[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTTGCT-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/TGCT-TP/11541779/TGCT-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/TGCT-TP/11544839/transformed.cor.cli.txt"

nPatients in clinical file=31, in cluster file=150, common to both=31
[1] "Reduce the number of clustering variables from 80 to 55."
[1] 55 31
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               10                21 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               10                21 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               11                20 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               11                20 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11                20 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11                20 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               12                19 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               12                19 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                25 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                25 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                9                22 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                9                22 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                25 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                25 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6                25 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6                25 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               28                 3 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               28                 3 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               27                 4 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               27                 4 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               25                 6 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               25                 6 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               24                 7 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               24                 7 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                28 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                28 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                24                  7 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                24                  7 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                 20 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                 20 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                 23 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                 23 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 27 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 27 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 26 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 26 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                 22 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                 22 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                12                 19 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                12                 19 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 26 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 26 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 9                 22 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 9                 22 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                 21 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                 21 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                27                  4 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                27                  4 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 6                 25 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 6                 25 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                25 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                25 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12                19 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12                19 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9                22 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9                22 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23                 8 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23                 8 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               25                 6 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               25                 6 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               21                10 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               21                10 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               19                12 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               19                12 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                5                26 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                5                26 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                5                26 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                5                26 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               18                13 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               18                13 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               16                15 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               16                15 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                20                 11 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                20                 11 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                20                 11 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                20                 11 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                20                 11 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                20                 11 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                24                  7 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                24                  7 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                24                  7 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                24                  7 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 5                 26 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 5                 26 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                 23 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                 23 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                 21 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                 21 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                 21 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                 21 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                10                 21 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                10                 21 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 26 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 26 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                25                  6 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                25                  6 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                26                  5 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                26                  5 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                14                 17 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                14                 17 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                17                 14 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                17                 14 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                 23 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                 23 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 28 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 28 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                 16 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                 16 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7                24 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7                24 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 31 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-2G-AAF6 TCGA-2G-AAFL TCGA-2G-AAFZ TCGA-2G-AAG9 TCGA-2G-AAGE TCGA-2G-AAGG 
        3113          428         1122         1926         2080         2067 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
        2801         2284         1814         3236         3498         3669 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG 
        3922         1869         2462         3823         1817         1819 
TCGA-2G-AAKD TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2X-A9D6 TCGA-SO-A8JP TCGA-X3-A8G4 
        3726         2651         3991            4          107          856 
TCGA-XE-A8H1 TCGA-XE-AANR TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A8S3 TCGA-ZM-AA05 
         209           14         1550           13          424          757 
TCGA-ZM-AA06 
        1197 
Variable 1:'AGE':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 3:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RACE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "ETHNICITY"            
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 31 columns, 0 survival variables, and 5 non-survival variables.
AGE, nv=19, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=10, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 
15 14  2 
[1] "table(vv)"
vv
   T1 T2+T3 
   15    16 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 
15 14  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 15

$Class1_nSamples
[1] 16

$Class0_label
[1] "T1"

$Class1_label
[1] "T2+T3"


   T1 T2+T3 
   15    16 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  1P GAIN MUTATED         1        0        1        1         1         1
  1P GAIN WILD-TYPE       4        1        1        2         0         0
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  1P GAIN MUTATED           0          0          1        4
  1P GAIN WILD-TYPE         2          2          0        9
D1V2, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IB                 1                 1
  STAGE II                 1                 2
  STAGE IIA                1                 0
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIB               0                 2
  STAGE IIIC               1                 0
  STAGE IS                 4                 9
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  1P GAIN MUTATED    3     7
  1P GAIN WILD-TYPE 12     9
D1V3, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1                  3                12
  T2+T3               7                 9
[1] 2 2
[1] FALSE
D1V4, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    3  2
  1P GAIN WILD-TYPE 10  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    2
  1P GAIN WILD-TYPE   10    2
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               3                10
  1               2                 2
[1] 2 2
[1] FALSE
D1V5, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    1  9
  1P GAIN WILD-TYPE  2 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    9
  1P GAIN WILD-TYPE    2   19
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO               9                19
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  1Q GAIN MUTATED         1        0        1        1         1         1
  1Q GAIN WILD-TYPE       4        1        1        2         0         0
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  1Q GAIN MUTATED           0          0          1        5
  1Q GAIN WILD-TYPE         2          2          0        8
D2V2, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IB                 1                 1
  STAGE II                 1                 2
  STAGE IIA                1                 0
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIB               0                 2
  STAGE IIIC               1                 0
  STAGE IS                 5                 8
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  1Q GAIN MUTATED    4     7
  1Q GAIN WILD-TYPE 11     9
D2V3, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1                  4                11
  T2+T3               7                 9
[1] 2 2
[1] FALSE
D2V4, binary
                   cls
clus                0 1
  1Q GAIN MUTATED   4 2
  1Q GAIN WILD-TYPE 9 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      4    2
  1Q GAIN WILD-TYPE    9    2
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0               4                 9
  1               2                 2
[1] 2 2
[1] FALSE
D2V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    1 10
  1Q GAIN WILD-TYPE  2 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1   10
  1Q GAIN WILD-TYPE    2   18
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              10                18
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  2P GAIN MUTATED         1        1        1        0         1         0
  2P GAIN WILD-TYPE       4        0        1        3         0         1
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  2P GAIN MUTATED           0          0          1        6
  2P GAIN WILD-TYPE         2          2          0        7
D3V2, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 1                 0
  STAGE IB                 1                 1
  STAGE II                 0                 3
  STAGE IIA                1                 0
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIB               0                 2
  STAGE IIIC               1                 0
  STAGE IS                 6                 7
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  2P GAIN MUTATED    7     4
  2P GAIN WILD-TYPE  8    12
D3V3, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1                  7                 8
  T2+T3               4                12
[1] 2 2
[1] FALSE
D3V4, binary
                   cls
clus                0 1
  2P GAIN MUTATED   7 2
  2P GAIN WILD-TYPE 6 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      7    2
  2P GAIN WILD-TYPE    6    2
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               7                 6
  1               2                 2
[1] 2 2
[1] FALSE
D3V5, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    0 11
  2P GAIN WILD-TYPE  3 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   11
  2P GAIN WILD-TYPE    3   17
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              11                17
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  2Q GAIN MUTATED         3        0        1        0         1         0
  2Q GAIN WILD-TYPE       2        1        1        3         0         1
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  2Q GAIN MUTATED           0          0          1        6
  2Q GAIN WILD-TYPE         2          2          0        7
D4V2, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                 0                 1
  STAGE IB                 1                 1
  STAGE II                 0                 3
  STAGE IIA                1                 0
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIB               0                 2
  STAGE IIIC               1                 0
  STAGE IS                 6                 7
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  2Q GAIN MUTATED    8     4
  2Q GAIN WILD-TYPE  7    12
D4V3, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1                  8                 7
  T2+T3               4                12
[1] 2 2
[1] FALSE
D4V4, binary
                   cls
clus                0 1
  2Q GAIN MUTATED   6 2
  2Q GAIN WILD-TYPE 7 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      6    2
  2Q GAIN WILD-TYPE    7    2
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               6                 7
  1               2                 2
[1] 2 2
[1] FALSE
D4V5, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    0 12
  2Q GAIN WILD-TYPE  3 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   12
  2Q GAIN WILD-TYPE    3   16
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              12                16
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  3P GAIN MUTATED         0        0        0        0         0         0
  3P GAIN WILD-TYPE       5        1        2        3         1         1
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  3P GAIN MUTATED           1          0          1        4
  3P GAIN WILD-TYPE         1          2          0        9
D5V2, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IB                 0                 2
  STAGE II                 0                 3
  STAGE IIA                0                 1
  STAGE IIC                0                 1
  STAGE III                1                 1
  STAGE IIIB               0                 2
  STAGE IIIC               1                 0
  STAGE IS                 4                 9
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  3P GAIN MUTATED    2     4
  3P GAIN WILD-TYPE 13    12
D5V3, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1                  2                13
  T2+T3               4                12
[1] 2 2
[1] FALSE
D5V4, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3  1
  3P GAIN WILD-TYPE 10  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    1
  3P GAIN WILD-TYPE   10    3
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               3                10
  1               1                 3
[1] 2 2
[1] FALSE
D5V5, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    1  5
  3P GAIN WILD-TYPE  2 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    5
  3P GAIN WILD-TYPE    2   23
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO               5                23
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  3Q GAIN MUTATED         0        0        0        0         0         0
  3Q GAIN WILD-TYPE       5        1        2        3         1         1
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  3Q GAIN MUTATED           2          0          1        6
  3Q GAIN WILD-TYPE         0          2          0        7
D6V2, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IB                 0                 2
  STAGE II                 0                 3
  STAGE IIA                0                 1
  STAGE IIC                0                 1
  STAGE III                2                 0
  STAGE IIIB               0                 2
  STAGE IIIC               1                 0
  STAGE IS                 6                 7
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  3Q GAIN MUTATED    4     5
  3Q GAIN WILD-TYPE 11    11
D6V3, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1                  4                11
  T2+T3               5                11
[1] 2 2
[1] FALSE
D6V4, binary
                   cls
clus                0 1
  3Q GAIN MUTATED   5 1
  3Q GAIN WILD-TYPE 8 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5    1
  3Q GAIN WILD-TYPE    8    3
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0               5                 8
  1               1                 3
[1] 2 2
[1] FALSE
D6V5, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    1  8
  3Q GAIN WILD-TYPE  2 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1    8
  3Q GAIN WILD-TYPE    2   20
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO               8                20
[1] 2 2
[1] FALSE

