[1] "ofn"       "-oTUVM-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/UVM-TP/22507229/UVM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UVM-TP/22534465/transformed.cor.cli.txt"

nPatients in clinical file=80, in cluster file=80, common to both=80
[1] "Reduce the number of clustering variables from 82 to 50."
[1] 50 80
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                72 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                72 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10                70 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10                70 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                8                72 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                8                72 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                7                73 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                7                73 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4                76 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4                76 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                3                77 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                3                77 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                77 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                77 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               38                42 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               38                42 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                64 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                64 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                9                71 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                9                71 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                8                72 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                8                72 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               39                41 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               39                41 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               53                27 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               53                27 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                5                75 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                5                75 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4                76 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4                76 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                 70 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                 70 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                 70 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                 70 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 77 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 77 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 77 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 77 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                 74 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                 74 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                 77 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                 77 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 76 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 76 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                 72 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                 72 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 9                 71 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 9                 71 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                 72 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                 72 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 9                 71 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 9                 71 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                14                 66 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                14                 66 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 75 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 75 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               10                70 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               10                70 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9                71 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9                71 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               19                61 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               19                61 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                77 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                77 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               43                37 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               43                37 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               43                37 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               43                37 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                77 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                77 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                77 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                77 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               17                63 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               17                63 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                76 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                76 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                77 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                77 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                8                72 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                8                72 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                7                73 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                7                73 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 77 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 77 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 77 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 77 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 76 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 76 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 77 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 77 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                16                 64 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                16                 64 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 77 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 77 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 77 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 77 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               12                68 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               12                68 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               13                67 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               13                67 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "RACE"                                
[14] "ETHNICITY"                           

Input Data has 14 rows and 80 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RACE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "1"                "52"                  
freq.contrast "52"               "1"                   
both >= 3     "FALSE"            "FALSE"               
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 80 columns, 1 survival variables, and 6 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "PATHOLOGIC_STAGE"  "PATHOLOGY_T_STAGE"
[4] "PATHOLOGY_M_STAGE" "GENDER"            "RADIATION_THERAPY"
YEARS_TO_BIRTH, nv=40, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T2 T3 T4 
14 32 34 
[1] "table(vv)"
vv
T2 T3 T4 
14 32 34 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T2 T3 T4 
14 32 34 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T2 T3 T4 
14 32 34 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1Q GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    5  3
  1Q GAIN WILD-TYPE 52 20
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                72 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                20 
$`1Q GAIN MUTATED`
TCGA-RZ-AB0B TCGA-V4-A9EK TCGA-V4-A9ET TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-VD-AA8O 
        4.90        33.80        44.78        24.13        20.84        19.92 
TCGA-WC-A883 TCGA-WC-A884 
        7.92         0.39 

$`1Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-V3-A9ZX TCGA-V3-A9ZY 
       32.28        51.98        35.01        14.89        15.45        15.09 
TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       82.16        13.64        26.56        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       35.44        13.08        38.30        22.03        12.79        24.53 
TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9EU TCGA-V4-A9EV 
       31.76        25.41        14.96        49.68        23.31        41.72 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 
       39.81        24.00        27.52        19.69        31.07        30.84 
TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 
       28.70         6.67        41.29        19.63        47.97        45.27 
TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF 
       46.82        38.73        44.52         3.75        26.99         1.32 
TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL 
        0.62        38.07        36.59        37.81         2.10        20.98 
TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8P 
        0.13         2.24        26.14         0.20         1.45         2.83 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W 
       20.91         0.20        14.04         1.61        85.48        55.99 
TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A 
       43.20        41.36        36.56        22.55        18.90         2.70 
TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       27.55        61.22        16.27        26.24        45.90        38.93 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.39              0.13 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            44.78             85.48 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            20.38             26.40 
[1] "0.4 - 44.8 (20.4)" "0.1 - 85.5 (26.4)"
[1] "hr=" "2.1"
D1V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  1Q GAIN MUTATED           0         2          3          2          0
  1Q GAIN WILD-TYPE        12        25         22          8          1
                   vv
clus                STAGE IV
  1Q GAIN MUTATED          1
  1Q GAIN WILD-TYPE        3
D1V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE IIA                0                12
  STAGE IIB                2                25
  STAGE IIIA               3                22
  STAGE IIIB               2                 8
  STAGE IIIC               0                 1
  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                T2 T3 T4
  1Q GAIN MUTATED    0  4  4
  1Q GAIN WILD-TYPE 14 28 30
D1V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T2               0                14
  T3               4                28
  T4               4                30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    7  1
  1Q GAIN WILD-TYPE 44  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      7    1
  1Q GAIN WILD-TYPE   44    3
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0               7                44
  1               1                 3
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    5  3
  1Q GAIN WILD-TYPE 30 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5    3
  1Q GAIN WILD-TYPE   30   42
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               5                30
  MALE                 3                42
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    7  0
  1Q GAIN WILD-TYPE 69  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      7    0
  1Q GAIN WILD-TYPE   69    3
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                7                69
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(2) Variable = 2P GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    7  3
  2P GAIN WILD-TYPE 50 20
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10                70 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3                20 
$`2P GAIN MUTATED`
TCGA-V4-A9E8 TCGA-V4-A9EI TCGA-V4-A9EK TCGA-VD-A8KJ TCGA-VD-A8KL TCGA-VD-AA8P 
       26.56        12.79        33.80        37.81        20.98         2.83 
TCGA-VD-AA8S TCGA-WC-A882 TCGA-YZ-A982 TCGA-YZ-A984 
       14.04        36.56        16.27        45.90 

$`2P GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       15.09        82.16        13.64        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EM 
       35.44        13.08        38.30        22.03        24.53        31.76 
TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV 
       25.41        14.96        49.68        44.78        23.31        41.72 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 
       39.81        24.00        27.52        19.69        31.07        30.84 
TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 
       24.13        28.70        20.84         6.67        41.29        19.63 
TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD 
       47.97        45.27        46.82        38.73        44.52         3.75 
TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KK 
       26.99         1.32         0.62        38.07        36.59         2.10 
TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O 
        0.13         2.24        26.14         0.20         1.45        19.92 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y 
       20.91         0.20         1.61        85.48        55.99        43.20 
TCGA-WC-A880 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A 
       41.36         7.92         0.39        22.55        18.90         2.70 
TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A985 
       27.55        61.22        26.24        38.93 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             2.83              0.13 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            45.90             85.48 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           23.770            25.775 
[1] "2.8 - 45.9 (23.8)" "0.1 - 85.5 (25.8)"
[1] "hr=" "1.2"
D2V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  2P GAIN MUTATED           1         6          1          2          0
  2P GAIN WILD-TYPE        11        21         24          8          1
                   vv
clus                STAGE IV
  2P GAIN MUTATED          0
  2P GAIN WILD-TYPE        4
D2V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE IIA                1                11
  STAGE IIB                6                21
  STAGE IIIA               1                24
  STAGE IIIB               2                 8
  STAGE IIIC               0                 1
  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                T2 T3 T4
  2P GAIN MUTATED    2  5  3
  2P GAIN WILD-TYPE 12 27 31
D2V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T2               2                12
  T3               5                27
  T4               3                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    6  0
  2P GAIN WILD-TYPE 45  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      6    0
  2P GAIN WILD-TYPE   45    4
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               6                45
  1               0                 4
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    6  4
  2P GAIN WILD-TYPE 29 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      6    4
  2P GAIN WILD-TYPE   29   41
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               6                29
  MALE                 4                41
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    9  1
  2P GAIN WILD-TYPE 67  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      9    1
  2P GAIN WILD-TYPE   67    2
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                9                67
  YES               1                 2
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2Q GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    6  2
  2Q GAIN WILD-TYPE 51 21
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                8                72 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                21 
$`2Q GAIN MUTATED`
TCGA-V4-A9E8 TCGA-V4-A9EK TCGA-VD-A8KJ TCGA-VD-A8KL TCGA-VD-AA8S TCGA-WC-A882 
       26.56        33.80        37.81        20.98        14.04        36.56 
TCGA-YZ-A982 TCGA-YZ-A984 
       16.27        45.90 

$`2Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       15.09        82.16        13.64        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       35.44        13.08        38.30        22.03        12.79        24.53 
TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU 
       31.76        25.41        14.96        49.68        44.78        23.31 
TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 
       41.72        39.81        24.00        27.52        19.69        31.07 
TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 
       30.84        24.13        28.70        20.84         6.67        41.29 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       19.63        47.97        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI 
        3.75        26.99         1.32         0.62        38.07        36.59 
TCGA-VD-A8KK TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N 
        2.10         0.13         2.24        26.14         0.20         1.45 
TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8T TCGA-WC-A87T 
       19.92         2.83        20.91         0.20         1.61        85.48 
TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 
       55.99        43.20        41.36         7.92         0.39        22.55 
TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A985 
       18.90         2.70        27.55        61.22        26.24        38.93 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            14.04              0.13 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            45.90             85.48 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            30.18             24.97 
[1] "14.0 - 45.9 (30.2)" "0.1 - 85.5 (25.0)" 
[1] "hr=" "1.3"
D3V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  2Q GAIN MUTATED           1         5          1          1          0
  2Q GAIN WILD-TYPE        11        22         24          9          1
                   vv
clus                STAGE IV
  2Q GAIN MUTATED          0
  2Q GAIN WILD-TYPE        4
D3V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE IIA                1                11
  STAGE IIB                5                22
  STAGE IIIA               1                24
  STAGE IIIB               1                 9
  STAGE IIIC               0                 1
  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                T2 T3 T4
  2Q GAIN MUTATED    2  4  2
  2Q GAIN WILD-TYPE 12 28 32
D3V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T2               2                12
  T3               4                28
  T4               2                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    4  0
  2Q GAIN WILD-TYPE 47  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4    0
  2Q GAIN WILD-TYPE   47    4
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               4                47
  1               0                 4
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    5  3
  2Q GAIN WILD-TYPE 30 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5    3
  2Q GAIN WILD-TYPE   30   42
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               5                30
  MALE                 3                42
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    8  0
  2Q GAIN WILD-TYPE 68  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      8    0
  2Q GAIN WILD-TYPE   68    3
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                8                68
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(4) Variable = 4P GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    5  2
  4P GAIN WILD-TYPE 52 21
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                7                73 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                21 
$`4P GAIN MUTATED`
TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9EI TCGA-V4-A9EU TCGA-V4-A9F5 TCGA-VD-A8KM 
       82.16        13.64        12.79        23.31         6.67         0.13 
TCGA-VD-AA8S 
       14.04 

$`4P GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED 
       15.09        26.56        40.96        44.32        24.43        35.44 
TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM 
       13.08        38.30        22.03        24.53        33.80        31.76 
TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EV TCGA-V4-A9EW 
       25.41        14.96        49.68        44.78        41.72        39.81 
TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 
       24.00        27.52        19.69        31.07        30.84        24.13 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 
       28.70        20.84        41.29        19.63        47.97        45.27 
TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF 
       46.82        38.73        44.52         3.75        26.99         1.32 
TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL 
        0.62        38.07        36.59        37.81         2.10        20.98 
TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P 
        2.24        26.14         0.20         1.45        19.92         2.83 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y 
       20.91         0.20         1.61        85.48        55.99        43.20 
TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 
       41.36        36.56         7.92         0.39        22.55        18.90 
TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 
        2.70        27.55        61.22        16.27        26.24        45.90 
TCGA-YZ-A985 
       38.93 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.13              0.20 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            82.16             85.48 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            13.64             26.56 
[1] "0.1 - 82.2 (13.6)" "0.2 - 85.5 (26.6)"
[1] "hr=" "1.4"
D4V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  4P GAIN MUTATED           1         1          1          2          1
  4P GAIN WILD-TYPE        11        26         24          8          0
                   vv
clus                STAGE IV
  4P GAIN MUTATED          1
  4P GAIN WILD-TYPE        3
D4V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE IIA                1                11
  STAGE IIB                1                26
  STAGE IIIA               1                24
  STAGE IIIB               2                 8
  STAGE IIIC               1                 0
  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                T2 T3 T4
  4P GAIN MUTATED    1  1  5
  4P GAIN WILD-TYPE 13 31 29
D4V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T2               1                13
  T3               1                31
  T4               5                29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    5  1
  4P GAIN WILD-TYPE 46  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      5    1
  4P GAIN WILD-TYPE   46    3
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               5                46
  1               1                 3
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    3  4
  4P GAIN WILD-TYPE 32 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3    4
  4P GAIN WILD-TYPE   32   41
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               3                32
  MALE                 4                41
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    6  1
  4P GAIN WILD-TYPE 70  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6    1
  4P GAIN WILD-TYPE   70    2
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                6                70
  YES               1                 2
[1] 2 2
[1] FALSE

Clustering(5) Variable = 4Q GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    3  1
  4Q GAIN WILD-TYPE 54 22
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4                76 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                22 
$`4Q GAIN MUTATED`
TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9EU TCGA-V4-A9F5 
       82.16        13.64        23.31         6.67 

$`4Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED 
       15.09        26.56        40.96        44.32        24.43        35.44 
TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK 
       13.08        38.30        22.03        12.79        24.53        33.80 
TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EV 
       31.76        25.41        14.96        49.68        44.78        41.72 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 
       39.81        24.00        27.52        19.69        31.07        30.84 
TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 
       24.13        28.70        20.84        41.29        19.63        47.97 
TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE 
       45.27        46.82        38.73        44.52         3.75        26.99 
TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK 
        1.32         0.62        38.07        36.59        37.81         2.10 
TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N 
       20.98         0.13         2.24        26.14         0.20         1.45 
TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T 
       19.92         2.83        20.91         0.20        14.04         1.61 
TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 
       85.48        55.99        43.20        41.36        36.56         7.92 
TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 
        0.39        22.55        18.90         2.70        27.55        61.22 
TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       16.27        26.24        45.90        38.93 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             6.67              0.13 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            82.16             85.48 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           18.475            26.190 
[1] "6.7 - 82.2 (18.5)" "0.1 - 85.5 (26.2)"
[1] "hr=" "1.3"
D5V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  4Q GAIN MUTATED           0         0          1          1          1
  4Q GAIN WILD-TYPE        12        27         24          9          0
                   vv
clus                STAGE IV
  4Q GAIN MUTATED          1
  4Q GAIN WILD-TYPE        3
D5V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE IIA                0                12
  STAGE IIB                0                27
  STAGE IIIA               1                24
  STAGE IIIB               1                 9
  STAGE IIIC               1                 0
  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                T2 T3 T4
  4Q GAIN MUTATED    0  0  4
  4Q GAIN WILD-TYPE 14 32 30
D5V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T2               0                14
  T3               0                32
  T4               4                30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    3  1
  4Q GAIN WILD-TYPE 48  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    1
  4Q GAIN WILD-TYPE   48    3
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               3                48
  1               1                 3
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    3  1
  4Q GAIN WILD-TYPE 32 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    1
  4Q GAIN WILD-TYPE   32   44
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               3                32
  MALE                 1                44
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    4  0
  4Q GAIN WILD-TYPE 72  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    0
  4Q GAIN WILD-TYPE   72    3
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                4                72
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(6) Variable = 5P GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    1  2
  5P GAIN WILD-TYPE 56 21
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                3                77 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                21 
$`5P GAIN MUTATED`
TCGA-V4-A9EO TCGA-V4-A9F3 TCGA-YZ-A984 
       25.41        28.70        45.90 

$`5P GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET 
       24.53        33.80        31.76        14.96        49.68        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ 
       23.31        41.72        39.81        24.00        27.52        19.69 
TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 
       31.07        30.84        24.13        20.84         6.67        41.29 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       19.63        47.97        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI 
        3.75        26.99         1.32         0.62        38.07        36.59 
TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO 
       37.81         2.10        20.98         0.13         2.24        26.14 
TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R 
        0.20         1.45        19.92         2.83        20.91         0.20 
TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 
       14.04         1.61        85.48        55.99        43.20        41.36 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A 
       36.56         7.92         0.39        22.55        18.90         2.70 
TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A985 
       27.55        61.22        16.27        26.24        38.93 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            25.41              0.13 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            45.90             85.48 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            28.70             24.53 
[1] "25.4 - 45.9 (28.7)" "0.1 - 85.5 (24.5)" 
[1] "hr=" "1.7"
D6V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  5P GAIN MUTATED           0         1          2          0          0
  5P GAIN WILD-TYPE        12        26         23         10          1
                   vv
clus                STAGE IV
  5P GAIN MUTATED          0
  5P GAIN WILD-TYPE        4
D6V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE IIA                0                12
  STAGE IIB                1                26
  STAGE IIIA               2                23
  STAGE IIIB               0                10
  STAGE IIIC               0                 1
  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                T2 T3 T4
  5P GAIN MUTATED    0  1  2
  5P GAIN WILD-TYPE 14 31 32
D6V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T2               0                14
  T3               1                31
  T4               2                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    2  0
  5P GAIN WILD-TYPE 49  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    0
  5P GAIN WILD-TYPE   49    4
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0               2                49
  1               0                 4
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    2  1
  5P GAIN WILD-TYPE 33 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    1
  5P GAIN WILD-TYPE   33   44
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               2                33
  MALE                 1                44
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    3  0
  5P GAIN WILD-TYPE 73  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3    0
  5P GAIN WILD-TYPE   73    3
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                3                73
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(7) Variable = 5Q GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    1  2
  5Q GAIN WILD-TYPE 56 21
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                77 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                21 
$`5Q GAIN MUTATED`
TCGA-V4-A9EO TCGA-V4-A9F3 TCGA-YZ-A984 
       25.41        28.70        45.90 

