] "hr=" "2.4"
D44V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         0        1        1        2         3        0
  15Q LOSS WILD-TYPE       3        0        0        9        16        4
D44V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 1                  0
  STAGE IB                 1                  0
  STAGE II                 2                  9
  STAGE III                3                 16
  STAGE IV                 0                  4
[1] 6 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     3
  15Q LOSS WILD-TYPE  5 15    12
D44V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                   2                  5
  T2                   2                 15
  T3+T4                3                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  15Q LOSS MUTATED    5  0  1
  15Q LOSS WILD-TYPE 20  6  4
D44V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                5                 20
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  15Q LOSS MUTATED    5  0  2
  15Q LOSS WILD-TYPE 26  2  4
D44V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                5                 26
  M1                0                  2
  MX                2                  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"
D44V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  6
  15Q LOSS WILD-TYPE  9 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    6
  15Q LOSS WILD-TYPE    9   23
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                1                  9
  MALE                  6                 23
[1] 2 2
[1] FALSE

Clustering(45) Variable = 16P LOSS MUTATION ANALYSIS
D45V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    1  4
  16P LOSS WILD-TYPE  9 25
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 34 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 25 
$`16P LOSS MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A4LM TCGA-MQ-A6BS TCGA-UT-A88G TCGA-UT-A97Y 
        6.08         5.19        13.61         2.50         4.73 

$`16P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        91.73        18.81        23.31 
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-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
        0.23        28.96         6.58        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        8.42         6.48        23.64        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-AA4M 
       21.44        14.27         4.67         2.76 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              2.50               0.23 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             13.61              91.73 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              5.19              14.63 
[1] "2.5 - 13.6 (5.2)"  "0.2 - 91.7 (14.6)"
[1] "hr=" "3.9"
D45V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         1        1        0        1         2        0
  16P LOSS WILD-TYPE       2        0        1       10        17        4
D45V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  1                  2
  STAGE IA                 1                  0
  STAGE IB                 0                  1
  STAGE II                 1                 10
  STAGE III                2                 17
  STAGE IV                 0                  4
[1] 6 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 LOSS MUTATED    2  1     2
  16P LOSS WILD-TYPE  5 16    13
D45V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                   2                  5
  T2                   1                 16
  T3+T4                2                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  16P LOSS MUTATED    5  0  0
  16P LOSS WILD-TYPE 20  6  5
D45V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                5                 20
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  16P LOSS MUTATED    4  0  1
  16P LOSS WILD-TYPE 27  2  5
D45V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                4                 27
  M1                0                  2
  MX                1                  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"
D45V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  4
  16P LOSS WILD-TYPE  9 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    4
  16P LOSS WILD-TYPE    9   25
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                1                  9
  MALE                  4                 25
[1] 2 2
[1] FALSE

Clustering(46) Variable = 16Q LOSS MUTATION ANALYSIS
D46V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    2  4
  16Q LOSS WILD-TYPE  8 25
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                 33 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 25 
$`16Q LOSS MUTATED`
TCGA-LK-A4O0 TCGA-LK-A4O6 TCGA-MQ-A6BS TCGA-UD-AABZ TCGA-UT-A88G TCGA-UT-A97Y 
        6.08         1.61        13.61         6.48         2.50         4.73 