Clustering(7) Variable = 6P GAIN MUTATION ANALYSIS
D7V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  6P GAIN MUTATED         1        0        1        0         1         1
  6P GAIN WILD-TYPE       4        1        1        3         0         0
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  6P GAIN MUTATED           0          0          1        1
  6P GAIN WILD-TYPE         2          2          0       12
D7V2, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IB                 1                 1
  STAGE II                 0                 3
  STAGE IIA                1                 0
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIB               0                 2
  STAGE IIIC               1                 0
  STAGE IS                 1                12
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  6P GAIN MUTATED    2     4
  6P GAIN WILD-TYPE 13    12
D7V3, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1                  2                13
  T2+T3               4                12
[1] 2 2
[1] FALSE
D7V4, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    1  2
  6P GAIN WILD-TYPE 12  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1    2
  6P GAIN WILD-TYPE   12    2
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               1                12
  1               2                 2
[1] 2 2
[1] FALSE
D7V5, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    0  6
  6P GAIN WILD-TYPE  3 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    6
  6P GAIN WILD-TYPE    3   22
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               6                22
[1] 2 2
[1] FALSE

Clustering(8) Variable = 6Q GAIN MUTATION ANALYSIS
D8V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  6Q GAIN MUTATED         1        0        1        0         1         1
  6Q GAIN WILD-TYPE       4        1        1        3         0         0
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  6Q GAIN MUTATED           0          0          1        1
  6Q GAIN WILD-TYPE         2          2          0       12
D8V2, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IB                 1                 1
  STAGE II                 0                 3
  STAGE IIA                1                 0
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIB               0                 2
  STAGE IIIC               1                 0
  STAGE IS                 1                12
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  6Q GAIN MUTATED    2     4
  6Q GAIN WILD-TYPE 13    12
D8V3, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1                  2                13
  T2+T3               4                12
[1] 2 2
[1] FALSE
D8V4, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    1  2
  6Q GAIN WILD-TYPE 12  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    2
  6Q GAIN WILD-TYPE   12    2
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               1                12
  1               2                 2
[1] 2 2
[1] FALSE
D8V5, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    0  6
  6Q GAIN WILD-TYPE  3 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    6
  6Q GAIN WILD-TYPE    3   22
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               6                22
[1] 2 2
[1] FALSE

Clustering(9) Variable = 7P GAIN MUTATION ANALYSIS
D9V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  7P GAIN MUTATED         4        1        2        3         1         1
  7P GAIN WILD-TYPE       1        0        0        0         0         0
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  7P GAIN MUTATED           2          2          1       11
  7P GAIN WILD-TYPE         0          0          0        2
D9V2, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  4                 1
  STAGE IA                 1                 0
  STAGE IB                 2                 0
  STAGE II                 3                 0
  STAGE IIA                1                 0
  STAGE IIC                1                 0
  STAGE III                2                 0
  STAGE IIIB               2                 0
  STAGE IIIC               1                 0
  STAGE IS                11                 2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  7P GAIN MUTATED   13    15
  7P GAIN WILD-TYPE  2     1
D9V3, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1                 13                 2
  T2+T3              15                 1
[1] 2 2
[1] FALSE
D9V4, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   12  4
  7P GAIN WILD-TYPE  1  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     12    4
  7P GAIN WILD-TYPE    1    0
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              12                 1
  1               4                 0
[1] 2 2
[1] FALSE
D9V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    1 27
  7P GAIN WILD-TYPE  2  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      1   27
  7P GAIN WILD-TYPE    2    1
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              27                 1
[1] 2 2
[1] FALSE

Clustering(10) Variable = 7Q GAIN MUTATION ANALYSIS
D10V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  7Q GAIN MUTATED         4        1        2        3         0         1
  7Q GAIN WILD-TYPE       1        0        0        0         1         0
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  7Q GAIN MUTATED           2          2          1       11
  7Q GAIN WILD-TYPE         0          0          0        2
D10V2, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  4                 1
  STAGE IA                 1                 0
  STAGE IB                 2                 0
  STAGE II                 3                 0
  STAGE IIA                0                 1
  STAGE IIC                1                 0
  STAGE III                2                 0
  STAGE IIIB               2                 0
  STAGE IIIC               1                 0
  STAGE IS                11                 2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  7Q GAIN MUTATED   13    14
  7Q GAIN WILD-TYPE  2     2
D10V3, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1                 13                 2
  T2+T3              14                 2
[1] 2 2
[1] FALSE
D10V4, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   12  3
  7Q GAIN WILD-TYPE  1  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     12    3
  7Q GAIN WILD-TYPE    1    1
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              12                 1
  1               3                 1
[1] 2 2
[1] FALSE
D10V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    1 26
  7Q GAIN WILD-TYPE  2  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1   26
  7Q GAIN WILD-TYPE    2    2
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              26                 2
[1] 2 2
[1] FALSE

Clustering(11) Variable = 8P GAIN MUTATION ANALYSIS
D11V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  8P GAIN MUTATED         5        0        1        2         1         1
  8P GAIN WILD-TYPE       0        1        1        1         0         0
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  8P GAIN MUTATED           2          2          0       11
  8P GAIN WILD-TYPE         0          0          1        2
D11V2, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  5                 0
  STAGE IA                 0                 1
  STAGE IB                 1                 1
  STAGE II                 2                 1
  STAGE IIA                1                 0
  STAGE IIC                1                 0
  STAGE III                2                 0
  STAGE IIIB               2                 0
  STAGE IIIC               0                 1
  STAGE IS                11                 2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  8P GAIN MUTATED   12    13
  8P GAIN WILD-TYPE  3     3
D11V3, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1                 12                 3
  T2+T3              13                 3
[1] 2 2
[1] FALSE
D11V4, binary
                   cls
clus                0 1
  8P GAIN MUTATED   9 3
  8P GAIN WILD-TYPE 4 1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9    3
  8P GAIN WILD-TYPE    4    1
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               9                 4
  1               3                 1
[1] 2 2
[1] FALSE
D11V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    3 22
  8P GAIN WILD-TYPE  0  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3   22
  8P GAIN WILD-TYPE    0    6
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 0
  NOT HISPANIC OR LATINO              22                 6
[1] 2 2
[1] FALSE