$`5Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET 
       24.53        33.80        31.76        14.96        49.68        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ 
       23.31        41.72        39.81        24.00        27.52        19.69 
TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 
       31.07        30.84        24.13        20.84         6.67        41.29 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       19.63        47.97        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI 
        3.75        26.99         1.32         0.62        38.07        36.59 
TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO 
       37.81         2.10        20.98         0.13         2.24        26.14 
TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R 
        0.20         1.45        19.92         2.83        20.91         0.20 
TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 
       14.04         1.61        85.48        55.99        43.20        41.36 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A 
       36.56         7.92         0.39        22.55        18.90         2.70 
TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A985 
       27.55        61.22        16.27        26.24        38.93 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            25.41              0.13 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            45.90             85.48 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            28.70             24.53 
[1] "25.4 - 45.9 (28.7)" "0.1 - 85.5 (24.5)" 
[1] "hr=" "1.7"
D7V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  5Q GAIN MUTATED           0         1          2          0          0
  5Q GAIN WILD-TYPE        12        26         23         10          1
                   vv
clus                STAGE IV
  5Q GAIN MUTATED          0
  5Q GAIN WILD-TYPE        4
D7V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE IIA                0                12
  STAGE IIB                1                26
  STAGE IIIA               2                23
  STAGE IIIB               0                10
  STAGE IIIC               0                 1
  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                T2 T3 T4
  5Q GAIN MUTATED    0  1  2
  5Q GAIN WILD-TYPE 14 31 32
D7V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T2               0                14
  T3               1                31
  T4               2                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    2  0
  5Q GAIN WILD-TYPE 49  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    0
  5Q GAIN WILD-TYPE   49    4
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               2                49
  1               0                 4
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    2  1
  5Q GAIN WILD-TYPE 33 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    1
  5Q GAIN WILD-TYPE   33   44
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               2                33
  MALE                 1                44
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    3  0
  5Q GAIN WILD-TYPE 73  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    0
  5Q GAIN WILD-TYPE   73    3
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                3                73
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(8) Variable = 6P GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   32  6
  6P GAIN WILD-TYPE 25 17
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               38                42 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                17 
$`6P GAIN MUTATED`
TCGA-WC-A87U TCGA-WC-A881 TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E8 
       51.98        35.01        15.45        15.09        82.16        26.56 
TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO 
       44.32        24.43        24.53        33.80        31.76        25.41 
TCGA-V4-A9ET TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EZ TCGA-V4-A9F2 TCGA-V4-A9F3 
       44.78        39.81        24.00        19.69        24.13        28.70 
TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-VD-A8K7 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       20.84        41.29        47.97        46.82        38.73        44.52 
TCGA-VD-A8KE TCGA-VD-A8KI TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO 
       26.99        36.59        20.98         0.13         2.24        26.14 
TCGA-VD-AA8S TCGA-WC-A87W TCGA-WC-A880 TCGA-WC-A884 TCGA-WC-A88A TCGA-WC-AA9E 
       14.04        55.99        41.36         0.39         2.70        27.55 
TCGA-YZ-A982 TCGA-YZ-A983 
       16.27        26.24 

$`6P GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9ED 
       32.28        14.89         4.90        13.64        40.96        35.44 
TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EQ TCGA-V4-A9ES 
       13.08        38.30        22.03        12.79        14.96        49.68 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EY TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F5 
       23.31        41.72        27.52        31.07        30.84         6.67 
TCGA-V4-A9F8 TCGA-VD-A8K8 TCGA-VD-A8KD TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH 
       19.63        45.27         3.75         1.32         0.62        38.07 
TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P 
       37.81         2.10         0.20         1.45        19.92         2.83 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87Y TCGA-WC-A882 
       20.91         0.20         1.61        85.48        43.20        36.56 
TCGA-WC-A883 TCGA-WC-A885 TCGA-WC-A888 TCGA-YZ-A980 TCGA-YZ-A984 TCGA-YZ-A985 
        7.92        22.55        18.90        61.22        45.90        38.93 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.13              0.20 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            82.16             85.48 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           26.775            21.470 
[1] "0.1 - 82.2 (26.8)" "0.2 - 85.5 (21.5)"
[1] "hr=" "3.3"
D8V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  6P GAIN MUTATED           7        14         12          4          0
  6P GAIN WILD-TYPE         5        13         13          6          1
                   vv
clus                STAGE IV
  6P GAIN MUTATED          1
  6P GAIN WILD-TYPE        3
D8V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE IIA                7                 5
  STAGE IIB               14                13
  STAGE IIIA              12                13
  STAGE IIIB               4                 6
  STAGE IIIC               0                 1
  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                T2 T3 T4
  6P GAIN MUTATED    8 15 15
  6P GAIN WILD-TYPE  6 17 19
D8V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T2               8                 6
  T3              15                17
  T4              15                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   22  1
  6P GAIN WILD-TYPE 29  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     22    1
  6P GAIN WILD-TYPE   29    3
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              22                29
  1               1                 3
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   18 20
  6P GAIN WILD-TYPE 17 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     18   20
  6P GAIN WILD-TYPE   17   25
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              18                17
  MALE                20                25
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   37  1
  6P GAIN WILD-TYPE 39  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     37    1
  6P GAIN WILD-TYPE   39    2
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               37                39
  YES               1                 2
[1] 2 2
[1] FALSE

Clustering(9) Variable = 6Q GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED   16  0
  6Q GAIN WILD-TYPE 41 23
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                64 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                0                23 
$`6Q GAIN MUTATED`
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9EA TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO 
       15.09        82.16        44.32        33.80        31.76        25.41 
TCGA-V4-A9ET TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-VD-A8K9 TCGA-VD-A8KB TCGA-VD-A8KE 
       44.78        24.13        20.84        46.82        44.52        26.99 
TCGA-VD-A8KN TCGA-VD-AA8S TCGA-WC-AA9E TCGA-YZ-A983 
        2.24        14.04        27.55        26.24 

$`6Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE 
       13.64        26.56        40.96        24.43        35.44        13.08 
TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EQ TCGA-V4-A9ES 
       38.30        22.03        12.79        24.53        14.96        49.68 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ 
       23.31        41.72        39.81        24.00        27.52        19.69 
TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 
       31.07        30.84        28.70         6.67        41.29        19.63 
TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8KA TCGA-VD-A8KD TCGA-VD-A8KF TCGA-VD-A8KG 
       47.97        45.27        38.73         3.75         1.32         0.62 
TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM 
       38.07        36.59        37.81         2.10        20.98         0.13 
TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q 
       26.14         0.20         1.45        19.92         2.83        20.91 
TCGA-VD-AA8R TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 
        0.20         1.61        85.48        55.99        43.20        41.36 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A 
       36.56         7.92         0.39        22.55        18.90         2.70 
TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A984 TCGA-YZ-A985 
       61.22        16.27        45.90        38.93 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             2.24              0.13 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            82.16             85.48 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           27.270            24.215 
[1] "2.2 - 82.2 (27.3)" "0.1 - 85.5 (24.2)"
[1] "hr="     "2.8e+08"
D9V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  6Q GAIN MUTATED           5         4          5          2          0
  6Q GAIN WILD-TYPE         7        23         20          8          1
                   vv
clus                STAGE IV
  6Q GAIN MUTATED          0
  6Q GAIN WILD-TYPE        4
D9V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE IIA                5                 7
  STAGE IIB                4                23
  STAGE IIIA               5                20
  STAGE IIIB               2                 8
  STAGE IIIC               0                 1
  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                T2 T3 T4
  6Q GAIN MUTATED    5  5  6
  6Q GAIN WILD-TYPE  9 27 28
D9V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T2               5                 9
  T3               5                27
  T4               6                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    9  0
  6Q GAIN WILD-TYPE 42  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      9    0
  6Q GAIN WILD-TYPE   42    4
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               9                42
  1               0                 4
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    8  8
  6Q GAIN WILD-TYPE 27 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      8    8
  6Q GAIN WILD-TYPE   27   37
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               8                27
  MALE                 8                37
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   15  1
  6Q GAIN WILD-TYPE 61  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     15    1
  6Q GAIN WILD-TYPE   61    2
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               15                61
  YES               1                 2
[1] 2 2
[1] FALSE

Clustering(10) Variable = 7P GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED    5  4
  7P GAIN WILD-TYPE 52 19
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                9                71 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                4                19 
$`7P GAIN MUTATED`
TCGA-V4-A9E9 TCGA-V4-A9EW TCGA-V4-A9F2 TCGA-VD-A8KF TCGA-VD-A8KH TCGA-VD-A8KL 
       40.96        39.81        24.13         1.32        38.07        20.98 
TCGA-VD-AA8O TCGA-WC-A88A TCGA-YZ-A984 
       19.92         2.70        45.90 

$`7P GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9EA TCGA-V4-A9EC 
       15.09        82.16        13.64        26.56        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       35.44        13.08        38.30        22.03        12.79        24.53 
TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET 
       33.80        31.76        25.41        14.96        49.68        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 
       23.31        41.72        24.00        27.52        19.69        31.07 
TCGA-V4-A9F1 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 
       30.84        28.70        20.84         6.67        41.29        19.63 
TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD 
       47.97        45.27        46.82        38.73        44.52         3.75 
TCGA-VD-A8KE TCGA-VD-A8KG TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KM 
       26.99         0.62        36.59        37.81         2.10         0.13 
TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8P TCGA-VD-AA8Q 
        2.24        26.14         0.20         1.45         2.83        20.91 
TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y 
        0.20        14.04         1.61        85.48        55.99        43.20 
TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 
       41.36        36.56         7.92         0.39        22.55        18.90 
TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A985 
       27.55        61.22        16.27        26.24        38.93 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             1.32              0.13 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            45.90             85.48 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            24.13             26.14 
[1] "1.3 - 45.9 (24.1)" "0.1 - 85.5 (26.1)"
[1] "hr=" "1.8"
D10V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  7P GAIN MUTATED           0         3          3          2          0
  7P GAIN WILD-TYPE        12        24         22          8          1
                   vv
clus                STAGE IV
  7P GAIN MUTATED          1
  7P GAIN WILD-TYPE        3
D10V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE IIA                0                12
  STAGE IIB                3                24
  STAGE IIIA               3                22
  STAGE IIIB               2                 8
  STAGE IIIC               0                 1
  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                T2 T3 T4
  7P GAIN MUTATED    0  4  5
  7P GAIN WILD-TYPE 14 28 29
D10V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T2               0                14
  T3               4                28
  T4               5                29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    4  1
  7P GAIN WILD-TYPE 47  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4    1
  7P GAIN WILD-TYPE   47    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0               4                47
  1               1                 3
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    4  5
  7P GAIN WILD-TYPE 31 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4    5
  7P GAIN WILD-TYPE   31   40
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               4                31
  MALE                 5                40
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    9  0
  7P GAIN WILD-TYPE 67  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9    0
  7P GAIN WILD-TYPE   67    3
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                9                67
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(11) Variable = 7Q GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED    4  4
  7Q GAIN WILD-TYPE 53 19
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                8                72 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                4                19 
$`7Q GAIN MUTATED`
TCGA-V4-A9EW TCGA-V4-A9F2 TCGA-VD-A8KF TCGA-VD-A8KH TCGA-VD-A8KL TCGA-VD-AA8O 
       39.81        24.13         1.32        38.07        20.98        19.92 
TCGA-WC-A88A TCGA-YZ-A984 
        2.70        45.90 

$`7Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES 
       24.53        33.80        31.76        25.41        14.96        49.68 
TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ 
       44.78        23.31        41.72        24.00        27.52        19.69 
TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 
       31.07        30.84        28.70        20.84         6.67        41.29 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       19.63        47.97        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KG TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK 
        3.75        26.99         0.62        36.59        37.81         2.10 
TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8P 
        0.13         2.24        26.14         0.20         1.45         2.83 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W 
       20.91         0.20        14.04         1.61        85.48        55.99 
TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 
       43.20        41.36        36.56         7.92         0.39        22.55 
TCGA-WC-A888 TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A985 
       18.90        27.55        61.22        16.27        26.24        38.93 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             1.32              0.13 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            45.90             85.48 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           22.555            26.190 
[1] "1.3 - 45.9 (22.6)" "0.1 - 85.5 (26.2)"
[1] "hr=" "2.1"
D11V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  7Q GAIN MUTATED           0         3          2          2          0
  7Q GAIN WILD-TYPE        12        24         23          8          1
                   vv
clus                STAGE IV
  7Q GAIN MUTATED          1
  7Q GAIN WILD-TYPE        3
D11V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE IIA                0                12
  STAGE IIB                3                24
  STAGE IIIA               2                23
  STAGE IIIB               2                 8
  STAGE IIIC               0                 1
  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                T2 T3 T4
  7Q GAIN MUTATED    0  4  4
  7Q GAIN WILD-TYPE 14 28 30
D11V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T2               0                14
  T3               4                28
  T4               4                30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    3  1
  7Q GAIN WILD-TYPE 48  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3    1
  7Q GAIN WILD-TYPE   48    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0               3                48
  1               1                 3
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4  4
  7Q GAIN WILD-TYPE 31 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    4
  7Q GAIN WILD-TYPE   31   41
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               4                31
  MALE                 4                41
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    8  0
  7Q GAIN WILD-TYPE 68  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8    0
  7Q GAIN WILD-TYPE   68    3
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                8                68
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(12) Variable = 8P GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   22 17
  8P GAIN WILD-TYPE 35  6
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               39                41 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               17                 6 
$`8P GAIN MUTATED`
TCGA-V4-A9EL TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E5 TCGA-V4-A9E7 
       32.28        14.89         4.90        15.45        82.16        13.64 
TCGA-V4-A9E8 TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EQ 
       26.56        38.30        12.79        33.80        31.76        14.96 
TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9F0 TCGA-V4-A9F1 
       44.78        23.31        39.81        24.00        31.07        30.84 
TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F8 TCGA-VD-A8K8 TCGA-VD-A8KB TCGA-VD-A8KD 
       24.13        28.70        19.63        45.27        44.52         3.75 
TCGA-VD-A8KI TCGA-VD-A8KL TCGA-VD-A8KN TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P 
       36.59        20.98         2.24         1.45        19.92         2.83 
TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87Y TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E 
       14.04         1.61        43.20        18.90         2.70        27.55 
TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A984 
       61.22        16.27        45.90 

$`8P GAIN WILD-TYPE`
TCGA-WC-A87U TCGA-WC-A881 TCGA-V3-A9ZY TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       51.98        35.01        15.09        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EO TCGA-V4-A9ES 
       35.44        13.08        22.03        24.53        25.41        49.68 
TCGA-V4-A9EV TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 
       41.72        27.52        19.69        20.84         6.67        41.29 
TCGA-VD-A8K7 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG 
       47.97        46.82        38.73        26.99         1.32         0.62 
TCGA-VD-A8KH TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KM TCGA-VD-A8KO TCGA-VD-AA8M 
       38.07        37.81         2.10         0.13        26.14         0.20 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A880 TCGA-WC-A882 
       20.91         0.20        85.48        55.99        41.36        36.56 
TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-YZ-A983 TCGA-YZ-A985 
        7.92         0.39        22.55        26.24        38.93 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             1.45              0.13 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            82.16             85.48 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            24.00             26.24 
[1] "1.4 - 82.2 (24.0)" "0.1 - 85.5 (26.2)"
[1] "hr=" "3.3"
D12V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  8P GAIN MUTATED           5        12         11          6          1
  8P GAIN WILD-TYPE         7        15         14          4          0
                   vv
clus                STAGE IV
  8P GAIN MUTATED          3
  8P GAIN WILD-TYPE        1
D12V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE IIA                5                 7
  STAGE IIB               12                15
  STAGE IIIA              11                14
  STAGE IIIB               6                 4
  STAGE IIIC               1                 0
  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                T2 T3 T4
  8P GAIN MUTATED    6 14 19
  8P GAIN WILD-TYPE  8 18 15
D12V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T2               6                 8
  T3              14                18
  T4              19                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"
D12V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   25  3
  8P GAIN WILD-TYPE 26  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     25    3
  8P GAIN WILD-TYPE   26    1
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              25                26
  1               3                 1
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   18 21
  8P GAIN WILD-TYPE 17 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     18   21
  8P GAIN WILD-TYPE   17   24
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              18                17
  MALE                21                24
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   35  3
  8P GAIN WILD-TYPE 41  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     35    3
  8P GAIN WILD-TYPE   41    0
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               35                41
  YES               3                 0
[1] 2 2
[1] FALSE