$`16Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
        3.55        80.84        91.73        18.81        23.31         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-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
        0.23        28.96         6.58        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D 
        8.42        23.64        14.99        13.35        23.77        21.44 
TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-AA4M 
       14.27         4.67         2.76 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              1.61               0.23 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             13.61              91.73 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             5.405             14.990 
[1] "1.6 - 13.6 (5.4)"  "0.2 - 91.7 (15.0)"
[1] "hr=" "3.4"
D46V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         1        1        0        2         2        0
  16Q LOSS WILD-TYPE       2        0        1        9        17        4
D46V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  1                  2
  STAGE IA                 1                  0
  STAGE IB                 0                  1
  STAGE II                 2                  9
  STAGE III                2                 17
  STAGE IV                 0                  4
[1] 6 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 LOSS MUTATED    2  2     2
  16Q LOSS WILD-TYPE  5 15    13
D46V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                   2                  5
  T2                   2                 15
  T3+T4                2                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  16Q LOSS MUTATED    5  1  0
  16Q LOSS WILD-TYPE 20  5  5
D46V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                5                 20
  N1                1                  5
  N2                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"
                    vv
clus                 M0 M1 MX
  16Q LOSS MUTATED    5  0  1
  16Q LOSS WILD-TYPE 26  2  5
D46V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0                5                 26
  M1                0                  2
  MX                1                  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"
D46V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    2  4
  16Q LOSS WILD-TYPE  8 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    4
  16Q LOSS WILD-TYPE    8   25
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                2                  8
  MALE                  4                 25
[1] 2 2
[1] FALSE

Clustering(47) Variable = 17P LOSS MUTATION ANALYSIS
D47V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED    4  5
  17P LOSS WILD-TYPE  6 24
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 30 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                 24 
$`17P LOSS MUTATED`
TCGA-LK-A4NW TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LN TCGA-SH-A7BH TCGA-SH-A9CT 
       17.95        13.61         0.23         6.58         7.99         8.42 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       13.35        23.77         2.50 

$`17P LOSS WILD-TYPE`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
        5.52         8.02         6.08         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        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-SC-A6LM TCGA-SH-A7BC TCGA-SH-A7BD TCGA-UD-AABZ TCGA-UD-AAC4 
       51.78        28.96        23.90        15.09         6.48        23.64 
TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       14.99        21.44        14.27         4.73         4.67         2.76 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.23               1.61 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             23.77              91.73 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              8.42              14.63 
[1] "0.2 - 23.8 (8.4)"  "1.6 - 91.7 (14.6)"
[1] "hr=" "1.2"
D47V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         0        0        1        3         4        1
  17P LOSS WILD-TYPE       3        1        0        8        15        3
D47V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 0                  1
  STAGE IB                 1                  0
  STAGE II                 3                  8
  STAGE III                4                 15
  STAGE IV                 1                  3
[1] 6 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    1  4     4
  17P LOSS WILD-TYPE  6 13    11
D47V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                   1                  6
  T2                   4                 13
  T3+T4                4                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  17P LOSS MUTATED    5  0  3
  17P LOSS WILD-TYPE 20  6  2
D47V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                5                 20
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  17P LOSS MUTATED    7  0  2
  17P LOSS WILD-TYPE 24  2  4
D47V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0                7                 24
  M1                0                  2
  MX                2                  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"
D47V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    1  8
  17P LOSS WILD-TYPE  9 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1    8
  17P LOSS WILD-TYPE    9   21
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                1                  9
  MALE                  8                 21
[1] 2 2
[1] FALSE

Clustering(48) Variable = 17Q LOSS MUTATION ANALYSIS
D48V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    0  3
  17Q LOSS WILD-TYPE 10 26
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 36 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 26 
$`17Q LOSS MUTATED`
TCGA-NQ-A57I TCGA-SH-A7BH TCGA-UT-A88G 
        0.23         7.99         2.50 