Clustering(12) Variable = 8Q GAIN MUTATION ANALYSIS
D12V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  8Q GAIN MUTATED         4        0        1        2         1         1
  8Q GAIN WILD-TYPE       1        1        1        1         0         0
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  8Q GAIN MUTATED           2          2          0       11
  8Q GAIN WILD-TYPE         0          0          1        2
D12V2, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  4                 1
  STAGE IA                 0                 1
  STAGE IB                 1                 1
  STAGE II                 2                 1
  STAGE IIA                1                 0
  STAGE IIC                1                 0
  STAGE III                2                 0
  STAGE IIIB               2                 0
  STAGE IIIC               0                 1
  STAGE IS                11                 2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  8Q GAIN MUTATED   10    14
  8Q GAIN WILD-TYPE  5     2
D12V3, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1                 10                 5
  T2+T3              14                 2
[1] 2 2
[1] FALSE
D12V4, binary
                   cls
clus                0 1
  8Q GAIN MUTATED   9 3
  8Q GAIN WILD-TYPE 4 1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      9    3
  8Q GAIN WILD-TYPE    4    1
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0               9                 4
  1               3                 1
[1] 2 2
[1] FALSE
D12V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    2 22
  8Q GAIN WILD-TYPE  1  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2   22
  8Q GAIN WILD-TYPE    1    6
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              22                 6
[1] 2 2
[1] FALSE

Clustering(13) Variable = 9Q GAIN MUTATION ANALYSIS
D13V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  9Q GAIN MUTATED         0        1        0        0         0         1
  9Q GAIN WILD-TYPE       5        0        2        3         1         0
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  9Q GAIN MUTATED           0          0          0        1
  9Q GAIN WILD-TYPE         2          2          1       12
D13V2, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 1                 0
  STAGE IB                 0                 2
  STAGE II                 0                 3
  STAGE IIA                0                 1
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIB               0                 2
  STAGE IIIC               0                 1
  STAGE IS                 1                12
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  9Q GAIN MUTATED    1     2
  9Q GAIN WILD-TYPE 14    14
D13V3, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1                  1                14
  T2+T3               2                14
[1] 2 2
[1] FALSE
D13V4, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    2  0
  9Q GAIN WILD-TYPE 11  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    0
  9Q GAIN WILD-TYPE   11    4
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               2                11
  1               0                 4
[1] 2 2
[1] FALSE
D13V5, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    0  3
  9Q GAIN WILD-TYPE  3 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    3
  9Q GAIN WILD-TYPE    3   25
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               3                25
[1] 2 2
[1] FALSE

Clustering(14) Variable = 12Q GAIN MUTATION ANALYSIS
D14V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  12Q GAIN MUTATED         3        1        2        2         1         1
  12Q GAIN WILD-TYPE       2        0        0        1         0         0
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  12Q GAIN MUTATED           1          2          1       10
  12Q GAIN WILD-TYPE         1          0          0        3
D14V2, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                  1                  0
  STAGE IB                  2                  0
  STAGE II                  2                  1
  STAGE IIA                 1                  0
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIB                2                  0
  STAGE IIIC                1                  0
  STAGE IS                 10                  3
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  12Q GAIN MUTATED   12    12
  12Q GAIN WILD-TYPE  3     4
D14V3, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                  12                  3
  T2+T3               12                  4
[1] 2 2
[1] FALSE
D14V4, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   10  4
  12Q GAIN WILD-TYPE  3  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     10    4
  12Q GAIN WILD-TYPE    3    0
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               10                  3
  1                4                  0
[1] 2 2
[1] FALSE
D14V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    2 22
  12Q GAIN WILD-TYPE  1  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   22
  12Q GAIN WILD-TYPE    1    6
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               22                  6
[1] 2 2
[1] FALSE

Clustering(15) Variable = 14Q GAIN MUTATION ANALYSIS
D15V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  14Q GAIN MUTATED         1        0        1        0         0         1
  14Q GAIN WILD-TYPE       4        1        1        3         1         0
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  14Q GAIN MUTATED           1          0          0        7
  14Q GAIN WILD-TYPE         1          2          1        6
D15V2, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  0                  3
  STAGE IIA                 0                  1
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIB                0                  2
  STAGE IIIC                0                  1
  STAGE IS                  7                  6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  14Q GAIN MUTATED    5     6
  14Q GAIN WILD-TYPE 10    10
D15V3, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                   5                 10
  T2+T3                6                 10
[1] 2 2
[1] FALSE
D15V4, binary
                    cls
clus                 0 1
  14Q GAIN MUTATED   4 0
  14Q GAIN WILD-TYPE 9 4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4    0
  14Q GAIN WILD-TYPE    9    4
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                4                  9
  1                0                  4
[1] 2 2
[1] FALSE
D15V5, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    1 10
  14Q GAIN WILD-TYPE  2 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   10
  14Q GAIN WILD-TYPE    2   18
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               10                 18
[1] 2 2
[1] FALSE

Clustering(16) Variable = 15Q GAIN MUTATION ANALYSIS
D16V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  15Q GAIN MUTATED         2        0        1        0         0         0
  15Q GAIN WILD-TYPE       3        1        1        3         1         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  15Q GAIN MUTATED           0          1          0        4
  15Q GAIN WILD-TYPE         2          1          1        9
D16V2, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  0                  3
  STAGE IIA                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIB                1                  1
  STAGE IIIC                0                  1
  STAGE IS                  4                  9
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  15Q GAIN MUTATED    5     3
  15Q GAIN WILD-TYPE 10    13
D16V3, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                   5                 10
  T2+T3                3                 13
[1] 2 2
[1] FALSE
D16V4, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    3  1
  15Q GAIN WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    1
  15Q GAIN WILD-TYPE   10    3
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                3                 10
  1                1                  3
[1] 2 2
[1] FALSE
D16V5, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    0  8
  15Q GAIN WILD-TYPE  3 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    8
  15Q GAIN WILD-TYPE    3   20
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                8                 20
[1] 2 2
[1] FALSE

Clustering(17) Variable = 16P GAIN MUTATION ANALYSIS
D17V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  16P GAIN MUTATED         0        0        1        0         1         0
  16P GAIN WILD-TYPE       5        1        1        3         0         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  16P GAIN MUTATED           0          0          1        1
  16P GAIN WILD-TYPE         2          2          0       12
D17V2, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  0                  3
  STAGE IIA                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIB                0                  2
  STAGE IIIC                1                  0
  STAGE IS                  1                 12
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  16P GAIN MUTATED    0     4
  16P GAIN WILD-TYPE 15    12
D17V3, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                   0                 15
  T2+T3                4                 12
[1] 2 2
[1] FALSE
D17V4, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    1  2
  16P GAIN WILD-TYPE 12  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    2
  16P GAIN WILD-TYPE   12    2
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                1                 12
  1                2                  2
[1] 2 2
[1] FALSE
D17V5, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    0  4
  16P GAIN WILD-TYPE  3 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0    4
  16P GAIN WILD-TYPE    3   24
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                4                 24
[1] 2 2
[1] FALSE

Clustering(18) Variable = 16Q GAIN MUTATION ANALYSIS
D18V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  16Q GAIN MUTATED         0        0        1        0         1         0
  16Q GAIN WILD-TYPE       5        1        1        3         0         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  16Q GAIN MUTATED           0          0          1        2
  16Q GAIN WILD-TYPE         2          2          0       11
D18V2, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  0                  3
  STAGE IIA                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIB                0                  2
  STAGE IIIC                1                  0
  STAGE IS                  2                 11
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  16Q GAIN MUTATED    1     4
  16Q GAIN WILD-TYPE 14    12
D18V3, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                   1                 14
  T2+T3                4                 12
[1] 2 2
[1] FALSE
D18V4, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    2  2
  16Q GAIN WILD-TYPE 11  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2    2
  16Q GAIN WILD-TYPE   11    2
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                2                 11
  1                2                  2
[1] 2 2
[1] FALSE
D18V5, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    0  5
  16Q GAIN WILD-TYPE  3 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0    5
  16Q GAIN WILD-TYPE    3   23
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                5                 23
[1] 2 2
[1] FALSE