Clustering(13) Variable = 8Q GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   32 21
  8Q GAIN WILD-TYPE 25  2
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               53                27 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               21                 2 
$`8Q GAIN MUTATED`
TCGA-V4-A9EL TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E5 TCGA-V4-A9E7 
       32.28        14.89         4.90        15.45        82.16        13.64 
TCGA-V4-A9E8 TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EJ 
       26.56        35.44        13.08        38.30        12.79        24.53 
TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ET TCGA-V4-A9EU 
       33.80        31.76        25.41        14.96        44.78        23.31 
TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 
       41.72        39.81        24.00        31.07        30.84        24.13 
TCGA-V4-A9F3 TCGA-V4-A9F8 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       28.70        19.63        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KK 
        3.75         1.32         0.62        38.07        36.59         2.10 
TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P 
       20.98         0.13         2.24         1.45        19.92         2.83 
TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87Y TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A888 
       14.04         1.61        43.20        36.56         7.92        18.90 
TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A984 
        2.70        27.55        61.22        16.27        45.90 

$`8Q GAIN WILD-TYPE`
TCGA-WC-A87U TCGA-WC-A881 TCGA-V3-A9ZY TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       51.98        35.01        15.09        40.96        44.32        24.43 
TCGA-V4-A9EH TCGA-V4-A9ES TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F4 TCGA-V4-A9F5 
       22.03        49.68        27.52        19.69        20.84         6.67 
TCGA-V4-A9F7 TCGA-VD-A8K7 TCGA-VD-A8KE TCGA-VD-A8KJ TCGA-VD-A8KO TCGA-VD-AA8M 
       41.29        47.97        26.99        37.81        26.14         0.20 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A880 TCGA-WC-A884 
       20.91         0.20        85.48        55.99        41.36         0.39 
TCGA-WC-A885 TCGA-YZ-A983 TCGA-YZ-A985 
       22.55        26.24        38.93 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.13              0.20 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            82.16             85.48 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            24.13             26.99 
[1] "0.1 - 82.2 (24.1)" "0.2 - 85.5 (27.0)"
[1] "hr=" "7.2"
D13V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  8Q GAIN MUTATED           7        17         16          8          1
  8Q GAIN WILD-TYPE         5        10          9          2          0
                   vv
clus                STAGE IV
  8Q GAIN MUTATED          3
  8Q GAIN WILD-TYPE        1
D13V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE IIA                7                 5
  STAGE IIB               17                10
  STAGE IIIA              16                 9
  STAGE IIIB               8                 2
  STAGE IIIC               1                 0
  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                T2 T3 T4
  8Q GAIN MUTATED    9 20 24
  8Q GAIN WILD-TYPE  5 12 10
D13V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T2               9                 5
  T3              20                12
  T4              24                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"
D13V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   32  3
  8Q GAIN WILD-TYPE 19  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     32    3
  8Q GAIN WILD-TYPE   19    1
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              32                19
  1               3                 1
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   23 30
  8Q GAIN WILD-TYPE 12 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     23   30
  8Q GAIN WILD-TYPE   12   15
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              23                12
  MALE                30                15
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   49  3
  8Q GAIN WILD-TYPE 27  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     49    3
  8Q GAIN WILD-TYPE   27    0
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               49                27
  YES               3                 0
[1] 2 2
[1] FALSE

Clustering(14) Variable = 9P GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    4  1
  9P GAIN WILD-TYPE 53 22
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                5                75 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                22 
$`9P GAIN MUTATED`
TCGA-V4-A9EW TCGA-VD-A8KE TCGA-VD-AA8P TCGA-VD-AA8S TCGA-YZ-A984 
       39.81        26.99         2.83        14.04        45.90 

$`9P GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES 
       24.53        33.80        31.76        25.41        14.96        49.68 
TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ 
       44.78        23.31        41.72        24.00        27.52        19.69 
TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 
       31.07        30.84        24.13        28.70        20.84         6.67 
TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA 
       41.29        19.63        47.97        45.27        46.82        38.73 
TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI 
       44.52         3.75         1.32         0.62        38.07        36.59 
TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO 
       37.81         2.10        20.98         0.13         2.24        26.14 
TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8T 
        0.20         1.45        19.92        20.91         0.20         1.61 
TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 
       85.48        55.99        43.20        41.36        36.56         7.92 
TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 
        0.39        22.55        18.90         2.70        27.55        61.22 
TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A985 
       16.27        26.24        38.93 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             2.83              0.13 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            45.90             85.48 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            26.99             25.41 
[1] "2.8 - 45.9 (27.0)" "0.1 - 85.5 (25.4)"
[1] "hr=" "1.5"
D14V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  9P GAIN MUTATED           2         2          1          0          0
  9P GAIN WILD-TYPE        10        25         24         10          1
                   vv
clus                STAGE IV
  9P GAIN MUTATED          0
  9P GAIN WILD-TYPE        4
D14V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE IIA                2                10
  STAGE IIB                2                25
  STAGE IIIA               1                24
  STAGE IIIB               0                10
  STAGE IIIC               0                 1
  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                T2 T3 T4
  9P GAIN MUTATED    2  2  1
  9P GAIN WILD-TYPE 12 30 33
D14V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T2               2                12
  T3               2                30
  T4               1                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    3  0
  9P GAIN WILD-TYPE 48  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    0
  9P GAIN WILD-TYPE   48    4
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               3                48
  1               0                 4
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    4  1
  9P GAIN WILD-TYPE 31 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      4    1
  9P GAIN WILD-TYPE   31   44
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               4                31
  MALE                 1                44
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    5  0
  9P GAIN WILD-TYPE 71  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5    0
  9P GAIN WILD-TYPE   71    3
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                5                71
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(15) Variable = 9Q GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    4  0
  9Q GAIN WILD-TYPE 53 23
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4                76 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                23 
$`9Q GAIN MUTATED`
TCGA-V4-A9ES TCGA-V4-A9EW TCGA-VD-A8KE TCGA-VD-AA8S 
       49.68        39.81        26.99        14.04 

$`9Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ET 
       24.53        33.80        31.76        25.41        14.96        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 
       23.31        41.72        24.00        27.52        19.69        31.07 
TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 
       30.84        24.13        28.70        20.84         6.67        41.29 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       19.63        47.97        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ 
        3.75         1.32         0.62        38.07        36.59        37.81 
TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M 
        2.10        20.98         0.13         2.24        26.14         0.20 
TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8T 
        1.45        19.92         2.83        20.91         0.20         1.61 
TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 
       85.48        55.99        43.20        41.36        36.56         7.92 
TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 
        0.39        22.55        18.90         2.70        27.55        61.22 
TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       16.27        26.24        45.90        38.93 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            14.04              0.13 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            49.68             85.48 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            33.40             24.97 
[1] "14.0 - 49.7 (33.4)" "0.1 - 85.5 (25.0)" 
[1] "hr="     "7.4e+07"
D15V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  9Q GAIN MUTATED           2         0          2          0          0
  9Q GAIN WILD-TYPE        10        27         23         10          1
                   vv
clus                STAGE IV
  9Q GAIN MUTATED          0
  9Q GAIN WILD-TYPE        4
D15V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE IIA                2                10
  STAGE IIB                0                27
  STAGE IIIA               2                23
  STAGE IIIB               0                10
  STAGE IIIC               0                 1
  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                T2 T3 T4
  9Q GAIN MUTATED    2  1  1
  9Q GAIN WILD-TYPE 12 31 33
D15V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T2               2                12
  T3               1                31
  T4               1                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    3  0
  9Q GAIN WILD-TYPE 48  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    0
  9Q GAIN WILD-TYPE   48    4
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               3                48
  1               0                 4
[1] 2 2
[1] FALSE
D15V6, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    3  1
  9Q GAIN WILD-TYPE 32 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    1
  9Q GAIN WILD-TYPE   32   44
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               3                32
  MALE                 1                44
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    4  0
  9Q GAIN WILD-TYPE 72  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4    0
  9Q GAIN WILD-TYPE   72    3
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                4                72
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(16) Variable = 11P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    7  3
  11P GAIN WILD-TYPE 50 20
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                 70 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 20 
$`11P GAIN MUTATED`
TCGA-V4-A9E5 TCGA-V4-A9E8 TCGA-V4-A9EO TCGA-V4-A9F2 TCGA-V4-A9F8 TCGA-VD-A8KG 
       82.16        26.56        25.41        24.13        19.63         0.62 
TCGA-VD-A8KL TCGA-WC-A888 TCGA-YZ-A982 TCGA-YZ-A984 
       20.98        18.90        16.27        45.90 

$`11P GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED 
       15.09        13.64        40.96        44.32        24.43        35.44 
TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK 
       13.08        38.30        22.03        12.79        24.53        33.80 
TCGA-V4-A9EM TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV 
       31.76        14.96        49.68        44.78        23.31        41.72 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 
       39.81        24.00        27.52        19.69        31.07        30.84 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-VD-A8K7 TCGA-VD-A8K8 
       28.70        20.84         6.67        41.29        47.97        45.27 
TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF 
       46.82        38.73        44.52         3.75        26.99         1.32 
TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KM TCGA-VD-A8KN 
       38.07        36.59        37.81         2.10         0.13         2.24 
TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q 
       26.14         0.20         1.45        19.92         2.83        20.91 
TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y 
        0.20        14.04         1.61        85.48        55.99        43.20 
TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A88A 
       41.36        36.56         7.92         0.39        22.55         2.70 
TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A985 
       27.55        61.22        26.24        38.93 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.62               0.13 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             82.16              85.48 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            22.555             26.615 
[1] "0.6 - 82.2 (22.6)" "0.1 - 85.5 (26.6)"
[1] "hr=" "1"  
D16V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  11P GAIN MUTATED           1         3          4          2          0
  11P GAIN WILD-TYPE        11        24         21          8          1
                    vv
clus                 STAGE IV
  11P GAIN MUTATED          0
  11P GAIN WILD-TYPE        4
D16V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE IIA                 1                 11
  STAGE IIB                 3                 24
  STAGE IIIA                4                 21
  STAGE IIIB                2                  8
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  11P GAIN MUTATED    1  4  5
  11P GAIN WILD-TYPE 13 28 29
D16V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T2                1                 13
  T3                4                 28
  T4                5                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    6  0
  11P GAIN WILD-TYPE 45  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6    0
  11P GAIN WILD-TYPE   45    4
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                6                 45
  1                0                  4
[1] 2 2
[1] FALSE
D16V6, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    6  4
  11P GAIN WILD-TYPE 29 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6    4
  11P GAIN WILD-TYPE   29   41
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                6                 29
  MALE                  4                 41
[1] 2 2
[1] FALSE
D16V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED   10  0
  11P GAIN WILD-TYPE 66  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     10    0
  11P GAIN WILD-TYPE   66    3
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                10                 66
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(17) Variable = 11Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    8  2
  11Q GAIN WILD-TYPE 49 21
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                 70 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 21 
$`11Q GAIN MUTATED`
TCGA-V4-A9E5 TCGA-V4-A9E8 TCGA-V4-A9EO TCGA-V4-A9F2 TCGA-V4-A9F8 TCGA-VD-A8KG 
       82.16        26.56        25.41        24.13        19.63         0.62 
TCGA-VD-A8KL TCGA-VD-A8KO TCGA-WC-A888 TCGA-YZ-A982 
       20.98        26.14        18.90        16.27 

$`11Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED 
       15.09        13.64        40.96        44.32        24.43        35.44 
TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK 
       13.08        38.30        22.03        12.79        24.53        33.80 
TCGA-V4-A9EM TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV 
       31.76        14.96        49.68        44.78        23.31        41.72 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 
       39.81        24.00        27.52        19.69        31.07        30.84 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-VD-A8K7 TCGA-VD-A8K8 
       28.70        20.84         6.67        41.29        47.97        45.27 
TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF 
       46.82        38.73        44.52         3.75        26.99         1.32 
TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KM TCGA-VD-A8KN 
       38.07        36.59        37.81         2.10         0.13         2.24 
TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R 
        0.20         1.45        19.92         2.83        20.91         0.20 
TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 
       14.04         1.61        85.48        55.99        43.20        41.36 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A88A TCGA-WC-AA9E 
       36.56         7.92         0.39        22.55         2.70        27.55 
TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       61.22        26.24        45.90        38.93 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.62               0.13 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             82.16              85.48 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            22.555             27.255 
[1] "0.6 - 82.2 (22.6)" "0.1 - 85.5 (27.3)"
[1] "hr=" "1.3"
D17V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  11Q GAIN MUTATED           2         2          4          2          0
  11Q GAIN WILD-TYPE        10        25         21          8          1
                    vv
clus                 STAGE IV
  11Q GAIN MUTATED          0
  11Q GAIN WILD-TYPE        4
D17V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE IIA                 2                 10
  STAGE IIB                 2                 25
  STAGE IIIA                4                 21
  STAGE IIIB                2                  8
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  11Q GAIN MUTATED    2  3  5
  11Q GAIN WILD-TYPE 12 29 29
D17V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T2                2                 12
  T3                3                 29
  T4                5                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    6  0
  11Q GAIN WILD-TYPE 45  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    0
  11Q GAIN WILD-TYPE   45    4
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                6                 45
  1                0                  4
[1] 2 2
[1] FALSE
D17V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    5  5
  11Q GAIN WILD-TYPE 30 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    5
  11Q GAIN WILD-TYPE   30   40
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                5                 30
  MALE                  5                 40
[1] 2 2
[1] FALSE
D17V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED   10  0
  11Q GAIN WILD-TYPE 66  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10    0
  11Q GAIN WILD-TYPE   66    3
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                10                 66
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(18) Variable = 12P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    2  1
  12P GAIN WILD-TYPE 55 22
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 77 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 1                 22 
$`12P GAIN MUTATED`
TCGA-V4-A9EO TCGA-VD-A8KL TCGA-YZ-A984 
       25.41        20.98        45.90 

$`12P GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET 
       24.53        33.80        31.76        14.96        49.68        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ 
       23.31        41.72        39.81        24.00        27.52        19.69 
TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 
       31.07        30.84        24.13        28.70        20.84         6.67 
TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA 
       41.29        19.63        47.97        45.27        46.82        38.73 
TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH 
       44.52         3.75        26.99         1.32         0.62        38.07 
TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO 
       36.59        37.81         2.10         0.13         2.24        26.14 
TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R 
        0.20         1.45        19.92         2.83        20.91         0.20 
TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 
       14.04         1.61        85.48        55.99        43.20        41.36 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A 
       36.56         7.92         0.39        22.55        18.90         2.70 
TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A985 
       27.55        61.22        16.27        26.24        38.93 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             20.98               0.13 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             45.90              85.48 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             25.41              26.14 
[1] "21.0 - 45.9 (25.4)" "0.1 - 85.5 (26.1)" 
[1] "hr=" "1.2"
D18V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  12P GAIN MUTATED           0         2          1          0          0
  12P GAIN WILD-TYPE        12        25         24         10          1
                    vv
clus                 STAGE IV
  12P GAIN MUTATED          0
  12P GAIN WILD-TYPE        4
D18V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE IIA                 0                 12
  STAGE IIB                 2                 25
  STAGE IIIA                1                 24
  STAGE IIIB                0                 10
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  12P GAIN MUTATED    0  2  1
  12P GAIN WILD-TYPE 14 30 33
D18V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T2                0                 14
  T3                2                 30
  T4                1                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1  0
  12P GAIN WILD-TYPE 50  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    0
  12P GAIN WILD-TYPE   50    4
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                1                 50
  1                0                  4
[1] 2 2
[1] FALSE
D18V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    2  1
  12P GAIN WILD-TYPE 33 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    1
  12P GAIN WILD-TYPE   33   44
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                2                 33
  MALE                  1                 44
[1] 2 2
[1] FALSE
D18V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    3  0
  12P GAIN WILD-TYPE 73  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3    0
  12P GAIN WILD-TYPE   73    3
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 3                 73
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(19) Variable = 12Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    2  1
  12Q GAIN WILD-TYPE 55 22
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 77 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                 22 
$`12Q GAIN MUTATED`
TCGA-V4-A9EO TCGA-VD-A8KL TCGA-YZ-A984 
       25.41        20.98        45.90 