$`17Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.20         1.61         3.55        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-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC 
       43.27        51.78        13.61        28.96         6.58        23.90 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 
       15.09         8.42         6.48        23.64        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       23.77        21.44        14.27         4.73         4.67         2.76 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.23               1.61 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              7.99              91.73 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              2.50              13.94 
[1] "0.2 - 8.0 (2.5)"   "1.6 - 91.7 (13.9)"
[1] "hr=" "8"  
D48V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED         0        0        1        0         2        0
  17Q LOSS WILD-TYPE       3        1        0       11        17        4
D48V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 0                  1
  STAGE IB                 1                  0
  STAGE II                 0                 11
  STAGE III                2                 17
  STAGE IV                 0                  4
[1] 6 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    1  0     2
  17Q LOSS WILD-TYPE  6 17    13
D48V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                   1                  6
  T2                   0                 17
  T3+T4                2                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  17Q LOSS MUTATED    2  0  0
  17Q LOSS WILD-TYPE 23  6  5
D48V5, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 34 
        TCGA-LK-A4NW         TCGA-LK-A4NY         TCGA-LK-A4NZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-LK-A4O0         TCGA-LK-A4O2         TCGA-LK-A4O4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-LK-A4O6         TCGA-LK-A4O7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MQ-A4KX         TCGA-MQ-A4LC         TCGA-MQ-A4LI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LJ         TCGA-MQ-A4LM         TCGA-MQ-A4LP 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LV         TCGA-MQ-A6BL         TCGA-MQ-A6BN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MQ-A6BQ         TCGA-MQ-A6BR         TCGA-MQ-A6BS 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-SC-A6LN         TCGA-SH-A7BC         TCGA-SH-A7BD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-SH-A9CT         TCGA-UD-AABZ         TCGA-UD-AAC4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-UD-AAC6         TCGA-UD-AAC7         TCGA-UT-A88C 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-UT-A88D         TCGA-UT-A88E         TCGA-UT-A97Y 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-YS-AA4M 
"17Q LOSS WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  17Q LOSS MUTATED    2  0  1
  17Q LOSS WILD-TYPE 29  2  5
D48V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                2                 29
  M1                0                  2
  MX                1                  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"
D48V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    1  2
  17Q LOSS WILD-TYPE  9 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    2
  17Q LOSS WILD-TYPE    9   27
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                1                  9
  MALE                  2                 27
[1] 2 2
[1] FALSE

Clustering(49) Variable = 18P LOSS MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    1  4
  18P LOSS WILD-TYPE  9 25
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 34 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 25 
$`18P LOSS MUTATED`
TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-UT-A88G 
       18.81         5.19        10.95        13.61         2.50 

$`18P LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ 
       12.20         1.61         3.55        80.84        91.73        23.31 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
       17.33         3.52        24.89        43.27        51.78         0.23 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
       28.96         6.58        23.90        15.09         7.99         8.42 
TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D 
        6.48        23.64        14.99        13.35        23.77        21.44 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       14.27         4.73         4.67         2.76 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              2.50               0.23 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             18.81              91.73 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             10.95              13.81 
[1] "2.5 - 18.8 (10.9)" "0.2 - 91.7 (13.8)"
[1] "hr=" "2"  
D49V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  18P LOSS MUTATED         0        0        0        3         2        0
  18P LOSS WILD-TYPE       3        1        1        8        17        4
D49V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 0                  1
  STAGE IB                 0                  1
  STAGE II                 3                  8
  STAGE III                2                 17
  STAGE IV                 0                  4
[1] 6 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    0  3     2
  18P LOSS WILD-TYPE  7 14    13
D49V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                   0                  7
  T2                   3                 14
  T3+T4                2                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  18P LOSS MUTATED    5  0  0
  18P LOSS WILD-TYPE 20  6  5
D49V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                5                 20
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  18P LOSS MUTATED    4  0  1
  18P LOSS WILD-TYPE 27  2  5
D49V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                4                 27
  M1                0                  2
  MX                1                  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"
D49V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    1  4
  18P LOSS WILD-TYPE  9 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    4
  18P LOSS WILD-TYPE    9   25
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                1                  9
  MALE                  4                 25
[1] 2 2
[1] FALSE

Clustering(50) Variable = 18Q LOSS MUTATION ANALYSIS
D50V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    1  6
  18Q LOSS WILD-TYPE  9 23
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                 32 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 6                 23 
$`18Q LOSS MUTATED`
TCGA-LK-A4NY TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-SC-A6LM 
        5.52        18.81         5.19        10.95        13.61        28.96 
TCGA-UT-A88G 
        2.50 