Clustering(19) Variable = 17P GAIN MUTATION ANALYSIS
D19V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  17P GAIN MUTATED         0        0        0        1         1         0
  17P GAIN WILD-TYPE       5        1        2        2         0         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  17P GAIN MUTATED           1          1          1        4
  17P GAIN WILD-TYPE         1          1          0        9
D19V2, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IB                  0                  2
  STAGE II                  1                  2
  STAGE IIA                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIB                1                  1
  STAGE IIIC                1                  0
  STAGE IS                  4                  9
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  17P GAIN MUTATED    2     7
  17P GAIN WILD-TYPE 13     9
D19V3, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                   2                 13
  T2+T3                7                  9
[1] 2 2
[1] FALSE
D19V4, binary
                    cls
clus                 0 1
  17P GAIN MUTATED   4 3
  17P GAIN WILD-TYPE 9 1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    3
  17P GAIN WILD-TYPE    9    1
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                4                  9
  1                3                  1
[1] 2 2
[1] FALSE
D19V5, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    0  9
  17P GAIN WILD-TYPE  3 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    9
  17P GAIN WILD-TYPE    3   19
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                9                 19
[1] 2 2
[1] FALSE

Clustering(20) Variable = 17Q GAIN MUTATION ANALYSIS
D20V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  17Q GAIN MUTATED         0        1        0        1         1         0
  17Q GAIN WILD-TYPE       5        0        2        2         0         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  17Q GAIN MUTATED           1          1          1        6
  17Q GAIN WILD-TYPE         1          1          0        7
D20V2, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  1                  0
  STAGE IB                  0                  2
  STAGE II                  1                  2
  STAGE IIA                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIB                1                  1
  STAGE IIIC                1                  0
  STAGE IS                  6                  7
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  17Q GAIN MUTATED    4     8
  17Q GAIN WILD-TYPE 11     8
D20V3, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                   4                 11
  T2+T3                8                  8
[1] 2 2
[1] FALSE
D20V4, binary
                    cls
clus                 0 1
  17Q GAIN MUTATED   7 3
  17Q GAIN WILD-TYPE 6 1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7    3
  17Q GAIN WILD-TYPE    6    1
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                7                  6
  1                3                  1
[1] 2 2
[1] FALSE
D20V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    0 12
  17Q GAIN WILD-TYPE  3 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   12
  17Q GAIN WILD-TYPE    3   16
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               12                 16
[1] 2 2
[1] FALSE

Clustering(21) Variable = 19P GAIN MUTATION ANALYSIS
D21V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  19P GAIN MUTATED         1        0        1        0         0         1
  19P GAIN WILD-TYPE       4        1        1        3         1         0
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  19P GAIN MUTATED           0          0          0        2
  19P GAIN WILD-TYPE         2          2          1       11
D21V2, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  0                  3
  STAGE IIA                 0                  1
  STAGE IIC                 1                  0
  STAGE III                 0                  2
  STAGE IIIB                0                  2
  STAGE IIIC                0                  1
  STAGE IS                  2                 11
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  19P GAIN MUTATED    3     2
  19P GAIN WILD-TYPE 12    14
D21V3, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                   3                 12
  T2+T3                2                 14
[1] 2 2
[1] FALSE
D21V4, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    2  0
  19P GAIN WILD-TYPE 11  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2    0
  19P GAIN WILD-TYPE   11    4
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                2                 11
  1                0                  4
[1] 2 2
[1] FALSE
D21V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    0  5
  19P GAIN WILD-TYPE  3 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    5
  19P GAIN WILD-TYPE    3   23
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                5                 23
[1] 2 2
[1] FALSE

Clustering(22) Variable = 20P GAIN MUTATION ANALYSIS
D22V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  20P GAIN MUTATED         1        0        1        0         0         1
  20P GAIN WILD-TYPE       4        1        1        3         1         0
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  20P GAIN MUTATED           1          0          1        4
  20P GAIN WILD-TYPE         1          2          0        9
D22V2, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  0                  3
  STAGE IIA                 0                  1
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIB                0                  2
  STAGE IIIC                1                  0
  STAGE IS                  4                  9
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  20P GAIN MUTATED    3     6
  20P GAIN WILD-TYPE 12    10
D22V3, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                   3                 12
  T2+T3                6                 10
[1] 2 2
[1] FALSE
D22V4, binary
                    cls
clus                 0 1
  20P GAIN MUTATED   5 1
  20P GAIN WILD-TYPE 8 3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5    1
  20P GAIN WILD-TYPE    8    3
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0                5                  8
  1                1                  3
[1] 2 2
[1] FALSE
D22V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    0  9
  20P GAIN WILD-TYPE  3 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      0    9
  20P GAIN WILD-TYPE    3   19
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                9                 19
[1] 2 2
[1] FALSE

Clustering(23) Variable = 20Q GAIN MUTATION ANALYSIS
D23V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  20Q GAIN MUTATED         1        0        1        0         1         1
  20Q GAIN WILD-TYPE       4        1        1        3         0         0
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  20Q GAIN MUTATED           1          0          1        4
  20Q GAIN WILD-TYPE         1          2          0        9
D23V2, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  0                  3
  STAGE IIA                 1                  0
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIB                0                  2
  STAGE IIIC                1                  0
  STAGE IS                  4                  9
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  20Q GAIN MUTATED    3     7
  20Q GAIN WILD-TYPE 12     9
D23V3, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                   3                 12
  T2+T3                7                  9
[1] 2 2
[1] FALSE
D23V4, binary
                    cls
clus                 0 1
  20Q GAIN MUTATED   5 2
  20Q GAIN WILD-TYPE 8 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5    2
  20Q GAIN WILD-TYPE    8    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0                5                  8
  1                2                  2
[1] 2 2
[1] FALSE
D23V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    0 10
  20Q GAIN WILD-TYPE  3 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0   10
  20Q GAIN WILD-TYPE    3   18
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               10                 18
[1] 2 2
[1] FALSE

Clustering(24) Variable = 21Q GAIN MUTATION ANALYSIS
D24V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  21Q GAIN MUTATED         5        1        2        3         1         1
  21Q GAIN WILD-TYPE       0        0        0        0         0         0
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  21Q GAIN MUTATED           1          2          1       10
  21Q GAIN WILD-TYPE         1          0          0        3
D24V2, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   5                  0
  STAGE IA                  1                  0
  STAGE IB                  2                  0
  STAGE II                  3                  0
  STAGE IIA                 1                  0
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIB                2                  0
  STAGE IIIC                1                  0
  STAGE IS                 10                  3
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  21Q GAIN MUTATED   14    13
  21Q GAIN WILD-TYPE  1     3
D24V3, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                  14                  1
  T2+T3               13                  3
[1] 2 2
[1] FALSE
D24V4, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   11  4
  21Q GAIN WILD-TYPE  2  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     11    4
  21Q GAIN WILD-TYPE    2    0
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               11                  2
  1                4                  0
[1] 2 2
[1] FALSE
D24V5, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    2 25
  21Q GAIN WILD-TYPE  1  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2   25
  21Q GAIN WILD-TYPE    1    3
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               25                  3
[1] 2 2
[1] FALSE