$`12Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET 
       24.53        33.80        31.76        14.96        49.68        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ 
       23.31        41.72        39.81        24.00        27.52        19.69 
TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 
       31.07        30.84        24.13        28.70        20.84         6.67 
TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA 
       41.29        19.63        47.97        45.27        46.82        38.73 
TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH 
       44.52         3.75        26.99         1.32         0.62        38.07 
TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO 
       36.59        37.81         2.10         0.13         2.24        26.14 
TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R 
        0.20         1.45        19.92         2.83        20.91         0.20 
TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 
       14.04         1.61        85.48        55.99        43.20        41.36 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A 
       36.56         7.92         0.39        22.55        18.90         2.70 
TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A985 
       27.55        61.22        16.27        26.24        38.93 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             20.98               0.13 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             45.90              85.48 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             25.41              26.14 
[1] "21.0 - 45.9 (25.4)" "0.1 - 85.5 (26.1)" 
[1] "hr=" "1.2"
D19V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  12Q GAIN MUTATED           0         2          1          0          0
  12Q GAIN WILD-TYPE        12        25         24         10          1
                    vv
clus                 STAGE IV
  12Q GAIN MUTATED          0
  12Q GAIN WILD-TYPE        4
D19V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE IIA                 0                 12
  STAGE IIB                 2                 25
  STAGE IIIA                1                 24
  STAGE IIIB                0                 10
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  12Q GAIN MUTATED    0  2  1
  12Q GAIN WILD-TYPE 14 30 33
D19V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T2                0                 14
  T3                2                 30
  T4                1                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1  0
  12Q GAIN WILD-TYPE 50  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    0
  12Q GAIN WILD-TYPE   50    4
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                1                 50
  1                0                  4
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    2  1
  12Q GAIN WILD-TYPE 33 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2    1
  12Q GAIN WILD-TYPE   33   44
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                2                 33
  MALE                  1                 44
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    3  0
  12Q GAIN WILD-TYPE 73  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3    0
  12Q GAIN WILD-TYPE   73    3
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 3                 73
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(20) Variable = 13Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    5  1
  13Q GAIN WILD-TYPE 52 22
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                 74 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 22 
$`13Q GAIN MUTATED`
TCGA-V4-A9E8 TCGA-V4-A9F2 TCGA-V4-A9F8 TCGA-VD-A8KL TCGA-WC-AA9E TCGA-YZ-A982 
       26.56        24.13        19.63        20.98        27.55        16.27 

$`13Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       15.09        82.16        13.64        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       35.44        13.08        38.30        22.03        12.79        24.53 
TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET 
       33.80        31.76        25.41        14.96        49.68        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ 
       23.31        41.72        39.81        24.00        27.52        19.69 
TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 
       31.07        30.84        28.70        20.84         6.67        41.29 
TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD 
       47.97        45.27        46.82        38.73        44.52         3.75 
TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ 
       26.99         1.32         0.62        38.07        36.59        37.81 
TCGA-VD-A8KK TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N 
        2.10         0.13         2.24        26.14         0.20         1.45 
TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T 
       19.92         2.83        20.91         0.20        14.04         1.61 
TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 
       85.48        55.99        43.20        41.36        36.56         7.92 
TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-YZ-A980 TCGA-YZ-A983 
        0.39        22.55        18.90         2.70        61.22        26.24 
TCGA-YZ-A984 TCGA-YZ-A985 
       45.90        38.93 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             16.27               0.13 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             27.55              85.48 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            22.555             26.190 
[1] "16.3 - 27.6 (22.6)" "0.1 - 85.5 (26.2)" 
[1] "hr=" "1.3"
D20V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  13Q GAIN MUTATED           1         1          3          1          0
  13Q GAIN WILD-TYPE        11        26         22          9          1
                    vv
clus                 STAGE IV
  13Q GAIN MUTATED          0
  13Q GAIN WILD-TYPE        4
D20V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE IIA                 1                 11
  STAGE IIB                 1                 26
  STAGE IIIA                3                 22
  STAGE IIIB                1                  9
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  13Q GAIN MUTATED    1  2  3
  13Q GAIN WILD-TYPE 13 30 31
D20V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T2                1                 13
  T3                2                 30
  T4                3                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    3  0
  13Q GAIN WILD-TYPE 48  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    0
  13Q GAIN WILD-TYPE   48    4
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                3                 48
  1                0                  4
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    3  3
  13Q GAIN WILD-TYPE 32 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    3
  13Q GAIN WILD-TYPE   32   42
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                3                 32
  MALE                  3                 42
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    5  1
  13Q GAIN WILD-TYPE 71  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5    1
  13Q GAIN WILD-TYPE   71    2
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 5                 71
  YES                1                  2
[1] 2 2
[1] FALSE

Clustering(21) Variable = 14Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    1  2
  14Q GAIN WILD-TYPE 56 21
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                 77 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                 21 
$`14Q GAIN MUTATED`
TCGA-V4-A9E8 TCGA-V4-A9EO TCGA-VD-AA8O 
       26.56        25.41        19.92 

$`14Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       15.09        82.16        13.64        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       35.44        13.08        38.30        22.03        12.79        24.53 
TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU 
       33.80        31.76        14.96        49.68        44.78        23.31 
TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 
       41.72        39.81        24.00        27.52        19.69        31.07 
TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 
       30.84        24.13        28.70        20.84         6.67        41.29 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       19.63        47.97        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI 
        3.75        26.99         1.32         0.62        38.07        36.59 
TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO 
       37.81         2.10        20.98         0.13         2.24        26.14 
TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S 
        0.20         1.45         2.83        20.91         0.20        14.04 
TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 
        1.61        85.48        55.99        43.20        41.36        36.56 
TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E 
        7.92         0.39        22.55        18.90         2.70        27.55 
TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       61.22        16.27        26.24        45.90        38.93 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             19.92               0.13 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             26.56              85.48 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             25.41              26.14 
[1] "19.9 - 26.6 (25.4)" "0.1 - 85.5 (26.1)" 
[1] "hr=" "3.2"
D21V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  14Q GAIN MUTATED           0         1          2          0          0
  14Q GAIN WILD-TYPE        12        26         23         10          1
                    vv
clus                 STAGE IV
  14Q GAIN MUTATED          0
  14Q GAIN WILD-TYPE        4
D21V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE IIA                 0                 12
  STAGE IIB                 1                 26
  STAGE IIIA                2                 23
  STAGE IIIB                0                 10
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  14Q GAIN MUTATED    0  1  2
  14Q GAIN WILD-TYPE 14 31 32
D21V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T2                0                 14
  T3                1                 31
  T4                2                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    3  0
  14Q GAIN WILD-TYPE 48  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3    0
  14Q GAIN WILD-TYPE   48    4
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                3                 48
  1                0                  4
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    0  3
  14Q GAIN WILD-TYPE 35 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    3
  14Q GAIN WILD-TYPE   35   42
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                0                 35
  MALE                  3                 42
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    3  0
  14Q GAIN WILD-TYPE 73  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3    0
  14Q GAIN WILD-TYPE   73    3
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 3                 73
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(22) Variable = 16P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    4  0
  16P GAIN WILD-TYPE 53 23
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 76 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 0                 23 
$`16P GAIN MUTATED`
TCGA-V4-A9EO TCGA-V4-A9EZ TCGA-VD-A8KM TCGA-WC-A884 
       25.41        19.69         0.13         0.39 

$`16P GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET 
       24.53        33.80        31.76        14.96        49.68        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9F0 
       23.31        41.72        39.81        24.00        27.52        31.07 
TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 
       30.84        24.13        28.70        20.84         6.67        41.29 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       19.63        47.97        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI 
        3.75        26.99         1.32         0.62        38.07        36.59 
TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M 
       37.81         2.10        20.98         2.24        26.14         0.20 
TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S 
        1.45        19.92         2.83        20.91         0.20        14.04 
TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 
        1.61        85.48        55.99        43.20        41.36        36.56 
TCGA-WC-A883 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 
        7.92        22.55        18.90         2.70        27.55        61.22 
TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       16.27        26.24        45.90        38.93 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.13               0.20 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             25.41              85.48 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             10.04              26.40 
[1] "0.1 - 25.4 (10.0)" "0.2 - 85.5 (26.4)"
[1] "hr="     "9300000"
D22V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  16P GAIN MUTATED           0         2          1          1          0
  16P GAIN WILD-TYPE        12        25         24          9          1
                    vv
clus                 STAGE IV
  16P GAIN MUTATED          0
  16P GAIN WILD-TYPE        4
D22V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE IIA                 0                 12
  STAGE IIB                 2                 25
  STAGE IIIA                1                 24
  STAGE IIIB                1                  9
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  16P GAIN MUTATED    0  2  2
  16P GAIN WILD-TYPE 14 30 32
D22V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T2                0                 14
  T3                2                 30
  T4                2                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V5, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    3  0
  16P GAIN WILD-TYPE 48  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    0
  16P GAIN WILD-TYPE   48    4
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                3                 48
  1                0                  4
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    2  2
  16P GAIN WILD-TYPE 33 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2    2
  16P GAIN WILD-TYPE   33   43
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                2                 33
  MALE                  2                 43
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    4  0
  16P GAIN WILD-TYPE 72  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    0
  16P GAIN WILD-TYPE   72    3
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 4                 72
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(23) Variable = 17P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    5  3
  17P GAIN WILD-TYPE 52 20
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                 72 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 20 
$`17P GAIN MUTATED`
TCGA-V4-A9E8 TCGA-V4-A9EO TCGA-V4-A9EZ TCGA-VD-A8KL TCGA-VD-AA8O TCGA-VD-AA8S 
       26.56        25.41        19.69        20.98        19.92        14.04 
TCGA-YZ-A982 TCGA-YZ-A984 
       16.27        45.90 

$`17P GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       15.09        82.16        13.64        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       35.44        13.08        38.30        22.03        12.79        24.53 
TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU 
       33.80        31.76        14.96        49.68        44.78        23.31 
TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9F0 TCGA-V4-A9F1 
       41.72        39.81        24.00        27.52        31.07        30.84 
TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 
       24.13        28.70        20.84         6.67        41.29        19.63 
TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD 
       47.97        45.27        46.82        38.73        44.52         3.75 
TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ 
       26.99         1.32         0.62        38.07        36.59        37.81 
TCGA-VD-A8KK TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N 
        2.10         0.13         2.24        26.14         0.20         1.45 
TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W 
        2.83        20.91         0.20         1.61        85.48        55.99 
TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 
       43.20        41.36        36.56         7.92         0.39        22.55 
TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A985 
       18.90         2.70        27.55        61.22        26.24        38.93 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             14.04               0.13 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             45.90              85.48 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            20.450             26.615 
[1] "14.0 - 45.9 (20.5)" "0.1 - 85.5 (26.6)" 
[1] "hr=" "1.5"
D23V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  17P GAIN MUTATED           1         4          2          1          0
  17P GAIN WILD-TYPE        11        23         23          9          1
                    vv
clus                 STAGE IV
  17P GAIN MUTATED          0
  17P GAIN WILD-TYPE        4
D23V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE IIA                 1                 11
  STAGE IIB                 4                 23
  STAGE IIIA                2                 23
  STAGE IIIB                1                  9
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  17P GAIN MUTATED    1  4  3
  17P GAIN WILD-TYPE 13 28 31
D23V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T2                1                 13
  T3                4                 28
  T4                3                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    5  0
  17P GAIN WILD-TYPE 46  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    0
  17P GAIN WILD-TYPE   46    4
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                5                 46
  1                0                  4
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    4  4
  17P GAIN WILD-TYPE 31 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    4
  17P GAIN WILD-TYPE   31   41
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                4                 31
  MALE                  4                 41
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    8  0
  17P GAIN WILD-TYPE 68  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      8    0
  17P GAIN WILD-TYPE   68    3
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 8                 68
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(24) Variable = 17Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    6  3
  17Q GAIN WILD-TYPE 51 20
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 9                 71 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 20 
$`17Q GAIN MUTATED`
TCGA-V4-A9E8 TCGA-V4-A9EK TCGA-V4-A9EO TCGA-V4-A9EZ TCGA-VD-A8KL TCGA-VD-AA8O 
       26.56        33.80        25.41        19.69        20.98        19.92 
TCGA-VD-AA8S TCGA-YZ-A982 TCGA-YZ-A984 
       14.04        16.27        45.90 

$`17Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       15.09        82.16        13.64        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       35.44        13.08        38.30        22.03        12.79        24.53 
TCGA-V4-A9EM TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV 
       31.76        14.96        49.68        44.78        23.31        41.72 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 
       39.81        24.00        27.52        31.07        30.84        24.13 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 
       28.70        20.84         6.67        41.29        19.63        47.97 
TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE 
       45.27        46.82        38.73        44.52         3.75        26.99 
TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK 
        1.32         0.62        38.07        36.59        37.81         2.10 
TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8P 
        0.13         2.24        26.14         0.20         1.45         2.83 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y 
       20.91         0.20         1.61        85.48        55.99        43.20 
TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 
       41.36        36.56         7.92         0.39        22.55        18.90 
TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A985 
        2.70        27.55        61.22        26.24        38.93 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             14.04               0.13 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             45.90              85.48 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             20.98              26.24 
[1] "14.0 - 45.9 (21.0)" "0.1 - 85.5 (26.2)" 
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  17Q GAIN MUTATED           1         5          2          1          0
  17Q GAIN WILD-TYPE        11        22         23          9          1
                    vv
clus                 STAGE IV
  17Q GAIN MUTATED          0
  17Q GAIN WILD-TYPE        4
D24V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE IIA                 1                 11
  STAGE IIB                 5                 22
  STAGE IIIA                2                 23
  STAGE IIIB                1                  9
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  17Q GAIN MUTATED    1  5  3
  17Q GAIN WILD-TYPE 13 27 31
D24V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T2                1                 13
  T3                5                 27
  T4                3                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    6  0
  17Q GAIN WILD-TYPE 45  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6    0
  17Q GAIN WILD-TYPE   45    4
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                6                 45
  1                0                  4
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    5  4
  17Q GAIN WILD-TYPE 30 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5    4
  17Q GAIN WILD-TYPE   30   41
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                5                 30
  MALE                  4                 41
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    9  0
  17Q GAIN WILD-TYPE 67  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      9    0
  17Q GAIN WILD-TYPE   67    3
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 9                 67
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(25) Variable = 20P GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    4  4
  20P GAIN WILD-TYPE 53 19
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                 72 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 4                 19 
$`20P GAIN MUTATED`
TCGA-V4-A9E8 TCGA-V4-A9EH TCGA-V4-A9EO TCGA-V4-A9F2 TCGA-VD-AA8O TCGA-VD-AA8Q 
       26.56        22.03        25.41        24.13        19.92        20.91 
TCGA-YZ-A982 TCGA-YZ-A984 
       16.27        45.90 

$`20P GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       15.09        82.16        13.64        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK 
       35.44        13.08        38.30        12.79        24.53        33.80 
TCGA-V4-A9EM TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV 
       31.76        14.96        49.68        44.78        23.31        41.72 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 
       39.81        24.00        27.52        19.69        31.07        30.84 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 
       28.70        20.84         6.67        41.29        19.63        47.97 
TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE 
       45.27        46.82        38.73        44.52         3.75        26.99 
TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK 
        1.32         0.62        38.07        36.59        37.81         2.10 
TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N 
       20.98         0.13         2.24        26.14         0.20         1.45 
TCGA-VD-AA8P TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W 
        2.83         0.20        14.04         1.61        85.48        55.99 
TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 
       43.20        41.36        36.56         7.92         0.39        22.55 
TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A985 
       18.90         2.70        27.55        61.22        26.24        38.93 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             16.27               0.13 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             45.90              85.48 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            23.080             26.615 
[1] "16.3 - 45.9 (23.1)" "0.1 - 85.5 (26.6)" 
[1] "hr=" "2"  
D25V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  20P GAIN MUTATED           0         3          3          2          0
  20P GAIN WILD-TYPE        12        24         22          8          1
                    vv
clus                 STAGE IV
  20P GAIN MUTATED          0
  20P GAIN WILD-TYPE        4
D25V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE IIA                 0                 12
  STAGE IIB                 3                 24
  STAGE IIIA                3                 22
  STAGE IIIB                2                  8
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  20P GAIN MUTATED    0  4  4
  20P GAIN WILD-TYPE 14 28 30
D25V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T2                0                 14
  T3                4                 28
  T4                4                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    6  0
  20P GAIN WILD-TYPE 45  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      6    0
  20P GAIN WILD-TYPE   45    4
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0                6                 45
  1                0                  4
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    3  5
  20P GAIN WILD-TYPE 32 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3    5
  20P GAIN WILD-TYPE   32   40
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                3                 32
  MALE                  5                 40
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    8  0
  20P GAIN WILD-TYPE 68  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      8    0
  20P GAIN WILD-TYPE   68    3
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 8                 68
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(26) Variable = 20Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED    4  5
  20Q GAIN WILD-TYPE 53 18
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 9                 71 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 5                 18 
$`20Q GAIN MUTATED`
TCGA-V4-A9E8 TCGA-V4-A9EH TCGA-V4-A9EO TCGA-V4-A9F2 TCGA-VD-AA8O TCGA-VD-AA8Q 
       26.56        22.03        25.41        24.13        19.92        20.91 
TCGA-WC-A883 TCGA-YZ-A982 TCGA-YZ-A984 
        7.92        16.27        45.90 