$`18Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         8.02         6.08         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LP 
        1.61         3.55        80.84        91.73        23.31        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LN 
        3.52        24.89        43.27        51.78         0.23         6.58 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 
       23.90        15.09         7.99         8.42         6.48        23.64 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y 
       14.99        13.35        23.77        21.44        14.27         4.73 
TCGA-XT-AASU TCGA-YS-AA4M 
        4.67         2.76 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              2.50               0.23 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             28.96              91.73 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             10.95              13.81 
[1] "2.5 - 29.0 (10.9)" "0.2 - 91.7 (13.8)"
[1] "hr=" "1.6"
D50V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED         0        0        0        3         3        1
  18Q LOSS WILD-TYPE       3        1        1        8        16        3
D50V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 0                  1
  STAGE IB                 0                  1
  STAGE II                 3                  8
  STAGE III                3                 16
  STAGE IV                 1                  3
[1] 6 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    0  3     4
  18Q LOSS WILD-TYPE  7 14    11
D50V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                   0                  7
  T2                   3                 14
  T3+T4                4                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  18Q LOSS MUTATED    6  0  0
  18Q LOSS WILD-TYPE 19  6  5
D50V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                6                 19
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  18Q LOSS MUTATED    6  0  1
  18Q LOSS WILD-TYPE 25  2  5
D50V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0                6                 25
  M1                0                  2
  MX                1                  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"
D50V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    3  4
  18Q LOSS WILD-TYPE  7 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    4
  18Q LOSS WILD-TYPE    7   25
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                3                  7
  MALE                  4                 25
[1] 2 2
[1] FALSE

Clustering(51) Variable = 19Q LOSS MUTATION ANALYSIS
D51V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    2  1
  19Q LOSS WILD-TYPE  8 28
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 36 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 28 
$`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-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.20         1.61         3.55        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-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       51.78        28.96         6.58        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        8.42         6.48        23.64        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       21.44        14.27         2.50         4.73         4.67         2.76 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.23               1.61 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             43.27              91.73 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            13.610             12.775 
[1] "0.2 - 43.3 (13.6)" "1.6 - 91.7 (12.8)"
[1] "hr=" "2.4"
D51V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         0        0        1        2         0        0
  19Q LOSS WILD-TYPE       3        1        0        9        19        4
D51V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 0                  1
  STAGE IB                 1                  0
  STAGE II                 2                  9
  STAGE III                0                 19
  STAGE IV                 0                  4
[1] 6 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    1  2     0
  19Q LOSS WILD-TYPE  6 15    15
D51V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                   1                  6
  T2                   2                 15
  T3+T4                0                 15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  19Q LOSS MUTATED    2  0  0
  19Q LOSS WILD-TYPE 23  6  5
D51V5, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 34 
        TCGA-LK-A4NW         TCGA-LK-A4NY         TCGA-LK-A4NZ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-LK-A4O0         TCGA-LK-A4O2         TCGA-LK-A4O4 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-LK-A4O5         TCGA-LK-A4O6         TCGA-LK-A4O7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MQ-A4KX         TCGA-MQ-A4LC         TCGA-MQ-A4LI 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LJ         TCGA-MQ-A4LM         TCGA-MQ-A4LP 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MQ-A4LV         TCGA-MQ-A6BL         TCGA-MQ-A6BN 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MQ-A6BR         TCGA-SC-A6LN         TCGA-SH-A7BC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-SH-A7BD         TCGA-SH-A7BH         TCGA-SH-A9CT 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-UD-AABZ         TCGA-UD-AAC4         TCGA-UD-AAC6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-UD-AAC7         TCGA-UT-A88C         TCGA-UT-A88D 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-UT-A88E         TCGA-UT-A88G         TCGA-UT-A97Y 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-YS-AA4M 
"19Q LOSS WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  19Q LOSS MUTATED    0  0  3
  19Q LOSS WILD-TYPE 31  2  3
D51V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                0                 31
  M1                0                  2
  MX                3                  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"
D51V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    0  3
  19Q LOSS WILD-TYPE 10 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    3
  19Q LOSS WILD-TYPE   10   26
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                0                 10
  MALE                  3                 26
[1] 2 2
[1] FALSE