Clustering(25) Variable = 22Q GAIN MUTATION ANALYSIS
D25V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  22Q GAIN MUTATED         3        0        1        0         0         0
  22Q GAIN WILD-TYPE       2        1        1        3         1         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  22Q GAIN MUTATED           0          0          0        2
  22Q GAIN WILD-TYPE         2          2          1       11
D25V2, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  0                  3
  STAGE IIA                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIB                0                  2
  STAGE IIIC                0                  1
  STAGE IS                  2                 11
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  22Q GAIN MUTATED    5     1
  22Q GAIN WILD-TYPE 10    15
D25V3, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                   5                 10
  T2+T3                1                 15
[1] 2 2
[1] FALSE
D25V4, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    2  0
  22Q GAIN WILD-TYPE 11  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2    0
  22Q GAIN WILD-TYPE   11    4
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                2                 11
  1                0                  4
[1] 2 2
[1] FALSE
D25V5, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    0  6
  22Q GAIN WILD-TYPE  3 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    6
  22Q GAIN WILD-TYPE    3   22
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                6                 22
[1] 2 2
[1] FALSE

Clustering(26) Variable = XQ GAIN MUTATION ANALYSIS
D26V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  XQ GAIN MUTATED         1        0        0        0         0         0
  XQ GAIN WILD-TYPE       4        1        2        3         1         1
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  XQ GAIN MUTATED           1          0          0        4
  XQ GAIN WILD-TYPE         1          2          1        9
D26V2, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IB                 0                 2
  STAGE II                 0                 3
  STAGE IIA                0                 1
  STAGE IIC                0                 1
  STAGE III                1                 1
  STAGE IIIB               0                 2
  STAGE IIIC               0                 1
  STAGE IS                 4                 9
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  XQ GAIN MUTATED    3     3
  XQ GAIN WILD-TYPE 12    13
D26V3, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1                  3                12
  T2+T3               3                13
[1] 2 2
[1] FALSE
D26V4, binary
                   cls
clus                0 1
  XQ GAIN MUTATED   4 0
  XQ GAIN WILD-TYPE 9 4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4    0
  XQ GAIN WILD-TYPE    9    4
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               4                 9
  1               0                 4
[1] 2 2
[1] FALSE
D26V5, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    0  6
  XQ GAIN WILD-TYPE  3 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    6
  XQ GAIN WILD-TYPE    3   22
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               6                22
[1] 2 2
[1] FALSE

Clustering(27) Variable = 3P LOSS MUTATION ANALYSIS
D27V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  3P LOSS MUTATED         3        1        1        0         0         0
  3P LOSS WILD-TYPE       2        0        1        3         1         1
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  3P LOSS MUTATED           1          2          0        4
  3P LOSS WILD-TYPE         1          0          1        9
D27V2, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                 1                 0
  STAGE IB                 1                 1
  STAGE II                 0                 3
  STAGE IIA                0                 1
  STAGE IIC                0                 1
  STAGE III                1                 1
  STAGE IIIB               2                 0
  STAGE IIIC               0                 1
  STAGE IS                 4                 9
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  3P LOSS MUTATED    5     7
  3P LOSS WILD-TYPE 10     9
D27V3, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1                  5                10
  T2+T3               7                 9
[1] 2 2
[1] FALSE
D27V4, binary
                   cls
clus                0 1
  3P LOSS MUTATED   6 2
  3P LOSS WILD-TYPE 7 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      6    2
  3P LOSS WILD-TYPE    7    2
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               6                 7
  1               2                 2
[1] 2 2
[1] FALSE
D27V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    1 11
  3P LOSS WILD-TYPE  2 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   11
  3P LOSS WILD-TYPE    2   17
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              11                17
[1] 2 2
[1] FALSE

Clustering(28) Variable = 3Q LOSS MUTATION ANALYSIS
D28V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  3Q LOSS MUTATED         2        1        1        0         0         0
  3Q LOSS WILD-TYPE       3        0        1        3         1         1
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  3Q LOSS MUTATED           0          1          0        4
  3Q LOSS WILD-TYPE         2          1          1        9
D28V2, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                 1                 0
  STAGE IB                 1                 1
  STAGE II                 0                 3
  STAGE IIA                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIB               1                 1
  STAGE IIIC               0                 1
  STAGE IS                 4                 9
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  3Q LOSS MUTATED    5     4
  3Q LOSS WILD-TYPE 10    12
D28V3, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1                  5                10
  T2+T3               4                12
[1] 2 2
[1] FALSE
D28V4, binary
                   cls
clus                0 1
  3Q LOSS MUTATED   6 1
  3Q LOSS WILD-TYPE 7 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6    1
  3Q LOSS WILD-TYPE    7    3
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               6                 7
  1               1                 3
[1] 2 2
[1] FALSE
D28V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    0  9
  3Q LOSS WILD-TYPE  3 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    9
  3Q LOSS WILD-TYPE    3   19
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               9                19
[1] 2 2
[1] FALSE

Clustering(29) Variable = 4P LOSS MUTATION ANALYSIS
D29V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  4P LOSS MUTATED         3        1        2        3         1         1
  4P LOSS WILD-TYPE       2        0        0        0         0         0
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  4P LOSS MUTATED           0          2          1        9
  4P LOSS WILD-TYPE         2          0          0        4
D29V2, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                 1                 0
  STAGE IB                 2                 0
  STAGE II                 3                 0
  STAGE IIA                1                 0
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIB               2                 0
  STAGE IIIC               1                 0
  STAGE IS                 9                 4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  4P LOSS MUTATED   10    13
  4P LOSS WILD-TYPE  5     3
D29V3, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1                 10                 5
  T2+T3              13                 3
[1] 2 2
[1] FALSE
D29V4, binary
                   cls
clus                0 1
  4P LOSS MUTATED   9 4
  4P LOSS WILD-TYPE 4 0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      9    4
  4P LOSS WILD-TYPE    4    0
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0               9                 4
  1               4                 0
[1] 2 2
[1] FALSE
D29V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    3 20
  4P LOSS WILD-TYPE  0  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3   20
  4P LOSS WILD-TYPE    0    8
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 0
  NOT HISPANIC OR LATINO              20                 8
[1] 2 2
[1] FALSE

Clustering(30) Variable = 4Q LOSS MUTATION ANALYSIS
D30V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  4Q LOSS MUTATED         3        1        2        3         1         0
  4Q LOSS WILD-TYPE       2        0        0        0         0         1
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  4Q LOSS MUTATED           1          2          1       11
  4Q LOSS WILD-TYPE         1          0          0        2
D30V2, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                 1                 0
  STAGE IB                 2                 0
  STAGE II                 3                 0
  STAGE IIA                1                 0
  STAGE IIC                0                 1
  STAGE III                1                 1
  STAGE IIIB               2                 0
  STAGE IIIC               1                 0
  STAGE IS                11                 2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  4Q LOSS MUTATED   11    14
  4Q LOSS WILD-TYPE  4     2
D30V3, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1                 11                 4
  T2+T3              14                 2
[1] 2 2
[1] FALSE
D30V4, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   11  4
  4Q LOSS WILD-TYPE  2  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     11    4
  4Q LOSS WILD-TYPE    2    0
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              11                 2
  1               4                 0
[1] 2 2
[1] FALSE
D30V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    3 22
  4Q LOSS WILD-TYPE  0  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3   22
  4Q LOSS WILD-TYPE    0    6
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 0
  NOT HISPANIC OR LATINO              22                 6
[1] 2 2
[1] FALSE

Clustering(31) Variable = 5P LOSS MUTATION ANALYSIS
D31V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  5P LOSS MUTATED         4        1        1        3         1         1
  5P LOSS WILD-TYPE       1        0        1        0         0         0
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  5P LOSS MUTATED           1          1          0        8
  5P LOSS WILD-TYPE         1          1          1        5
D31V2, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  4                 1
  STAGE IA                 1                 0
  STAGE IB                 1                 1
  STAGE II                 3                 0
  STAGE IIA                1                 0
  STAGE IIC                1                 0
  STAGE III                1                 1
  STAGE IIIB               1                 1
  STAGE IIIC               0                 1
  STAGE IS                 8                 5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  5P LOSS MUTATED   13     8
  5P LOSS WILD-TYPE  2     8
D31V3, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1                 13                 2
  T2+T3               8                 8
[1] 2 2
[1] FALSE
D31V4, binary
                   cls
clus                0 1
  5P LOSS MUTATED   7 2
  5P LOSS WILD-TYPE 6 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      7    2
  5P LOSS WILD-TYPE    6    2
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               7                 6
  1               2                 2
[1] 2 2
[1] FALSE
D31V5, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    2 19
  5P LOSS WILD-TYPE  1  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2   19
  5P LOSS WILD-TYPE    1    9
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              19                 9
[1] 2 2
[1] FALSE