$`20Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       15.09        82.16        13.64        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK 
       35.44        13.08        38.30        12.79        24.53        33.80 
TCGA-V4-A9EM TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV 
       31.76        14.96        49.68        44.78        23.31        41.72 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 
       39.81        24.00        27.52        19.69        31.07        30.84 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 
       28.70        20.84         6.67        41.29        19.63        47.97 
TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE 
       45.27        46.82        38.73        44.52         3.75        26.99 
TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK 
        1.32         0.62        38.07        36.59        37.81         2.10 
TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N 
       20.98         0.13         2.24        26.14         0.20         1.45 
TCGA-VD-AA8P TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W 
        2.83         0.20        14.04         1.61        85.48        55.99 
TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 
       43.20        41.36        36.56         0.39        22.55        18.90 
TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A985 
        2.70        27.55        61.22        26.24        38.93 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              7.92               0.13 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             45.90              85.48 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             22.03              26.99 
[1] "7.9 - 45.9 (22.0)" "0.1 - 85.5 (27.0)"
[1] "hr=" "2.6"
D26V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  20Q GAIN MUTATED           0         3          4          2          0
  20Q GAIN WILD-TYPE        12        24         21          8          1
                    vv
clus                 STAGE IV
  20Q GAIN MUTATED          0
  20Q GAIN WILD-TYPE        4
D26V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE IIA                 0                 12
  STAGE IIB                 3                 24
  STAGE IIIA                4                 21
  STAGE IIIB                2                  8
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  20Q GAIN MUTATED    0  5  4
  20Q GAIN WILD-TYPE 14 27 30
D26V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T2                0                 14
  T3                5                 27
  T4                4                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    7  0
  20Q GAIN WILD-TYPE 44  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      7    0
  20Q GAIN WILD-TYPE   44    4
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0                7                 44
  1                0                  4
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    4  5
  20Q GAIN WILD-TYPE 31 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4    5
  20Q GAIN WILD-TYPE   31   40
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                4                 31
  MALE                  5                 40
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    9  0
  20Q GAIN WILD-TYPE 67  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      9    0
  20Q GAIN WILD-TYPE   67    3
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 9                 67
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(27) Variable = 21Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    9  5
  21Q GAIN WILD-TYPE 48 18
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                14                 66 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 18 
$`21Q GAIN MUTATED`
TCGA-V4-A9E8 TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9F2 TCGA-V4-A9F5 TCGA-VD-A8K9 
       26.56        25.41        14.96        24.13         6.67        46.82 
TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-AA8O TCGA-WC-A883 TCGA-WC-A884 
        2.10        20.98         0.13        19.92         7.92         0.39 
TCGA-YZ-A982 TCGA-YZ-A984 
       16.27        45.90 

$`21Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       15.09        82.16        13.64        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       35.44        13.08        38.30        22.03        12.79        24.53 
TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV 
       33.80        31.76        49.68        44.78        23.31        41.72 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 
       39.81        24.00        27.52        19.69        31.07        30.84 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 
       28.70        20.84        41.29        19.63        47.97        45.27 
TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG 
       38.73        44.52         3.75        26.99         1.32         0.62 
TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M 
       38.07        36.59        37.81         2.24        26.14         0.20 
TCGA-VD-AA8N TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T 
        1.45         2.83        20.91         0.20        14.04         1.61 
TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A885 
       85.48        55.99        43.20        41.36        36.56        22.55 
TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A985 
       18.90         2.70        27.55        61.22        26.24        38.93 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.13               0.20 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             46.82              85.48 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            18.095             27.535 
[1] "0.1 - 46.8 (18.1)" "0.2 - 85.5 (27.5)"
[1] "hr=" "1.9"
D27V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  21Q GAIN MUTATED           1         4          6          2          0
  21Q GAIN WILD-TYPE        11        23         19          8          1
                    vv
clus                 STAGE IV
  21Q GAIN MUTATED          1
  21Q GAIN WILD-TYPE        3
D27V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE IIA                 1                 11
  STAGE IIB                 4                 23
  STAGE IIIA                6                 19
  STAGE IIIB                2                  8
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  21Q GAIN MUTATED    1  6  7
  21Q GAIN WILD-TYPE 13 26 27
D27V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T2                1                 13
  T3                6                 26
  T4                7                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V5, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    7  1
  21Q GAIN WILD-TYPE 44  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7    1
  21Q GAIN WILD-TYPE   44    3
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                7                 44
  1                1                  3
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    8  6
  21Q GAIN WILD-TYPE 27 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8    6
  21Q GAIN WILD-TYPE   27   39
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                8                 27
  MALE                  6                 39
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   14  0
  21Q GAIN WILD-TYPE 62  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     14    0
  21Q GAIN WILD-TYPE   62    3
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                14                 62
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(28) Variable = 22Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    4  1
  22Q GAIN WILD-TYPE 53 22
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 75 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 22 
$`22Q GAIN MUTATED`
TCGA-V4-A9EZ TCGA-V4-A9F2 TCGA-VD-A8KL TCGA-YZ-A982 TCGA-YZ-A984 
       19.69        24.13        20.98        16.27        45.90 

$`22Q GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES 
       24.53        33.80        31.76        25.41        14.96        49.68 
TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY 
       44.78        23.31        41.72        39.81        24.00        27.52 
TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 
       31.07        30.84        28.70        20.84         6.67        41.29 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       19.63        47.97        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI 
        3.75        26.99         1.32         0.62        38.07        36.59 
TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M 
       37.81         2.10         0.13         2.24        26.14         0.20 
TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S 
        1.45        19.92         2.83        20.91         0.20        14.04 
TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 
        1.61        85.48        55.99        43.20        41.36        36.56 
TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E 
        7.92         0.39        22.55        18.90         2.70        27.55 
TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A985 
       61.22        26.24        38.93 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             16.27               0.13 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             45.90              85.48 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             20.98              26.24 
[1] "16.3 - 45.9 (21.0)" "0.1 - 85.5 (26.2)" 
[1] "hr=" "1.5"
D28V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  22Q GAIN MUTATED           0         3          1          1          0
  22Q GAIN WILD-TYPE        12        24         24          9          1
                    vv
clus                 STAGE IV
  22Q GAIN MUTATED          0
  22Q GAIN WILD-TYPE        4
D28V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE IIA                 0                 12
  STAGE IIB                 3                 24
  STAGE IIIA                1                 24
  STAGE IIIB                1                  9
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  22Q GAIN MUTATED    0  4  1
  22Q GAIN WILD-TYPE 14 28 33
D28V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T2                0                 14
  T3                4                 28
  T4                1                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V5, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    2  0
  22Q GAIN WILD-TYPE 49  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2    0
  22Q GAIN WILD-TYPE   49    4
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                2                 49
  1                0                  4
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    5  0
  22Q GAIN WILD-TYPE 30 45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      5    0
  22Q GAIN WILD-TYPE   30   45
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                5                 30
  MALE                  0                 45
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    5  0
  22Q GAIN WILD-TYPE 71  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      5    0
  22Q GAIN WILD-TYPE   71    3
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 5                 71
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(29) Variable = XP GAIN MUTATION ANALYSIS
D29V1, survival
                   sevent
clus2                0  1
  XP GAIN MUTATED    9  1
  XP GAIN WILD-TYPE 48 22
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               10                70 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                22 
$`XP GAIN MUTATED`
TCGA-V4-A9E5 TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9ES TCGA-V4-A9F2 
       82.16        33.80        31.76        25.41        49.68        24.13 
TCGA-VD-A8KG TCGA-VD-A8KL TCGA-VD-AA8S TCGA-YZ-A984 
        0.62        20.98        14.04        45.90 

$`XP GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       15.09        13.64        26.56        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       35.44        13.08        38.30        22.03        12.79        24.53 
TCGA-V4-A9EQ TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX 
       14.96        44.78        23.31        41.72        39.81        24.00 
TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F3 TCGA-V4-A9F4 
       27.52        19.69        31.07        30.84        28.70        20.84 
TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 
        6.67        41.29        19.63        47.97        45.27        46.82 
TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KH 
       38.73        44.52         3.75        26.99         1.32        38.07 
TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO 
       36.59        37.81         2.10         0.13         2.24        26.14 
TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R 
        0.20         1.45        19.92         2.83        20.91         0.20 
TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 
        1.61        85.48        55.99        43.20        41.36        36.56 
TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E 
        7.92         0.39        22.55        18.90         2.70        27.55 
TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A985 
       61.22        16.27        26.24        38.93 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.62              0.13 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            82.16             85.48 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           28.585            25.335 
[1] "0.6 - 82.2 (28.6)" "0.1 - 85.5 (25.3)"
[1] "hr=" "4.4"
D29V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  XP GAIN MUTATED           2         3          4          1          0
  XP GAIN WILD-TYPE        10        24         21          9          1
                   vv
clus                STAGE IV
  XP GAIN MUTATED          0
  XP GAIN WILD-TYPE        4
D29V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE IIA                2                10
  STAGE IIB                3                24
  STAGE IIIA               4                21
  STAGE IIIB               1                 9
  STAGE IIIC               0                 1
  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                T2 T3 T4
  XP GAIN MUTATED    2  5  3
  XP GAIN WILD-TYPE 12 27 31
D29V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T2               2                12
  T3               5                27
  T4               3                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V5, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    7  0
  XP GAIN WILD-TYPE 44  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      7    0
  XP GAIN WILD-TYPE   44    4
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0               7                44
  1               0                 4
[1] 2 2
[1] FALSE
D29V6, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    7  3
  XP GAIN WILD-TYPE 28 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      7    3
  XP GAIN WILD-TYPE   28   42
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               7                28
  MALE                 3                42
[1] 2 2
[1] FALSE
D29V7, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   10  0
  XP GAIN WILD-TYPE 66  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     10    0
  XP GAIN WILD-TYPE   66    3
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               10                66
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(30) Variable = XQ GAIN MUTATION ANALYSIS
D30V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    8  1
  XQ GAIN WILD-TYPE 49 22
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9                71 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                22 
$`XQ GAIN MUTATED`
TCGA-V4-A9E5 TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9F2 TCGA-VD-A8KG 
       82.16        33.80        31.76        25.41        24.13         0.62 
TCGA-VD-A8KL TCGA-VD-AA8S TCGA-YZ-A984 
       20.98        14.04        45.90 

$`XQ GAIN WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       15.09        13.64        26.56        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       35.44        13.08        38.30        22.03        12.79        24.53 
TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW 
       14.96        49.68        44.78        23.31        41.72        39.81 
TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F3 
       24.00        27.52        19.69        31.07        30.84        28.70 
TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 
       20.84         6.67        41.29        19.63        47.97        45.27 
TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF 
       46.82        38.73        44.52         3.75        26.99         1.32 
TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KM TCGA-VD-A8KN 
       38.07        36.59        37.81         2.10         0.13         2.24 
TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q 
       26.14         0.20         1.45        19.92         2.83        20.91 
TCGA-VD-AA8R TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 
        0.20         1.61        85.48        55.99        43.20        41.36 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A 
       36.56         7.92         0.39        22.55        18.90         2.70 
TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A985 
       27.55        61.22        16.27        26.24        38.93 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.62              0.13 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            82.16             85.48 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            25.41             26.14 
[1] "0.6 - 82.2 (25.4)" "0.1 - 85.5 (26.1)"
[1] "hr=" "3.4"
D30V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  XQ GAIN MUTATED           2         3          3          1          0
  XQ GAIN WILD-TYPE        10        24         22          9          1
                   vv
clus                STAGE IV
  XQ GAIN MUTATED          0
  XQ GAIN WILD-TYPE        4
D30V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE IIA                2                10
  STAGE IIB                3                24
  STAGE IIIA               3                22
  STAGE IIIB               1                 9
  STAGE IIIC               0                 1
  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                T2 T3 T4
  XQ GAIN MUTATED    2  4  3
  XQ GAIN WILD-TYPE 12 28 31
D30V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T2               2                12
  T3               4                28
  T4               3                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    6  0
  XQ GAIN WILD-TYPE 45  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6    0
  XQ GAIN WILD-TYPE   45    4
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               6                45
  1               0                 4
[1] 2 2
[1] FALSE
D30V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    6  3
  XQ GAIN WILD-TYPE 29 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6    3
  XQ GAIN WILD-TYPE   29   42
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               6                29
  MALE                 3                42
[1] 2 2
[1] FALSE
D30V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    9  0
  XQ GAIN WILD-TYPE 67  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      9    0
  XQ GAIN WILD-TYPE   67    3
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                9                67
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(31) Variable = 1P LOSS MUTATION ANALYSIS
D31V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   13  6
  1P LOSS WILD-TYPE 44 17
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               19                61 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                17 
$`1P LOSS MUTATED`
TCGA-WC-A881 TCGA-WC-AA9A TCGA-V4-A9E7 TCGA-V4-A9EE TCGA-V4-A9EO TCGA-V4-A9EQ 
       35.01        14.89        13.64        13.08        25.41        14.96 
TCGA-V4-A9ES TCGA-V4-A9EW TCGA-V4-A9EZ TCGA-V4-A9F5 TCGA-V4-A9F8 TCGA-VD-A8KA 
       49.68        39.81        19.69         6.67        19.63        38.73 
TCGA-VD-AA8O TCGA-VD-AA8P TCGA-WC-A87W TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-AA9E 
       19.92         2.83        55.99        36.56         7.92        27.55 
TCGA-YZ-A982 
       16.27 

$`1P LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E5 
       32.28        51.98         4.90        15.45        15.09        82.16 
TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EF 
       26.56        40.96        44.32        24.43        35.44        38.30 
TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9ET 
       22.03        12.79        24.53        33.80        31.76        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9F0 TCGA-V4-A9F1 
       23.31        41.72        24.00        27.52        31.07        30.84 
TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-VD-A8K7 TCGA-VD-A8K8 
       24.13        28.70        20.84        41.29        47.97        45.27 
TCGA-VD-A8K9 TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG 
       46.82        44.52         3.75        26.99         1.32         0.62 
TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM 
       38.07        36.59        37.81         2.10        20.98         0.13 
TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8Q TCGA-VD-AA8R 
        2.24        26.14         0.20         1.45        20.91         0.20 
TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A884 
       14.04         1.61        85.48        43.20        41.36         0.39 
TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A984 
       22.55        18.90         2.70        61.22        26.24        45.90 
TCGA-YZ-A985 
       38.93 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             2.83              0.13 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            55.99             85.48 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            19.69             26.56 
[1] "2.8 - 56.0 (19.7)" "0.1 - 85.5 (26.6)"
[1] "hr=" "1.3"
D31V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  1P LOSS MUTATED           3         7          7          1          0
  1P LOSS WILD-TYPE         9        20         18          9          1
                   vv
clus                STAGE IV
  1P LOSS MUTATED          1
  1P LOSS WILD-TYPE        3
D31V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE IIA                3                 9
  STAGE IIB                7                20
  STAGE IIIA               7                18
  STAGE IIIB               1                 9
  STAGE IIIC               0                 1
  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                T2 T3 T4
  1P LOSS MUTATED    4  8  7
  1P LOSS WILD-TYPE 10 24 27
D31V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T2               4                10
  T3               8                24
  T4               7                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   14  1
  1P LOSS WILD-TYPE 37  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     14    1
  1P LOSS WILD-TYPE   37    3
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              14                37
  1               1                 3
[1] 2 2
[1] FALSE
D31V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   10  9
  1P LOSS WILD-TYPE 25 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     10    9
  1P LOSS WILD-TYPE   25   36
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              10                25
  MALE                 9                36
[1] 2 2
[1] FALSE
D31V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   18  1
  1P LOSS WILD-TYPE 58  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     18    1
  1P LOSS WILD-TYPE   58    2
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               18                58
  YES               1                 2
[1] 2 2
[1] FALSE

Clustering(32) Variable = 1Q LOSS MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    2  1
  1Q LOSS WILD-TYPE 55 22
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                77 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                22 
$`1Q LOSS MUTATED`
TCGA-V4-A9EE TCGA-V4-A9ES TCGA-VD-AA8P 
       13.08        49.68         2.83 