Clustering(52) Variable = 20P LOSS MUTATION ANALYSIS
D52V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    4  3
  20P LOSS WILD-TYPE  6 26
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                 32 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 26 
$`20P LOSS MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SC-A6LN 
       17.95         6.08        12.20        43.27        13.61         6.58 
TCGA-UT-A88E 
       14.27 

$`20P LOSS WILD-TYPE`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-LK-A4O7 
        5.52         8.02         1.87        31.20         1.61         3.55 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       80.84        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM 
        3.52        10.95        24.89        51.78         0.23        28.96 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 
       23.90        15.09         7.99         8.42         6.48        23.64 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88G TCGA-UT-A97Y 
       14.99        13.35        23.77        21.44         2.50         4.73 
TCGA-XT-AASU TCGA-YS-AA4M 
        4.67         2.76 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              6.08               0.23 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             43.27              91.73 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             13.61              12.15 
[1] "6.1 - 43.3 (13.6)" "0.2 - 91.7 (12.1)"
[1] "hr=" "1.7"
D52V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         1        1        0        2         2        1
  20P LOSS WILD-TYPE       2        0        1        9        17        3
D52V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  1                  2
  STAGE IA                 1                  0
  STAGE IB                 0                  1
  STAGE II                 2                  9
  STAGE III                2                 17
  STAGE IV                 1                  3
[1] 6 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  3     2
  20P LOSS WILD-TYPE  5 14    13
D52V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                   2                  5
  T2                   3                 14
  T3+T4                2                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  20P LOSS MUTATED    5  0  2
  20P LOSS WILD-TYPE 20  6  3
D52V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                5                 20
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  20P LOSS MUTATED    5  0  2
  20P LOSS WILD-TYPE 26  2  4
D52V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                5                 26
  M1                0                  2
  MX                2                  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"
D52V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    1  6
  20P LOSS WILD-TYPE  9 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    6
  20P LOSS WILD-TYPE    9   23
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                1                  9
  MALE                  6                 23
[1] 2 2
[1] FALSE

Clustering(53) Variable = 21Q LOSS MUTATION ANALYSIS
D53V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    2  3
  21Q LOSS WILD-TYPE  8 26
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 5                 34 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 26 
$`21Q LOSS MUTATED`
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A9CT 
        6.08         1.87        13.61         0.23         8.42 

$`21Q LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 
       17.95         5.52         8.02        31.20        12.20         1.61 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
        3.55        80.84        91.73        18.81        23.31         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-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-UD-AABZ 
       28.96         6.58        23.90        15.09         7.99         6.48 
TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E 
       23.64        14.99        13.35        23.77        21.44        14.27 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
        2.50         4.73         4.67         2.76 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.23               1.61 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             13.61              91.73 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              6.08              14.63 
[1] "0.2 - 13.6 (6.1)"  "1.6 - 91.7 (14.6)"
[1] "hr=" "2.6"
D53V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED         0        1        1        2         1        0
  21Q LOSS WILD-TYPE       3        0        0        9        18        4
D53V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  0                  3
  STAGE IA                 1                  0
  STAGE IB                 1                  0
  STAGE II                 2                  9
  STAGE III                1                 18
  STAGE IV                 0                  4
[1] 6 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  2     1
  21Q LOSS WILD-TYPE  5 15    14
D53V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                   2                  5
  T2                   2                 15
  T3+T4                1                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  21Q LOSS MUTATED    4  0  0
  21Q LOSS WILD-TYPE 21  6  5
D53V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                4                 21
  N1                0                  6
  N2                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"
                    vv
clus                 M0 M1 MX
  21Q LOSS MUTATED    3  0  2
  21Q LOSS WILD-TYPE 28  2  4
D53V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0                3                 28
  M1                0                  2
  MX                2                  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"
D53V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    1  4
  21Q LOSS WILD-TYPE  9 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1    4
  21Q LOSS WILD-TYPE    9   25
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                1                  9
  MALE                  4                 25
[1] 2 2
[1] FALSE