Clustering(32) Variable = 5Q LOSS MUTATION ANALYSIS
D32V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  5Q LOSS MUTATED         4        1        1        3         1         1
  5Q LOSS WILD-TYPE       1        0        1        0         0         0
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  5Q LOSS MUTATED           0          0          0        8
  5Q LOSS WILD-TYPE         2          2          1        5
D32V2, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  4                 1
  STAGE IA                 1                 0
  STAGE IB                 1                 1
  STAGE II                 3                 0
  STAGE IIA                1                 0
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIB               0                 2
  STAGE IIIC               0                 1
  STAGE IS                 8                 5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  5Q LOSS MUTATED   13     6
  5Q LOSS WILD-TYPE  2    10
D32V3, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1                 13                 2
  T2+T3               6                10
[1] 2 2
[1] FALSE
D32V4, binary
                   cls
clus                0 1
  5Q LOSS MUTATED   7 1
  5Q LOSS WILD-TYPE 6 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7    1
  5Q LOSS WILD-TYPE    6    3
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               7                 6
  1               1                 3
[1] 2 2
[1] FALSE
D32V5, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    2 17
  5Q LOSS WILD-TYPE  1 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2   17
  5Q LOSS WILD-TYPE    1   11
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              17                11
[1] 2 2
[1] FALSE

Clustering(33) Variable = 6P LOSS MUTATION ANALYSIS
D33V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  6P LOSS MUTATED         1        0        0        0         0         0
  6P LOSS WILD-TYPE       4        1        2        3         1         1
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  6P LOSS MUTATED           0          0          0        4
  6P LOSS WILD-TYPE         2          2          1        9
D33V2, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IB                 0                 2
  STAGE II                 0                 3
  STAGE IIA                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIB               0                 2
  STAGE IIIC               0                 1
  STAGE IS                 4                 9
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  6P LOSS MUTATED    3     2
  6P LOSS WILD-TYPE 12    14
D33V3, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1                  3                12
  T2+T3               2                14
[1] 2 2
[1] FALSE
D33V4, binary
                   cls
clus                0 1
  6P LOSS MUTATED   4 0
  6P LOSS WILD-TYPE 9 4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4    0
  6P LOSS WILD-TYPE    9    4
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0               4                 9
  1               0                 4
[1] 2 2
[1] FALSE
D33V5, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    1  4
  6P LOSS WILD-TYPE  2 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1    4
  6P LOSS WILD-TYPE    2   24
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO               4                24
[1] 2 2
[1] FALSE

Clustering(34) Variable = 6Q LOSS MUTATION ANALYSIS
D34V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  6Q LOSS MUTATED         1        0        0        0         0         0
  6Q LOSS WILD-TYPE       4        1        2        3         1         1
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  6Q LOSS MUTATED           0          0          0        4
  6Q LOSS WILD-TYPE         2          2          1        9
D34V2, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IB                 0                 2
  STAGE II                 0                 3
  STAGE IIA                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIB               0                 2
  STAGE IIIC               0                 1
  STAGE IS                 4                 9
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  6Q LOSS MUTATED    3     2
  6Q LOSS WILD-TYPE 12    14
D34V3, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1                  3                12
  T2+T3               2                14
[1] 2 2
[1] FALSE
D34V4, binary
                   cls
clus                0 1
  6Q LOSS MUTATED   4 0
  6Q LOSS WILD-TYPE 9 4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    0
  6Q LOSS WILD-TYPE    9    4
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0               4                 9
  1               0                 4
[1] 2 2
[1] FALSE
D34V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    1  4
  6Q LOSS WILD-TYPE  2 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1    4
  6Q LOSS WILD-TYPE    2   24
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO               4                24
[1] 2 2
[1] FALSE

Clustering(35) Variable = 9P LOSS MUTATION ANALYSIS
D35V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  9P LOSS MUTATED         3        0        1        2         1         0
  9P LOSS WILD-TYPE       2        1        1        1         0         1
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  9P LOSS MUTATED           0          2          1        8
  9P LOSS WILD-TYPE         2          0          0        5
D35V2, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                 0                 1
  STAGE IB                 1                 1
  STAGE II                 2                 1
  STAGE IIA                1                 0
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIB               2                 0
  STAGE IIIC               1                 0
  STAGE IS                 8                 5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  9P LOSS MUTATED    8    10
  9P LOSS WILD-TYPE  7     6
D35V3, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1                  8                 7
  T2+T3              10                 6
[1] 2 2
[1] FALSE
D35V4, binary
                   cls
clus                0 1
  9P LOSS MUTATED   9 4
  9P LOSS WILD-TYPE 4 0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      9    4
  9P LOSS WILD-TYPE    4    0
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0               9                 4
  1               4                 0
[1] 2 2
[1] FALSE
D35V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    1 17
  9P LOSS WILD-TYPE  2 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1   17
  9P LOSS WILD-TYPE    2   11
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              17                11
[1] 2 2
[1] FALSE

Clustering(36) Variable = 9Q LOSS MUTATION ANALYSIS
D36V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  9Q LOSS MUTATED         3        0        1        2         1         0
  9Q LOSS WILD-TYPE       2        1        1        1         0         1
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  9Q LOSS MUTATED           0          2          1        6
  9Q LOSS WILD-TYPE         2          0          0        7
D36V2, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                 0                 1
  STAGE IB                 1                 1
  STAGE II                 2                 1
  STAGE IIA                1                 0
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIB               2                 0
  STAGE IIIC               1                 0
  STAGE IS                 6                 7
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  9Q LOSS MUTATED    7     9
  9Q LOSS WILD-TYPE  8     7
D36V3, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1                  7                 8
  T2+T3               9                 7
[1] 2 2
[1] FALSE
D36V4, binary
                   cls
clus                0 1
  9Q LOSS MUTATED   7 4
  9Q LOSS WILD-TYPE 6 0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      7    4
  9Q LOSS WILD-TYPE    6    0
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0               7                 6
  1               4                 0
[1] 2 2
[1] FALSE
D36V5, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    0 16
  9Q LOSS WILD-TYPE  3 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      0   16
  9Q LOSS WILD-TYPE    3   12
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              16                12
[1] 2 2
[1] FALSE

Clustering(37) Variable = 10P LOSS MUTATION ANALYSIS
D37V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  10P LOSS MUTATED         2        0        1        3         1         0
  10P LOSS WILD-TYPE       3        1        1        0         0         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  10P LOSS MUTATED           1          2          1        9
  10P LOSS WILD-TYPE         1          0          0        4
D37V2, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  3                  0
  STAGE IIA                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIB                2                  0
  STAGE IIIC                1                  0
  STAGE IS                  9                  4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  10P LOSS MUTATED   10    10
  10P LOSS WILD-TYPE  5     6
D37V3, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                  10                  5
  T2+T3               10                  6
[1] 2 2
[1] FALSE
D37V4, binary
                    cls
clus                 0 1
  10P LOSS MUTATED   8 4
  10P LOSS WILD-TYPE 5 0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8    4
  10P LOSS WILD-TYPE    5    0
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                8                  5
  1                4                  0
[1] 2 2
[1] FALSE
D37V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    1 19
  10P LOSS WILD-TYPE  2  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   19
  10P LOSS WILD-TYPE    2    9
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               19                  9
[1] 2 2
[1] FALSE