$`1Q LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       24.43        35.44        38.30        22.03        12.79        24.53 
TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ET TCGA-V4-A9EU 
       33.80        31.76        25.41        14.96        44.78        23.31 
TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 
       41.72        39.81        24.00        27.52        19.69        31.07 
TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 
       30.84        24.13        28.70        20.84         6.67        41.29 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       19.63        47.97        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI 
        3.75        26.99         1.32         0.62        38.07        36.59 
TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO 
       37.81         2.10        20.98         0.13         2.24        26.14 
TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S 
        0.20         1.45        19.92        20.91         0.20        14.04 
TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 
        1.61        85.48        55.99        43.20        41.36        36.56 
TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E 
        7.92         0.39        22.55        18.90         2.70        27.55 
TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       61.22        16.27        26.24        45.90        38.93 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             2.83              0.13 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            49.68             85.48 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            13.08             26.14 
[1] "2.8 - 49.7 (13.1)" "0.1 - 85.5 (26.1)"
[1] "hr=" "1.2"
D32V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  1Q LOSS MUTATED           0         2          1          0          0
  1Q LOSS WILD-TYPE        12        25         24         10          1
                   vv
clus                STAGE IV
  1Q LOSS MUTATED          0
  1Q LOSS WILD-TYPE        4
D32V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE IIA                0                12
  STAGE IIB                2                25
  STAGE IIIA               1                24
  STAGE IIIB               0                10
  STAGE IIIC               0                 1
  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                T2 T3 T4
  1Q LOSS MUTATED    0  3  0
  1Q LOSS WILD-TYPE 14 29 34
D32V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T2               0                14
  T3               3                29
  T4               0                34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V5, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3  0
  1Q LOSS WILD-TYPE 48  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    0
  1Q LOSS WILD-TYPE   48    4
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               3                48
  1               0                 4
[1] 2 2
[1] FALSE
D32V6, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    2  1
  1Q LOSS WILD-TYPE 33 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    1
  1Q LOSS WILD-TYPE   33   44
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               2                33
  MALE                 1                44
[1] 2 2
[1] FALSE
D32V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3  0
  1Q LOSS WILD-TYPE 73  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    0
  1Q LOSS WILD-TYPE   73    3
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                3                73
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(33) Variable = 3P LOSS MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   22 21
  3P LOSS WILD-TYPE 35  2
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               43                37 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               21                 2 
$`3P LOSS MUTATED`
TCGA-V4-A9EL TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E7 TCGA-V4-A9E8 
       32.28        14.89         4.90        15.45        13.64        26.56 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EO TCGA-V4-A9EQ 
       35.44        13.08        38.30        12.79        25.41        14.96 
TCGA-V4-A9ES TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9F0 
       49.68        23.31        41.72        39.81        24.00        31.07 
TCGA-V4-A9F1 TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F8 TCGA-VD-A8K8 TCGA-VD-A8KA 
       30.84        28.70         6.67        19.63        45.27        38.73 
TCGA-VD-A8KD TCGA-VD-A8KF TCGA-VD-A8KI TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM 
        3.75         1.32        36.59         2.10        20.98         0.13 
TCGA-VD-A8KN TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8T TCGA-WC-A87Y 
        2.24         1.45        19.92         2.83         1.61        43.20 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A888 TCGA-WC-A88A TCGA-YZ-A980 TCGA-YZ-A984 
       36.56         7.92        18.90         2.70        61.22        45.90 
TCGA-YZ-A985 
       38.93 

$`3P LOSS WILD-TYPE`
TCGA-WC-A87U TCGA-WC-A881 TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E9 TCGA-V4-A9EA 
       51.98        35.01        15.09        82.16        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9ET 
       24.43        22.03        24.53        33.80        31.76        44.78 
TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-VD-A8K7 
       27.52        19.69        24.13        20.84        41.29        47.97 
TCGA-VD-A8K9 TCGA-VD-A8KB TCGA-VD-A8KE TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KJ 
       46.82        44.52        26.99         0.62        38.07        37.81 
TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-WC-A87T 
       26.14         0.20        20.91         0.20        14.04        85.48 
TCGA-WC-A87W TCGA-WC-A880 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-AA9E TCGA-YZ-A982 
       55.99        41.36         0.39        22.55        27.55        16.27 
TCGA-YZ-A983 
       26.24 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.13              0.20 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            61.22             85.48 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            20.98             27.52 
[1] "0.1 - 61.2 (21.0)" "0.2 - 85.5 (27.5)"
[1] "hr=" "14" 
D33V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  3P LOSS MUTATED           3        14         16          4          1
  3P LOSS WILD-TYPE         9        13          9          6          0
                   vv
clus                STAGE IV
  3P LOSS MUTATED          4
  3P LOSS WILD-TYPE        0
D33V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE IIA                3                 9
  STAGE IIB               14                13
  STAGE IIIA              16                 9
  STAGE IIIB               4                 6
  STAGE IIIC               1                 0
  STAGE IV                 4                 0
[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                T2 T3 T4
  3P LOSS MUTATED    5 17 21
  3P LOSS WILD-TYPE  9 15 13
D33V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T2               5                 9
  T3              17                15
  T4              21                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"
D33V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   26  4
  3P LOSS WILD-TYPE 25  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     26    4
  3P LOSS WILD-TYPE   25    0
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              26                25
  1               4                 0
[1] 2 2
[1] FALSE
D33V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   19 24
  3P LOSS WILD-TYPE 16 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     19   24
  3P LOSS WILD-TYPE   16   21
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              19                16
  MALE                24                21
[1] 2 2
[1] FALSE
D33V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   40  2
  3P LOSS WILD-TYPE 36  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     40    2
  3P LOSS WILD-TYPE   36    1
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               40                36
  YES               2                 1
[1] 2 2
[1] FALSE

Clustering(34) Variable = 3Q LOSS MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED   22 21
  3Q LOSS WILD-TYPE 35  2
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               43                37 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               21                 2 
$`3Q LOSS MUTATED`
TCGA-V4-A9EL TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E7 TCGA-V4-A9E8 
       32.28        14.89         4.90        15.45        13.64        26.56 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EO TCGA-V4-A9EQ 
       35.44        13.08        38.30        12.79        25.41        14.96 
TCGA-V4-A9ES TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9F0 
       49.68        23.31        41.72        39.81        24.00        31.07 
TCGA-V4-A9F1 TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F8 TCGA-VD-A8K8 TCGA-VD-A8KA 
       30.84        28.70         6.67        19.63        45.27        38.73 
TCGA-VD-A8KD TCGA-VD-A8KF TCGA-VD-A8KI TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM 
        3.75         1.32        36.59         2.10        20.98         0.13 
TCGA-VD-A8KN TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8T TCGA-WC-A87Y 
        2.24         1.45        19.92         2.83         1.61        43.20 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A888 TCGA-WC-A88A TCGA-YZ-A980 TCGA-YZ-A984 
       36.56         7.92        18.90         2.70        61.22        45.90 
TCGA-YZ-A985 
       38.93 

$`3Q LOSS WILD-TYPE`
TCGA-WC-A87U TCGA-WC-A881 TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E9 TCGA-V4-A9EA 
       51.98        35.01        15.09        82.16        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9ET 
       24.43        22.03        24.53        33.80        31.76        44.78 
TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-VD-A8K7 
       27.52        19.69        24.13        20.84        41.29        47.97 
TCGA-VD-A8K9 TCGA-VD-A8KB TCGA-VD-A8KE TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KJ 
       46.82        44.52        26.99         0.62        38.07        37.81 
TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-WC-A87T 
       26.14         0.20        20.91         0.20        14.04        85.48 
TCGA-WC-A87W TCGA-WC-A880 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-AA9E TCGA-YZ-A982 
       55.99        41.36         0.39        22.55        27.55        16.27 
TCGA-YZ-A983 
       26.24 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.13              0.20 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            61.22             85.48 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            20.98             27.52 
[1] "0.1 - 61.2 (21.0)" "0.2 - 85.5 (27.5)"
[1] "hr=" "14" 
D34V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  3Q LOSS MUTATED           3        14         16          4          1
  3Q LOSS WILD-TYPE         9        13          9          6          0
                   vv
clus                STAGE IV
  3Q LOSS MUTATED          4
  3Q LOSS WILD-TYPE        0
D34V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE IIA                3                 9
  STAGE IIB               14                13
  STAGE IIIA              16                 9
  STAGE IIIB               4                 6
  STAGE IIIC               1                 0
  STAGE IV                 4                 0
[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                T2 T3 T4
  3Q LOSS MUTATED    5 17 21
  3Q LOSS WILD-TYPE  9 15 13
D34V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T2               5                 9
  T3              17                15
  T4              21                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"
D34V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   26  4
  3Q LOSS WILD-TYPE 25  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     26    4
  3Q LOSS WILD-TYPE   25    0
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              26                25
  1               4                 0
[1] 2 2
[1] FALSE
D34V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   19 24
  3Q LOSS WILD-TYPE 16 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     19   24
  3Q LOSS WILD-TYPE   16   21
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              19                16
  MALE                24                21
[1] 2 2
[1] FALSE
D34V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   40  2
  3Q LOSS WILD-TYPE 36  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     40    2
  3Q LOSS WILD-TYPE   36    1
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               40                36
  YES               2                 1
[1] 2 2
[1] FALSE

Clustering(35) Variable = 4Q LOSS MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    2  1
  4Q LOSS WILD-TYPE 55 22
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                77 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                22 
$`4Q LOSS MUTATED`
TCGA-V4-A9F1 TCGA-VD-AA8O TCGA-WC-AA9E 
       30.84        19.92        27.55 

$`4Q LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES 
       24.53        33.80        31.76        25.41        14.96        49.68 
TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY 
       44.78        23.31        41.72        39.81        24.00        27.52 
TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 
       19.69        31.07        24.13        28.70        20.84         6.67 
TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA 
       41.29        19.63        47.97        45.27        46.82        38.73 
TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH 
       44.52         3.75        26.99         1.32         0.62        38.07 
TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN 
       36.59        37.81         2.10        20.98         0.13         2.24 
TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R 
       26.14         0.20         1.45         2.83        20.91         0.20 
TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 
       14.04         1.61        85.48        55.99        43.20        41.36 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A 
       36.56         7.92         0.39        22.55        18.90         2.70 
TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       61.22        16.27        26.24        45.90        38.93 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            19.92              0.13 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            30.84             85.48 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            27.55             25.41 
[1] "19.9 - 30.8 (27.6)" "0.1 - 85.5 (25.4)" 
[1] "hr=" "1.4"
D35V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  4Q LOSS MUTATED           1         2          0          0          0
  4Q LOSS WILD-TYPE        11        25         25         10          1
                   vv
clus                STAGE IV
  4Q LOSS MUTATED          0
  4Q LOSS WILD-TYPE        4
D35V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE IIA                1                11
  STAGE IIB                2                25
  STAGE IIIA               0                25
  STAGE IIIB               0                10
  STAGE IIIC               0                 1
  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                T2 T3 T4
  4Q LOSS MUTATED    1  2  0
  4Q LOSS WILD-TYPE 13 30 34
D35V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T2               1                13
  T3               2                30
  T4               0                34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    2  0
  4Q LOSS WILD-TYPE 49  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2    0
  4Q LOSS WILD-TYPE   49    4
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0               2                49
  1               0                 4
[1] 2 2
[1] FALSE
D35V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  2
  4Q LOSS WILD-TYPE 34 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    2
  4Q LOSS WILD-TYPE   34   43
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               1                34
  MALE                 2                43
[1] 2 2
[1] FALSE
D35V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    2  1
  4Q LOSS WILD-TYPE 74  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2    1
  4Q LOSS WILD-TYPE   74    2
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                2                74
  YES               1                 2
[1] 2 2
[1] FALSE

Clustering(36) Variable = 5Q LOSS MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    3  0
  5Q LOSS WILD-TYPE 54 23
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                77 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                0                23 
$`5Q LOSS MUTATED`
TCGA-VD-AA8P TCGA-WC-A87W TCGA-YZ-A982 
        2.83        55.99        16.27 

$`5Q LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES 
       24.53        33.80        31.76        25.41        14.96        49.68 
TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY 
       44.78        23.31        41.72        39.81        24.00        27.52 
TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 
       19.69        31.07        30.84        24.13        28.70        20.84 
TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 
        6.67        41.29        19.63        47.97        45.27        46.82 
TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG 
       38.73        44.52         3.75        26.99         1.32         0.62 
TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM 
       38.07        36.59        37.81         2.10        20.98         0.13 
TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8Q 
        2.24        26.14         0.20         1.45        19.92        20.91 
TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87Y TCGA-WC-A880 
        0.20        14.04         1.61        85.48        43.20        41.36 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A 
       36.56         7.92         0.39        22.55        18.90         2.70 
TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       27.55        61.22        26.24        45.90        38.93 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             2.83              0.13 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            55.99             85.48 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            16.27             26.14 
[1] "2.8 - 56.0 (16.3)" "0.1 - 85.5 (26.1)"
[1] "hr="     "2.8e+07"
D36V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  5Q LOSS MUTATED           1         1          0          1          0
  5Q LOSS WILD-TYPE        11        26         25          9          1
                   vv
clus                STAGE IV
  5Q LOSS MUTATED          0
  5Q LOSS WILD-TYPE        4
D36V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE IIA                1                11
  STAGE IIB                1                26
  STAGE IIIA               0                25
  STAGE IIIB               1                 9
  STAGE IIIC               0                 1
  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                T2 T3 T4
  5Q LOSS MUTATED    1  1  1
  5Q LOSS WILD-TYPE 13 31 33
D36V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T2               1                13
  T3               1                31
  T4               1                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V5, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    2  0
  5Q LOSS WILD-TYPE 49  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2    0
  5Q LOSS WILD-TYPE   49    4
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               2                49
  1               0                 4
[1] 2 2
[1] FALSE
D36V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    3  0
  5Q LOSS WILD-TYPE 32 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3    0
  5Q LOSS WILD-TYPE   32   45
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               3                32
  MALE                 0                45
[1] 2 2
[1] FALSE
D36V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    3  0
  5Q LOSS WILD-TYPE 73  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3    0
  5Q LOSS WILD-TYPE   73    3
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                3                73
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(37) Variable = 6Q LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    9  8
  6Q LOSS WILD-TYPE 48 15
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               17                63 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                8                15 
$`6Q LOSS MUTATED`
TCGA-V4-A9EL TCGA-WC-A881 TCGA-V3-A9ZX TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 
       32.28        35.01        15.45        13.64        26.56        40.96 
TCGA-V4-A9EI TCGA-V4-A9EU TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EZ TCGA-V4-A9F0 
       12.79        23.31        39.81        24.00        19.69        31.07 
TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-VD-A8KI TCGA-VD-AA8N TCGA-WC-A88A 
       28.70         6.67        36.59         1.45         2.70 

$`6Q LOSS WILD-TYPE`
TCGA-WC-A87U TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9EA 
       51.98        14.89         4.90        15.09        82.16        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EJ 
       24.43        35.44        13.08        38.30        22.03        24.53 
TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET 
       33.80        31.76        25.41        14.96        49.68        44.78 
TCGA-V4-A9EV TCGA-V4-A9EY TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-V4-A9F7 
       41.72        27.52        30.84        24.13        20.84        41.29 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       19.63        47.97        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KJ 
        3.75        26.99         1.32         0.62        38.07        37.81 
TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M 
        2.10        20.98         0.13         2.24        26.14         0.20 
TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T 
       19.92         2.83        20.91         0.20        14.04         1.61 
TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 
       85.48        55.99        43.20        41.36        36.56         7.92 
TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 
        0.39        22.55        18.90        27.55        61.22        16.27 
TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       26.24        45.90        38.93 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             1.45              0.13 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            40.96             85.48 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            24.00             26.14 
[1] "1.4 - 41.0 (24.0)" "0.1 - 85.5 (26.1)"
[1] "hr=" "3.1"
D37V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  6Q LOSS MUTATED           0         5          7          2          1
  6Q LOSS WILD-TYPE        12        22         18          8          0
                   vv
clus                STAGE IV
  6Q LOSS MUTATED          2
  6Q LOSS WILD-TYPE        2
D37V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE IIA                0                12
  STAGE IIB                5                22
  STAGE IIIA               7                18
  STAGE IIIB               2                 8
  STAGE IIIC               1                 0
  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                T2 T3 T4
  6Q LOSS MUTATED    1  4 12
  6Q LOSS WILD-TYPE 13 28 22
D37V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T2               1                13
  T3               4                28
  T4              12                22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   13  2
  6Q LOSS WILD-TYPE 38  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     13    2
  6Q LOSS WILD-TYPE   38    2
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              13                38
  1               2                 2
[1] 2 2
[1] FALSE
D37V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    6 11
  6Q LOSS WILD-TYPE 29 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      6   11
  6Q LOSS WILD-TYPE   29   34
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               6                29
  MALE                11                34
[1] 2 2
[1] FALSE
D37V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   16  1
  6Q LOSS WILD-TYPE 60  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     16    1
  6Q LOSS WILD-TYPE   60    2
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               16                60
  YES               1                 2
[1] 2 2
[1] FALSE

Clustering(38) Variable = 8P LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    3  1
  8P LOSS WILD-TYPE 54 22
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                76 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                22 
$`8P LOSS MUTATED`
TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-VD-A8KF TCGA-VD-A8KJ 
       20.84         6.67         1.32        37.81 