Clustering(54) Variable = 22Q LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    9 22
  22Q LOSS WILD-TYPE  1  7
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                31                  8 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                22                  7 
$`22Q LOSS MUTATED`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08         1.87        12.20         1.61 
TCGA-LK-A4O7 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
        3.55        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
        3.52        24.89        43.27        13.61         0.23        28.96 
TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 
        6.58        23.90        15.09         8.42         6.48        23.64 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G 
       14.99        13.35        23.77        21.44        14.27         2.50 
TCGA-UT-A97Y 
        4.73 

$`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 
TCGA-XT-AASU TCGA-YS-AA4M 
        4.67         2.76 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.23               2.76 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             91.73              80.84 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             13.35              14.45 
[1] "0.2 - 91.7 (13.3)" "2.8 - 80.8 (14.4)"
[1] "hr=" "1.1"
D54V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED         2        1        1       10        15        2
  22Q LOSS WILD-TYPE       1        0        0        1         4        2
D54V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  2                  1
  STAGE IA                 1                  0
  STAGE IB                 1                  0
  STAGE II                10                  1
  STAGE III               15                  4
  STAGE IV                 2                  2
[1] 6 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    4 15    12
  22Q LOSS WILD-TYPE  3  2     3
D54V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                   4                  3
  T2                  15                  2
  T3+T4               12                  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"
                    vv
clus                 N0 N1 N2
  22Q LOSS MUTATED   21  4  4
  22Q LOSS WILD-TYPE  4  2  1
D54V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               21                  4
  N1                4                  2
  N2                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"
                    vv
clus                 M0 M1 MX
  22Q LOSS MUTATED   26  1  4
  22Q LOSS WILD-TYPE  5  1  2
D54V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               26                  5
  M1                1                  1
  MX                4                  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"
D54V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    8 23
  22Q LOSS WILD-TYPE  2  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      8   23
  22Q LOSS WILD-TYPE    2    6
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                8                  2
  MALE                 23                  6
[1] 2 2
[1] FALSE

Clustering(55) Variable = XQ LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    4  8
  XQ LOSS WILD-TYPE  6 21
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               12                27 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                8                21 
$`XQ LOSS MUTATED`
TCGA-LK-A4NY TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LP TCGA-MQ-A6BS TCGA-SC-A6LN 
        5.52         3.55        18.81        17.33        13.61         6.58 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88E 
       15.09         8.42         6.48        14.99        13.35        14.27 

$`XQ LOSS WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         8.02         6.08         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV 
        1.61        80.84        91.73        23.31         5.19         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM 
       10.95        24.89        43.27        51.78         0.23        28.96 
TCGA-SH-A7BC TCGA-SH-A7BH TCGA-UD-AAC4 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88G 
       23.90         7.99        23.64        23.77        21.44         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
        4.73         4.67         2.76 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             3.55              0.23 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            18.81             91.73 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            13.48             12.20 
[1] "3.5 - 18.8 (13.5)" "0.2 - 91.7 (12.2)"
[1] "hr=" "1.5"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         1        0        0        6         4        1
  XQ LOSS WILD-TYPE       2        1        1        5        15        3
D55V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 1                 2
  STAGE IA                0                 1
  STAGE IB                0                 1
  STAGE II                6                 5
  STAGE III               4                15
  STAGE IV                1                 3
[1] 6 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    1  8     3
  XQ LOSS WILD-TYPE  6  9    12
D55V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1                  1                 6
  T2                  8                 9
  T3+T4               3                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  XQ LOSS MUTATED   10  1  1
  XQ LOSS WILD-TYPE 15  5  4
D55V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              10                15
  N1               1                 5
  N2               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"
                   vv
clus                M0 M1 MX
  XQ LOSS MUTATED   10  1  1
  XQ LOSS WILD-TYPE 21  1  5
D55V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              10                21
  M1               1                 1
  MX               1                 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"
D55V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    2 10
  XQ LOSS WILD-TYPE  8 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   10
  XQ LOSS WILD-TYPE    8   19
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               2                 8
  MALE                10                19
[1] 2 2
[1] FALSE