Clustering(38) Variable = 10Q LOSS MUTATION ANALYSIS
D38V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  10Q LOSS MUTATED         3        0        1        3         1         0
  10Q LOSS WILD-TYPE       2        1        1        0         0         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  10Q LOSS MUTATED           1          2          1        8
  10Q LOSS WILD-TYPE         1          0          0        5
D38V2, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  3                  0
  STAGE IIA                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIB                2                  0
  STAGE IIIC                1                  0
  STAGE IS                  8                  5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  10Q LOSS MUTATED   11     9
  10Q LOSS WILD-TYPE  4     7
D38V3, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                  11                  4
  T2+T3                9                  7
[1] 2 2
[1] FALSE
D38V4, binary
                    cls
clus                 0 1
  10Q LOSS MUTATED   8 4
  10Q LOSS WILD-TYPE 5 0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      8    4
  10Q LOSS WILD-TYPE    5    0
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                8                  5
  1                4                  0
[1] 2 2
[1] FALSE
D38V5, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    0 20
  10Q LOSS WILD-TYPE  3  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0   20
  10Q LOSS WILD-TYPE    3    8
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               20                  8
[1] 2 2
[1] FALSE

Clustering(39) Variable = 11P LOSS MUTATION ANALYSIS
D39V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  11P LOSS MUTATED         3        0        1        3         0         1
  11P LOSS WILD-TYPE       2        1        1        0         1         0
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  11P LOSS MUTATED           1          2          1        8
  11P LOSS WILD-TYPE         1          0          0        5
D39V2, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  3                  0
  STAGE IIA                 0                  1
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIB                2                  0
  STAGE IIIC                1                  0
  STAGE IS                  8                  5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  11P LOSS MUTATED    9    11
  11P LOSS WILD-TYPE  6     5
D39V3, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                   9                  6
  T2+T3               11                  5
[1] 2 2
[1] FALSE
D39V4, binary
                    cls
clus                 0 1
  11P LOSS MUTATED   7 3
  11P LOSS WILD-TYPE 6 1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      7    3
  11P LOSS WILD-TYPE    6    1
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                7                  6
  1                3                  1
[1] 2 2
[1] FALSE
D39V5, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    2 18
  11P LOSS WILD-TYPE  1 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2   18
  11P LOSS WILD-TYPE    1   10
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               18                 10
[1] 2 2
[1] FALSE

Clustering(40) Variable = 11Q LOSS MUTATION ANALYSIS
D40V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  11Q LOSS MUTATED         4        0        1        3         1         1
  11Q LOSS WILD-TYPE       1        1        1        0         0         0
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  11Q LOSS MUTATED           1          2          1       10
  11Q LOSS WILD-TYPE         1          0          0        3
D40V2, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   4                  1
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  3                  0
  STAGE IIA                 1                  0
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIB                2                  0
  STAGE IIIC                1                  0
  STAGE IS                 10                  3
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  11Q LOSS MUTATED   11    13
  11Q LOSS WILD-TYPE  4     3
D40V3, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                  11                  4
  T2+T3               13                  3
[1] 2 2
[1] FALSE
D40V4, binary
                    cls
clus                 0 1
  11Q LOSS MUTATED   9 4
  11Q LOSS WILD-TYPE 4 0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      9    4
  11Q LOSS WILD-TYPE    4    0
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                9                  4
  1                4                  0
[1] 2 2
[1] FALSE
D40V5, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    2 22
  11Q LOSS WILD-TYPE  1  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2   22
  11Q LOSS WILD-TYPE    1    6
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               22                  6
[1] 2 2
[1] FALSE

Clustering(41) Variable = 13Q LOSS MUTATION ANALYSIS
D41V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  13Q LOSS MUTATED         4        1        2        2         1         1
  13Q LOSS WILD-TYPE       1        0        0        1         0         0
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  13Q LOSS MUTATED           1          2          1        9
  13Q LOSS WILD-TYPE         1          0          0        4
D41V2, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   4                  1
  STAGE IA                  1                  0
  STAGE IB                  2                  0
  STAGE II                  2                  1
  STAGE IIA                 1                  0
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIB                2                  0
  STAGE IIIC                1                  0
  STAGE IS                  9                  4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  13Q LOSS MUTATED   11    13
  13Q LOSS WILD-TYPE  4     3
D41V3, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                  11                  4
  T2+T3               13                  3
[1] 2 2
[1] FALSE
D41V4, binary
                    cls
clus                 0 1
  13Q LOSS MUTATED   9 4
  13Q LOSS WILD-TYPE 4 0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9    4
  13Q LOSS WILD-TYPE    4    0
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0                9                  4
  1                4                  0
[1] 2 2
[1] FALSE
D41V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    3 21
  13Q LOSS WILD-TYPE  0  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3   21
  13Q LOSS WILD-TYPE    0    7
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  0
  NOT HISPANIC OR LATINO               21                  7
[1] 2 2
[1] FALSE

Clustering(42) Variable = 14Q LOSS MUTATION ANALYSIS
D42V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  14Q LOSS MUTATED         0        0        0        1         1         0
  14Q LOSS WILD-TYPE       5        1        2        2         0         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  14Q LOSS MUTATED           0          0          1        2
  14Q LOSS WILD-TYPE         2          2          0       11
D42V2, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IB                  0                  2
  STAGE II                  1                  2
  STAGE IIA                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIB                0                  2
  STAGE IIIC                1                  0
  STAGE IS                  2                 11
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  14Q LOSS MUTATED    2     3
  14Q LOSS WILD-TYPE 13    13
D42V3, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                   2                 13
  T2+T3                3                 13
[1] 2 2
[1] FALSE
D42V4, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    2  2
  14Q LOSS WILD-TYPE 11  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2    2
  14Q LOSS WILD-TYPE   11    2
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0                2                 11
  1                2                  2
[1] 2 2
[1] FALSE
D42V5, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    0  5
  14Q LOSS WILD-TYPE  3 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0    5
  14Q LOSS WILD-TYPE    3   23
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                5                 23
[1] 2 2
[1] FALSE

Clustering(43) Variable = 15Q LOSS MUTATION ANALYSIS
D43V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  15Q LOSS MUTATED         0        1        1        1         1         0
  15Q LOSS WILD-TYPE       5        0        1        2         0         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  15Q LOSS MUTATED           0          0          1        3
  15Q LOSS WILD-TYPE         2          2          0       10
D43V2, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  1                  0
  STAGE IB                  1                  1
  STAGE II                  1                  2
  STAGE IIA                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIB                0                  2
  STAGE IIIC                1                  0
  STAGE IS                  3                 10
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  15Q LOSS MUTATED    3     5
  15Q LOSS WILD-TYPE 12    11
D43V3, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                   3                 12
  T2+T3                5                 11
[1] 2 2
[1] FALSE
D43V4, binary
                    cls
clus                 0 1
  15Q LOSS MUTATED   4 2
  15Q LOSS WILD-TYPE 9 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4    2
  15Q LOSS WILD-TYPE    9    2
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0                4                  9
  1                2                  2
[1] 2 2
[1] FALSE
D43V5, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  7
  15Q LOSS WILD-TYPE  2 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    7
  15Q LOSS WILD-TYPE    2   21
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO                7                 21
[1] 2 2
[1] FALSE

Clustering(44) Variable = 16P LOSS MUTATION ANALYSIS
D44V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  16P LOSS MUTATED         1        0        1        1         0         0
  16P LOSS WILD-TYPE       4        1        1        2         1         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  16P LOSS MUTATED           1          0          0        6
  16P LOSS WILD-TYPE         1          2          1        7
D44V2, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  1                  2
  STAGE IIA                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIB                0                  2
  STAGE IIIC                0                  1
  STAGE IS                  6                  7
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  16P LOSS MUTATED    4     6
  16P LOSS WILD-TYPE 11    10
D44V3, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                   4                 11
  T2+T3                6                 10
[1] 2 2
[1] FALSE
D44V4, binary
                    cls
clus                 0 1
  16P LOSS MUTATED   5 0
  16P LOSS WILD-TYPE 8 4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5    0
  16P LOSS WILD-TYPE    8    4
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                5                  8
  1                0                  4
[1] 2 2
[1] FALSE
D44V5, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    3  7
  16P LOSS WILD-TYPE  0 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    7
  16P LOSS WILD-TYPE    0   21
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  0
  NOT HISPANIC OR LATINO                7                 21
[1] 2 2
[1] FALSE