$`8P LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES 
       24.53        33.80        31.76        25.41        14.96        49.68 
TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY 
       44.78        23.31        41.72        39.81        24.00        27.52 
TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F7 
       19.69        31.07        30.84        24.13        28.70        41.29 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       19.63        47.97        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KK 
        3.75        26.99         0.62        38.07        36.59         2.10 
TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N 
       20.98         0.13         2.24        26.14         0.20         1.45 
TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T 
       19.92         2.83        20.91         0.20        14.04         1.61 
TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 
       85.48        55.99        43.20        41.36        36.56         7.92 
TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 
        0.39        22.55        18.90         2.70        27.55        61.22 
TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       16.27        26.24        45.90        38.93 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             1.32              0.13 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            37.81             85.48 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           13.755            26.190 
[1] "1.3 - 37.8 (13.8)" "0.1 - 85.5 (26.2)"
[1] "hr=" "1.6"
D38V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  8P LOSS MUTATED           0         1          1          1          0
  8P LOSS WILD-TYPE        12        26         24          9          1
                   vv
clus                STAGE IV
  8P LOSS MUTATED          1
  8P LOSS WILD-TYPE        3
D38V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE IIA                0                12
  STAGE IIB                1                26
  STAGE IIIA               1                24
  STAGE IIIB               1                 9
  STAGE IIIC               0                 1
  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                T2 T3 T4
  8P LOSS MUTATED    0  1  3
  8P LOSS WILD-TYPE 14 31 31
D38V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T2               0                14
  T3               1                31
  T4               3                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V5, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    1  1
  8P LOSS WILD-TYPE 50  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    1
  8P LOSS WILD-TYPE   50    3
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               1                50
  1               1                 3
[1] 2 2
[1] FALSE
D38V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    1  3
  8P LOSS WILD-TYPE 34 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    3
  8P LOSS WILD-TYPE   34   42
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               1                34
  MALE                 3                42
[1] 2 2
[1] FALSE
D38V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    4  0
  8P LOSS WILD-TYPE 72  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    0
  8P LOSS WILD-TYPE   72    3
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                4                72
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(39) Variable = 8Q LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    3  0
  8Q LOSS WILD-TYPE 54 23
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                77 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                23 
$`8Q LOSS MUTATED`
TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-VD-A8KJ 
       20.84         6.67        37.81 

$`8Q LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES 
       24.53        33.80        31.76        25.41        14.96        49.68 
TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY 
       44.78        23.31        41.72        39.81        24.00        27.52 
TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F7 
       19.69        31.07        30.84        24.13        28.70        41.29 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       19.63        47.97        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI 
        3.75        26.99         1.32         0.62        38.07        36.59 
TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M 
        2.10        20.98         0.13         2.24        26.14         0.20 
TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S 
        1.45        19.92         2.83        20.91         0.20        14.04 
TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 
        1.61        85.48        55.99        43.20        41.36        36.56 
TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E 
        7.92         0.39        22.55        18.90         2.70        27.55 
TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       61.22        16.27        26.24        45.90        38.93 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             6.67              0.13 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            37.81             85.48 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            20.84             26.14 
[1] "6.7 - 37.8 (20.8)" "0.1 - 85.5 (26.1)"
[1] "hr="     "2.6e+07"
D39V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  8Q LOSS MUTATED           0         1          1          0          0
  8Q LOSS WILD-TYPE        12        26         24         10          1
                   vv
clus                STAGE IV
  8Q LOSS MUTATED          1
  8Q LOSS WILD-TYPE        3
D39V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE IIA                0                12
  STAGE IIB                1                26
  STAGE IIIA               1                24
  STAGE IIIB               0                10
  STAGE IIIC               0                 1
  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                T2 T3 T4
  8Q LOSS MUTATED    0  1  2
  8Q LOSS WILD-TYPE 14 31 32
D39V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T2               0                14
  T3               1                31
  T4               2                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V5, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    1  1
  8Q LOSS WILD-TYPE 50  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    1
  8Q LOSS WILD-TYPE   50    3
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               1                50
  1               1                 3
[1] 2 2
[1] FALSE
D39V6, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    1  2
  8Q LOSS WILD-TYPE 34 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    2
  8Q LOSS WILD-TYPE   34   43
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               1                34
  MALE                 2                43
[1] 2 2
[1] FALSE
D39V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    3  0
  8Q LOSS WILD-TYPE 73  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    0
  8Q LOSS WILD-TYPE   73    3
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                3                73
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(40) Variable = 9P LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED    4  4
  9P LOSS WILD-TYPE 53 19
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                8                72 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4                19 
$`9P LOSS MUTATED`
TCGA-V4-A9EE TCGA-V4-A9EI TCGA-V4-A9EX TCGA-V4-A9EZ TCGA-VD-A8KH TCGA-VD-A8KL 
       13.08        12.79        24.00        19.69        38.07        20.98 
TCGA-VD-AA8O TCGA-VD-AA8T 
       19.92         1.61 

$`9P LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EK 
       24.43        35.44        38.30        22.03        24.53        33.80 
TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU 
       31.76        25.41        14.96        49.68        44.78        23.31 
TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EY TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 
       41.72        39.81        27.52        31.07        30.84        24.13 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 
       28.70        20.84         6.67        41.29        19.63        47.97 
TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE 
       45.27        46.82        38.73        44.52         3.75        26.99 
TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KM 
        1.32         0.62        36.59        37.81         2.10         0.13 
TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8P TCGA-VD-AA8Q 
        2.24        26.14         0.20         1.45         2.83        20.91 
TCGA-VD-AA8R TCGA-VD-AA8S TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 
        0.20        14.04        85.48        55.99        43.20        41.36 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A 
       36.56         7.92         0.39        22.55        18.90         2.70 
TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       27.55        61.22        16.27        26.24        45.90        38.93 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             1.61              0.13 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            38.07             85.48 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           19.805            26.775 
[1] "1.6 - 38.1 (19.8)" "0.1 - 85.5 (26.8)"
[1] "hr=" "3.5"
D40V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  9P LOSS MUTATED           1         4          1          2          0
  9P LOSS WILD-TYPE        11        23         24          8          1
                   vv
clus                STAGE IV
  9P LOSS MUTATED          0
  9P LOSS WILD-TYPE        4
D40V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE IIA                1                11
  STAGE IIB                4                23
  STAGE IIIA               1                24
  STAGE IIIB               2                 8
  STAGE IIIC               0                 1
  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                T2 T3 T4
  9P LOSS MUTATED    1  4  3
  9P LOSS WILD-TYPE 13 28 31
D40V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T2               1                13
  T3               4                28
  T4               3                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    6  0
  9P LOSS WILD-TYPE 45  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6    0
  9P LOSS WILD-TYPE   45    4
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0               6                45
  1               0                 4
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    4  4
  9P LOSS WILD-TYPE 31 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4    4
  9P LOSS WILD-TYPE   31   41
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               4                31
  MALE                 4                41
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    7  1
  9P LOSS WILD-TYPE 69  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      7    1
  9P LOSS WILD-TYPE   69    2
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                7                69
  YES               1                 2
[1] 2 2
[1] FALSE

Clustering(41) Variable = 9Q LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    3  4
  9Q LOSS WILD-TYPE 54 19
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                7                73 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                4                19 
$`9Q LOSS MUTATED`
TCGA-V4-A9EE TCGA-V4-A9EI TCGA-V4-A9EX TCGA-V4-A9EZ TCGA-VD-A8KH TCGA-VD-A8KL 
       13.08        12.79        24.00        19.69        38.07        20.98 
TCGA-VD-AA8O 
       19.92 

$`9Q LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EK 
       24.43        35.44        38.30        22.03        24.53        33.80 
TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU 
       31.76        25.41        14.96        49.68        44.78        23.31 
TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EY TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 
       41.72        39.81        27.52        31.07        30.84        24.13 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 
       28.70        20.84         6.67        41.29        19.63        47.97 
TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE 
       45.27        46.82        38.73        44.52         3.75        26.99 
TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KM 
        1.32         0.62        36.59        37.81         2.10         0.13 
TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8P TCGA-VD-AA8Q 
        2.24        26.14         0.20         1.45         2.83        20.91 
TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y 
        0.20        14.04         1.61        85.48        55.99        43.20 
TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 
       41.36        36.56         7.92         0.39        22.55        18.90 
TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 
        2.70        27.55        61.22        16.27        26.24        45.90 
TCGA-YZ-A985 
       38.93 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            12.79              0.13 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            38.07             85.48 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            19.92             26.56 
[1] "12.8 - 38.1 (19.9)" "0.1 - 85.5 (26.6)" 
[1] "hr=" "3.6"
D41V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  9Q LOSS MUTATED           0         4          1          2          0
  9Q LOSS WILD-TYPE        12        23         24          8          1
                   vv
clus                STAGE IV
  9Q LOSS MUTATED          0
  9Q LOSS WILD-TYPE        4
D41V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE IIA                0                12
  STAGE IIB                4                23
  STAGE IIIA               1                24
  STAGE IIIB               2                 8
  STAGE IIIC               0                 1
  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                T2 T3 T4
  9Q LOSS MUTATED    0  4  3
  9Q LOSS WILD-TYPE 14 28 31
D41V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T2               0                14
  T3               4                28
  T4               3                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V5, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    5  0
  9Q LOSS WILD-TYPE 46  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5    0
  9Q LOSS WILD-TYPE   46    4
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0               5                46
  1               0                 4
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    3  4
  9Q LOSS WILD-TYPE 32 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3    4
  9Q LOSS WILD-TYPE   32   41
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               3                32
  MALE                 4                41
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    6  1
  9Q LOSS WILD-TYPE 70  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      6    1
  9Q LOSS WILD-TYPE   70    2
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                6                70
  YES               1                 2
[1] 2 2
[1] FALSE

Clustering(42) Variable = 12P LOSS MUTATION ANALYSIS
D42V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    2  1
  12P LOSS WILD-TYPE 55 22
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 77 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 22 
$`12P LOSS MUTATED`
TCGA-V4-A9EC TCGA-V4-A9EK TCGA-VD-AA8O 
       24.43        33.80        19.92 

$`12P LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       35.44        13.08        38.30        22.03        12.79        24.53 
TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU 
       31.76        25.41        14.96        49.68        44.78        23.31 
TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 
       41.72        39.81        24.00        27.52        19.69        31.07 
TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 
       30.84        24.13        28.70        20.84         6.67        41.29 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       19.63        47.97        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI 
        3.75        26.99         1.32         0.62        38.07        36.59 
TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO 
       37.81         2.10        20.98         0.13         2.24        26.14 
TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S 
        0.20         1.45         2.83        20.91         0.20        14.04 
TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 
        1.61        85.48        55.99        43.20        41.36        36.56 
TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E 
        7.92         0.39        22.55        18.90         2.70        27.55 
TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       61.22        16.27        26.24        45.90        38.93 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             19.92               0.13 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             33.80              85.48 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             24.43              26.14 
[1] "19.9 - 33.8 (24.4)" "0.1 - 85.5 (26.1)" 
[1] "hr=" "1.4"
D42V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  12P LOSS MUTATED           0         3          0          0          0
  12P LOSS WILD-TYPE        12        24         25         10          1
                    vv
clus                 STAGE IV
  12P LOSS MUTATED          0
  12P LOSS WILD-TYPE        4
D42V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE IIA                 0                 12
  STAGE IIB                 3                 24
  STAGE IIIA                0                 25
  STAGE IIIB                0                 10
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  12P LOSS MUTATED    0  3  0
  12P LOSS WILD-TYPE 14 29 34
D42V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T2                0                 14
  T3                3                 29
  T4                0                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V5, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    3  0
  12P LOSS WILD-TYPE 48  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    0
  12P LOSS WILD-TYPE   48    4
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                3                 48
  1                0                  4
[1] 2 2
[1] FALSE
D42V6, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    2  1
  12P LOSS WILD-TYPE 33 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    1
  12P LOSS WILD-TYPE   33   44
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                 33
  MALE                  1                 44
[1] 2 2
[1] FALSE
D42V7, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    3  0
  12P LOSS WILD-TYPE 73  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    0
  12P LOSS WILD-TYPE   73    3
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 3                 73
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(43) Variable = 13Q LOSS MUTATION ANALYSIS
D43V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    3  0
  13Q LOSS WILD-TYPE 54 23
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 77 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                 23 
$`13Q LOSS MUTATED`
TCGA-V4-A9ES TCGA-V4-A9EZ TCGA-V4-A9F1 
       49.68        19.69        30.84 

$`13Q LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ET 
       24.53        33.80        31.76        25.41        14.96        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9F0 
       23.31        41.72        39.81        24.00        27.52        31.07 
TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 
       24.13        28.70        20.84         6.67        41.29        19.63 
TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD 
       47.97        45.27        46.82        38.73        44.52         3.75 
TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ 
       26.99         1.32         0.62        38.07        36.59        37.81 
TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M 
        2.10        20.98         0.13         2.24        26.14         0.20 
TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S 
        1.45        19.92         2.83        20.91         0.20        14.04 
TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 
        1.61        85.48        55.99        43.20        41.36        36.56 
TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E 
        7.92         0.39        22.55        18.90         2.70        27.55 
TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       61.22        16.27        26.24        45.90        38.93 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             19.69               0.13 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             49.68              85.48 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             30.84              25.41 
[1] "19.7 - 49.7 (30.8)" "0.1 - 85.5 (25.4)" 
[1] "hr="     "2.7e+07"
D43V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  13Q LOSS MUTATED           0         2          1          0          0
  13Q LOSS WILD-TYPE        12        25         24         10          1
                    vv
clus                 STAGE IV
  13Q LOSS MUTATED          0
  13Q LOSS WILD-TYPE        4
D43V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE IIA                 0                 12
  STAGE IIB                 2                 25
  STAGE IIIA                1                 24
  STAGE IIIB                0                 10
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  13Q LOSS MUTATED    0  3  0
  13Q LOSS WILD-TYPE 14 29 34
D43V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T2                0                 14
  T3                3                 29
  T4                0                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    3  0
  13Q LOSS WILD-TYPE 48  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3    0
  13Q LOSS WILD-TYPE   48    4
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0                3                 48
  1                0                  4
[1] 2 2
[1] FALSE
D43V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    3  0
  13Q LOSS WILD-TYPE 32 45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3    0
  13Q LOSS WILD-TYPE   32   45
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                3                 32
  MALE                  0                 45
[1] 2 2
[1] FALSE
D43V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    3  0
  13Q LOSS WILD-TYPE 73  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3    0
  13Q LOSS WILD-TYPE   73    3
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 3                 73
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(44) Variable = 15Q LOSS MUTATION ANALYSIS
D44V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    3  1
  15Q LOSS WILD-TYPE 54 22
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 76 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                 22 
$`15Q LOSS MUTATED`
TCGA-V4-A9ES TCGA-V4-A9EZ TCGA-VD-A8KH TCGA-VD-AA8O 
       49.68        19.69        38.07        19.92 

$`15Q LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ET 
       24.53        33.80        31.76        25.41        14.96        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9F0 
       23.31        41.72        39.81        24.00        27.52        31.07 
TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 
       30.84        24.13        28.70        20.84         6.67        41.29 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       19.63        47.97        45.27        46.82        38.73        44.52 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KI TCGA-VD-A8KJ 
        3.75        26.99         1.32         0.62        36.59        37.81 
TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M 
        2.10        20.98         0.13         2.24        26.14         0.20 
TCGA-VD-AA8N TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T 
        1.45         2.83        20.91         0.20        14.04         1.61 
TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 
       85.48        55.99        43.20        41.36        36.56         7.92 
TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 
        0.39        22.55        18.90         2.70        27.55        61.22 
TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       16.27        26.24        45.90        38.93 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             19.69               0.13 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             49.68              85.48 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            28.995             25.775 
[1] "19.7 - 49.7 (29.0)" "0.1 - 85.5 (25.8)" 
[1] "hr=" "1.5"
D44V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  15Q LOSS MUTATED           0         2          1          1          0
  15Q LOSS WILD-TYPE        12        25         24          9          1
                    vv
clus                 STAGE IV
  15Q LOSS MUTATED          0
  15Q LOSS WILD-TYPE        4
D44V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE IIA                 0                 12
  STAGE IIB                 2                 25
  STAGE IIIA                1                 24
  STAGE IIIB                1                  9
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  15Q LOSS MUTATED    0  3  1
  15Q LOSS WILD-TYPE 14 29 33
D44V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T2                0                 14
  T3                3                 29
  T4                1                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V5, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    3  0
  15Q LOSS WILD-TYPE 48  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3    0
  15Q LOSS WILD-TYPE   48    4
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0                3                 48
  1                0                  4
[1] 2 2
[1] FALSE
D44V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    2  2
  15Q LOSS WILD-TYPE 33 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    2
  15Q LOSS WILD-TYPE   33   43
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                2                 33
  MALE                  2                 43
[1] 2 2
[1] FALSE
D44V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    4  0
  15Q LOSS WILD-TYPE 72  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4    0
  15Q LOSS WILD-TYPE   72    3
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 4                 72
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(45) Variable = 16P LOSS MUTATION ANALYSIS
D45V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    1  2
  16P LOSS WILD-TYPE 56 21
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 77 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 21 
$`16P LOSS MUTATED`
TCGA-RZ-AB0B TCGA-V4-A9E5 TCGA-V4-A9EQ 
        4.90        82.16        14.96 

$`16P LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-V3-A9ZX TCGA-V3-A9ZY 
       32.28        51.98        35.01        14.89        15.45        15.09 
TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED 
       13.64        26.56        40.96        44.32        24.43        35.44 
TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK 
       13.08        38.30        22.03        12.79        24.53        33.80 
TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV 
       31.76        25.41        49.68        44.78        23.31        41.72 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 
       39.81        24.00        27.52        19.69        31.07        30.84 
TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 
       24.13        28.70        20.84         6.67        41.29        19.63 
TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD 
       47.97        45.27        46.82        38.73        44.52         3.75 
TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ 
       26.99         1.32         0.62        38.07        36.59        37.81 
TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M 
        2.10        20.98         0.13         2.24        26.14         0.20 
TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S 
        1.45        19.92         2.83        20.91         0.20        14.04 
TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 
        1.61        85.48        55.99        43.20        41.36        36.56 
TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E 
        7.92         0.39        22.55        18.90         2.70        27.55 
TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       61.22        16.27        26.24        45.90        38.93 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              4.90               0.13 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             82.16              85.48 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             14.96              26.14 
[1] "4.9 - 82.2 (15.0)" "0.1 - 85.5 (26.1)"
[1] "hr=" "1.9"
D45V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  16P LOSS MUTATED           0         0          1          1          0
  16P LOSS WILD-TYPE        12        27         24          9          1
                    vv
clus                 STAGE IV
  16P LOSS MUTATED          1
  16P LOSS WILD-TYPE        3
D45V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE IIA                 0                 12
  STAGE IIB                 0                 27
  STAGE IIIA                1                 24
  STAGE IIIB                1                  9
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  16P LOSS MUTATED    0  0  3
  16P LOSS WILD-TYPE 14 32 31
D45V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T2                0                 14
  T3                0                 32
  T4                3                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    2  1
  16P LOSS WILD-TYPE 49  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    1
  16P LOSS WILD-TYPE   49    3
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                2                 49
  1                1                  3
[1] 2 2
[1] FALSE
D45V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    2  1
  16P LOSS WILD-TYPE 33 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    1
  16P LOSS WILD-TYPE   33   44
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                2                 33
  MALE                  1                 44
[1] 2 2
[1] FALSE
D45V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    2  0
  16P LOSS WILD-TYPE 74  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    0
  16P LOSS WILD-TYPE   74    3
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 2                 74
  YES                0                  3
[1] 2 2
[1] FALSE

Clustering(46) Variable = 16Q LOSS MUTATION ANALYSIS
D46V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   10  6
  16Q LOSS WILD-TYPE 47 17
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                16                 64 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                 17 
$`16Q LOSS MUTATED`
TCGA-V4-A9EL TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E5 
       32.28        35.01        14.89         4.90        15.45        82.16 
TCGA-V4-A9E7 TCGA-V4-A9EI TCGA-V4-A9EQ TCGA-V4-A9EU TCGA-V4-A9EZ TCGA-VD-A8KM 
       13.64        12.79        14.96        23.31        19.69         0.13 
TCGA-VD-AA8N TCGA-WC-A884 TCGA-WC-A88A TCGA-WC-AA9E 
        1.45         0.39         2.70        27.55 

$`16Q LOSS WILD-TYPE`
TCGA-WC-A87U TCGA-V3-A9ZY TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       51.98        15.09        26.56        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EK 
       35.44        13.08        38.30        22.03        24.53        33.80 
TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EV TCGA-V4-A9EW 
       31.76        25.41        49.68        44.78        41.72        39.81 
TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 
       24.00        27.52        31.07        30.84        24.13        28.70 
TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 
       20.84         6.67        41.29        19.63        47.97        45.27 
TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF 
       46.82        38.73        44.52         3.75        26.99         1.32 
TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL 
        0.62        38.07        36.59        37.81         2.10        20.98 
TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q 
        2.24        26.14         0.20        19.92         2.83        20.91 
TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y 
        0.20        14.04         1.61        85.48        55.99        43.20 
TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A885 TCGA-WC-A888 TCGA-YZ-A980 
       41.36        36.56         7.92        22.55        18.90        61.22 
TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       16.27        26.24        45.90        38.93 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.13               0.20 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             82.16              85.48 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            14.925             27.255 
[1] "0.1 - 82.2 (14.9)" "0.2 - 85.5 (27.3)"
[1] "hr=" "2.5"
D46V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  16Q LOSS MUTATED           2         5          3          3          1
  16Q LOSS WILD-TYPE        10        22         22          7          0
                    vv
clus                 STAGE IV
  16Q LOSS MUTATED          2
  16Q LOSS WILD-TYPE        2
D46V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE IIA                 2                 10
  STAGE IIB                 5                 22
  STAGE IIIA                3                 22
  STAGE IIIB                3                  7
  STAGE IIIC                1                  0
  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                 T2 T3 T4
  16Q LOSS MUTATED    3  4  9
  16Q LOSS WILD-TYPE 11 28 25
D46V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T2                3                 11
  T3                4                 28
  T4                9                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   10  2
  16Q LOSS WILD-TYPE 41  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     10    2
  16Q LOSS WILD-TYPE   41    2
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               10                 41
  1                2                  2
[1] 2 2
[1] FALSE
D46V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    6 10
  16Q LOSS WILD-TYPE 29 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      6   10
  16Q LOSS WILD-TYPE   29   35
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                6                 29
  MALE                 10                 35
[1] 2 2
[1] FALSE
D46V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   13  2
  16Q LOSS WILD-TYPE 63  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     13    2
  16Q LOSS WILD-TYPE   63    1
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                13                 63
  YES                2                  1
[1] 2 2
[1] FALSE

Clustering(47) Variable = 19P LOSS MUTATION ANALYSIS
D47V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    2  1
  19P LOSS WILD-TYPE 55 22
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 77 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 22 
$`19P LOSS MUTATED`
TCGA-V4-A9E8 TCGA-WC-AA9E TCGA-YZ-A982 
       26.56        27.55        16.27 

$`19P LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       15.09        82.16        13.64        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       35.44        13.08        38.30        22.03        12.79        24.53 
TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET 
       33.80        31.76        25.41        14.96        49.68        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ 
       23.31        41.72        39.81        24.00        27.52        19.69 
TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 
       31.07        30.84        24.13        28.70        20.84         6.67 
TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA 
       41.29        19.63        47.97        45.27        46.82        38.73 
TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH 
       44.52         3.75        26.99         1.32         0.62        38.07 
TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN 
       36.59        37.81         2.10        20.98         0.13         2.24 
TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q 
       26.14         0.20         1.45        19.92         2.83        20.91 
TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y 
        0.20        14.04         1.61        85.48        55.99        43.20 
TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 
       41.36        36.56         7.92         0.39        22.55        18.90 
TCGA-WC-A88A TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
        2.70        61.22        26.24        45.90        38.93 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             16.27               0.13 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             27.55              85.48 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             26.56              25.41 
[1] "16.3 - 27.6 (26.6)" "0.1 - 85.5 (25.4)" 
[1] "hr=" "1.5"
D47V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  19P LOSS MUTATED           1         0          1          1          0
  19P LOSS WILD-TYPE        11        27         24          9          1
                    vv
clus                 STAGE IV
  19P LOSS MUTATED          0
  19P LOSS WILD-TYPE        4
D47V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE IIA                 1                 11
  STAGE IIB                 0                 27
  STAGE IIIA                1                 24
  STAGE IIIB                1                  9
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  19P LOSS MUTATED    1  0  2
  19P LOSS WILD-TYPE 13 32 32
D47V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T2                1                 13
  T3                0                 32
  T4                2                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V5, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    1  0
  19P LOSS WILD-TYPE 50  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1    0
  19P LOSS WILD-TYPE   50    4
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                1                 50
  1                0                  4
[1] 2 2
[1] FALSE
D47V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    1  2
  19P LOSS WILD-TYPE 34 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1    2
  19P LOSS WILD-TYPE   34   43
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                1                 34
  MALE                  2                 43
[1] 2 2
[1] FALSE
D47V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    2  1
  19P LOSS WILD-TYPE 74  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    1
  19P LOSS WILD-TYPE   74    2
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 2                 74
  YES                1                  2
[1] 2 2
[1] FALSE

Clustering(48) Variable = 19Q LOSS MUTATION ANALYSIS
D48V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    2  1
  19Q LOSS WILD-TYPE 55 22
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 77 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 22 
$`19Q LOSS MUTATED`
TCGA-V4-A9E8 TCGA-WC-AA9E TCGA-YZ-A982 
       26.56        27.55        16.27 

$`19Q LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       15.09        82.16        13.64        40.96        44.32        24.43 
TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       35.44        13.08        38.30        22.03        12.79        24.53 
TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET 
       33.80        31.76        25.41        14.96        49.68        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ 
       23.31        41.72        39.81        24.00        27.52        19.69 
TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 
       31.07        30.84        24.13        28.70        20.84         6.67 
TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA 
       41.29        19.63        47.97        45.27        46.82        38.73 
TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH 
       44.52         3.75        26.99         1.32         0.62        38.07 
TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN 
       36.59        37.81         2.10        20.98         0.13         2.24 
TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q 
       26.14         0.20         1.45        19.92         2.83        20.91 
TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y 
        0.20        14.04         1.61        85.48        55.99        43.20 
TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 
       41.36        36.56         7.92         0.39        22.55        18.90 
TCGA-WC-A88A TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
        2.70        61.22        26.24        45.90        38.93 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             16.27               0.13 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             27.55              85.48 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             26.56              25.41 
[1] "16.3 - 27.6 (26.6)" "0.1 - 85.5 (25.4)" 
[1] "hr=" "1.5"
D48V2, continuous
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  19Q LOSS MUTATED           1         0          1          1          0
  19Q LOSS WILD-TYPE        11        27         24          9          1
                    vv
clus                 STAGE IV
  19Q LOSS MUTATED          0
  19Q LOSS WILD-TYPE        4
D48V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE IIA                 1                 11
  STAGE IIB                 0                 27
  STAGE IIIA                1                 24
  STAGE IIIB                1                  9
  STAGE IIIC                0                  1
  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                 T2 T3 T4
  19Q LOSS MUTATED    1  0  2
  19Q LOSS WILD-TYPE 13 32 32
D48V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T2                1                 13
  T3                0                 32
  T4                2                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V5, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    1  0
  19Q LOSS WILD-TYPE 50  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    0
  19Q LOSS WILD-TYPE   50    4
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                1                 50
  1                0                  4
[1] 2 2
[1] FALSE
D48V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    1  2
  19Q LOSS WILD-TYPE 34 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    2
  19Q LOSS WILD-TYPE   34   43
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                1                 34
  MALE                  2                 43
[1] 2 2
[1] FALSE
D48V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  1
  19Q LOSS WILD-TYPE 74  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    1
  19Q LOSS WILD-TYPE   74    2
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 2                 74
  YES                1                  2
[1] 2 2
[1] FALSE

Clustering(49) Variable = XP LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED    9  3
  XP LOSS WILD-TYPE 48 20
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               12                68 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                3                20 
$`XP LOSS MUTATED`
TCGA-WC-AA9A TCGA-V4-A9E7 TCGA-V4-A9EZ TCGA-V4-A9F1 TCGA-V4-A9F5 TCGA-VD-A8KH 
       14.89        13.64        19.69        30.84         6.67        38.07 
TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8T TCGA-WC-A87W TCGA-WC-AA9E 
        1.45        19.92         2.83         1.61        55.99        27.55 

$`XP LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY 
       32.28        51.98        35.01         4.90        15.45        15.09 
TCGA-V4-A9E5 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED 
       82.16        26.56        40.96        44.32        24.43        35.44 
TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK 
       13.08        38.30        22.03        12.79        24.53        33.80 
TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU 
       31.76        25.41        14.96        49.68        44.78        23.31 
TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9F0 TCGA-V4-A9F2 
       41.72        39.81        24.00        27.52        31.07        24.13 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 
       28.70        20.84        41.29        19.63        47.97        45.27 
TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF 
       46.82        38.73        44.52         3.75        26.99         1.32 
TCGA-VD-A8KG TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM 
        0.62        36.59        37.81         2.10        20.98         0.13 
TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S 
        2.24        26.14         0.20        20.91         0.20        14.04 
TCGA-WC-A87T TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 
       85.48        43.20        41.36        36.56         7.92         0.39 
TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 
       22.55        18.90         2.70        61.22        16.27        26.24 
TCGA-YZ-A984 TCGA-YZ-A985 
       45.90        38.93 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             1.45              0.13 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            55.99             85.48 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            17.29             26.40 
[1] "1.4 - 56.0 (17.3)" "0.1 - 85.5 (26.4)"
[1] "hr=" "1.2"
D49V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  XP LOSS MUTATED           4         5          1          1          0
  XP LOSS WILD-TYPE         8        22         24          9          1
                   vv
clus                STAGE IV
  XP LOSS MUTATED          1
  XP LOSS WILD-TYPE        3
D49V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE IIA                4                 8
  STAGE IIB                5                22
  STAGE IIIA               1                24
  STAGE IIIB               1                 9
  STAGE IIIC               0                 1
  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                T2 T3 T4
  XP LOSS MUTATED    4  5  3
  XP LOSS WILD-TYPE 10 27 31
D49V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T2               4                10
  T3               5                27
  T4               3                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V5, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    8  1
  XP LOSS WILD-TYPE 43  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      8    1
  XP LOSS WILD-TYPE   43    3
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0               8                43
  1               1                 3
[1] 2 2
[1] FALSE
D49V6, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    7  5
  XP LOSS WILD-TYPE 28 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      7    5
  XP LOSS WILD-TYPE   28   40
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE               7                28
  MALE                 5                40
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   11  1
  XP LOSS WILD-TYPE 65  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     11    1
  XP LOSS WILD-TYPE   65    2
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               11                65
  YES               1                 2
[1] 2 2
[1] FALSE

Clustering(50) Variable = XQ LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   10  3
  XQ LOSS WILD-TYPE 47 20
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               13                67 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                20 
$`XQ LOSS MUTATED`
TCGA-WC-AA9A TCGA-V4-A9E7 TCGA-V4-A9ES TCGA-V4-A9EZ TCGA-V4-A9F1 TCGA-V4-A9F5 
       14.89        13.64        49.68        19.69        30.84         6.67 
TCGA-VD-A8KH TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8T TCGA-WC-A87W 
       38.07         1.45        19.92         2.83         1.61        55.99 
TCGA-WC-AA9E 
       27.55 

$`XQ LOSS WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY 
       32.28        51.98        35.01         4.90        15.45        15.09 
TCGA-V4-A9E5 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED 
       82.16        26.56        40.96        44.32        24.43        35.44 
TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK 
       13.08        38.30        22.03        12.79        24.53        33.80 
TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV 
       31.76        25.41        14.96        44.78        23.31        41.72 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9F0 TCGA-V4-A9F2 TCGA-V4-A9F3 
       39.81        24.00        27.52        31.07        24.13        28.70 
TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 
       20.84        41.29        19.63        47.97        45.27        46.82 
TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG 
       38.73        44.52         3.75        26.99         1.32         0.62 
TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN 
       36.59        37.81         2.10        20.98         0.13         2.24 
TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-WC-A87T 
       26.14         0.20        20.91         0.20        14.04        85.48 
TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 
       43.20        41.36        36.56         7.92         0.39        22.55 
TCGA-WC-A888 TCGA-WC-A88A TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 
       18.90         2.70        61.22        16.27        26.24        45.90 
TCGA-YZ-A985 
       38.93 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             1.45              0.13 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            55.99             85.48 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            19.69             26.24 
[1] "1.4 - 56.0 (19.7)" "0.1 - 85.5 (26.2)"
[1] "hr=" "1.1"
D50V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  XQ LOSS MUTATED           4         5          2          1          0
  XQ LOSS WILD-TYPE         8        22         23          9          1
                   vv
clus                STAGE IV
  XQ LOSS MUTATED          1
  XQ LOSS WILD-TYPE        3
D50V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE IIA                4                 8
  STAGE IIB                5                22
  STAGE IIIA               2                23
  STAGE IIIB               1                 9
  STAGE IIIC               0                 1
  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                T2 T3 T4
  XQ LOSS MUTATED    4  6  3
  XQ LOSS WILD-TYPE 10 26 31
D50V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T2               4                10
  T3               6                26
  T4               3                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    9  1
  XQ LOSS WILD-TYPE 42  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      9    1
  XQ LOSS WILD-TYPE   42    3
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0               9                42
  1               1                 3
[1] 2 2
[1] FALSE
D50V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    8  5
  XQ LOSS WILD-TYPE 27 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      8    5
  XQ LOSS WILD-TYPE   27   40
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               8                27
  MALE                 5                40
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   12  1
  XQ LOSS WILD-TYPE 64  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     12    1
  XQ LOSS WILD-TYPE   64    2
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               12                64
  YES               1                 2
[1] 2 2
[1] FALSE