Clustering(45) Variable = 16Q LOSS MUTATION ANALYSIS
D45V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  16Q LOSS MUTATED         1        0        1        1         0         0
  16Q LOSS WILD-TYPE       4        1        1        2         1         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  16Q LOSS MUTATED           1          0          0        6
  16Q LOSS WILD-TYPE         1          2          1        7
D45V2, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  1                  2
  STAGE IIA                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIB                0                  2
  STAGE IIIC                0                  1
  STAGE IS                  6                  7
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  16Q LOSS MUTATED    4     6
  16Q LOSS WILD-TYPE 11    10
D45V3, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                   4                 11
  T2+T3                6                 10
[1] 2 2
[1] FALSE
D45V4, binary
                    cls
clus                 0 1
  16Q LOSS MUTATED   5 0
  16Q LOSS WILD-TYPE 8 4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5    0
  16Q LOSS WILD-TYPE    8    4
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                5                  8
  1                0                  4
[1] 2 2
[1] FALSE
D45V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3  7
  16Q LOSS WILD-TYPE  0 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    7
  16Q LOSS WILD-TYPE    0   21
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  0
  NOT HISPANIC OR LATINO                7                 21
[1] 2 2
[1] FALSE

Clustering(46) Variable = 17P LOSS MUTATION ANALYSIS
D46V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  17P LOSS MUTATED         2        0        1        1         0         0
  17P LOSS WILD-TYPE       3        1        1        2         1         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  17P LOSS MUTATED           1          1          0        4
  17P LOSS WILD-TYPE         1          1          1        9
D46V2, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  1                  2
  STAGE IIA                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIB                1                  1
  STAGE IIIC                0                  1
  STAGE IS                  4                  9
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  17P LOSS MUTATED    6     4
  17P LOSS WILD-TYPE  9    12
D46V3, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                   6                  9
  T2+T3                4                 12
[1] 2 2
[1] FALSE
D46V4, binary
                    cls
clus                 0 1
  17P LOSS MUTATED   4 1
  17P LOSS WILD-TYPE 9 3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4    1
  17P LOSS WILD-TYPE    9    3
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0                4                  9
  1                1                  3
[1] 2 2
[1] FALSE
D46V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    1  9
  17P LOSS WILD-TYPE  2 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1    9
  17P LOSS WILD-TYPE    2   19
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO                9                 19
[1] 2 2
[1] FALSE

Clustering(47) Variable = 17Q LOSS MUTATION ANALYSIS
D47V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  17Q LOSS MUTATED         1        0        1        0         0         0
  17Q LOSS WILD-TYPE       4        1        1        3         1         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  17Q LOSS MUTATED           1          1          0        1
  17Q LOSS WILD-TYPE         1          1          1       12
D47V2, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IB                  1                  1
  STAGE II                  0                  3
  STAGE IIA                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIB                1                  1
  STAGE IIIC                0                  1
  STAGE IS                  1                 12
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  17Q LOSS MUTATED    2     3
  17Q LOSS WILD-TYPE 13    13
D47V3, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                   2                 13
  T2+T3                3                 13
[1] 2 2
[1] FALSE
D47V4, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    1  1
  17Q LOSS WILD-TYPE 12  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    1
  17Q LOSS WILD-TYPE   12    3
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0                1                 12
  1                1                  3
[1] 2 2
[1] FALSE
D47V5, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    0  5
  17Q LOSS WILD-TYPE  3 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0    5
  17Q LOSS WILD-TYPE    3   23
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                5                 23
[1] 2 2
[1] FALSE

Clustering(48) Variable = 18P LOSS MUTATION ANALYSIS
D48V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  18P LOSS MUTATED         3        1        2        3         0         0
  18P LOSS WILD-TYPE       2        0        0        0         1         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  18P LOSS MUTATED           1          2          1       12
  18P LOSS WILD-TYPE         1          0          0        1
D48V2, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                  1                  0
  STAGE IB                  2                  0
  STAGE II                  3                  0
  STAGE IIA                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIB                2                  0
  STAGE IIIC                1                  0
  STAGE IS                 12                  1
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  18P LOSS MUTATED   12    13
  18P LOSS WILD-TYPE  3     3
D48V3, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                  12                  3
  T2+T3               13                  3
[1] 2 2
[1] FALSE
D48V4, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   11  3
  18P LOSS WILD-TYPE  2  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     11    3
  18P LOSS WILD-TYPE    2    1
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               11                  2
  1                3                  1
[1] 2 2
[1] FALSE
D48V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    3 22
  18P LOSS WILD-TYPE  0  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   22
  18P LOSS WILD-TYPE    0    6
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  0
  NOT HISPANIC OR LATINO               22                  6
[1] 2 2
[1] FALSE

Clustering(49) Variable = 18Q LOSS MUTATION ANALYSIS
D49V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  18Q LOSS MUTATED         4        1        2        3         0         0
  18Q LOSS WILD-TYPE       1        0        0        0         1         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  18Q LOSS MUTATED           1          2          1       12
  18Q LOSS WILD-TYPE         1          0          0        1
D49V2, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   4                  1
  STAGE IA                  1                  0
  STAGE IB                  2                  0
  STAGE II                  3                  0
  STAGE IIA                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIB                2                  0
  STAGE IIIC                1                  0
  STAGE IS                 12                  1
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  18Q LOSS MUTATED   13    13
  18Q LOSS WILD-TYPE  2     3
D49V3, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                  13                  2
  T2+T3               13                  3
[1] 2 2
[1] FALSE
D49V4, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   12  3
  18Q LOSS WILD-TYPE  1  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     12    3
  18Q LOSS WILD-TYPE    1    1
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               12                  1
  1                3                  1
[1] 2 2
[1] FALSE
D49V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    3 23
  18Q LOSS WILD-TYPE  0  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3   23
  18Q LOSS WILD-TYPE    0    5
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  0
  NOT HISPANIC OR LATINO               23                  5
[1] 2 2
[1] FALSE

Clustering(50) Variable = 19P LOSS MUTATION ANALYSIS
D50V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  19P LOSS MUTATED         0        0        0        2         1         0
  19P LOSS WILD-TYPE       5        1        2        1         0         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  19P LOSS MUTATED           0          1          1        9
  19P LOSS WILD-TYPE         2          1          0        4
D50V2, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IB                  0                  2
  STAGE II                  2                  1
  STAGE IIA                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIB                1                  1
  STAGE IIIC                1                  0
  STAGE IS                  9                  4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  19P LOSS MUTATED    5     9
  19P LOSS WILD-TYPE 10     7
D50V3, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                   5                 10
  T2+T3                9                  7
[1] 2 2
[1] FALSE
D50V4, binary
                    cls
clus                 0 1
  19P LOSS MUTATED   6 3
  19P LOSS WILD-TYPE 7 1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      6    3
  19P LOSS WILD-TYPE    7    1
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                6                  7
  1                3                  1
[1] 2 2
[1] FALSE
D50V5, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    2 12
  19P LOSS WILD-TYPE  1 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2   12
  19P LOSS WILD-TYPE    1   16
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               12                 16
[1] 2 2
[1] FALSE

Clustering(51) Variable = 19Q LOSS MUTATION ANALYSIS
D51V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  19Q LOSS MUTATED         0        0        0        3         1         0
  19Q LOSS WILD-TYPE       5        1        2        0         0         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  19Q LOSS MUTATED           1          1          1       10
  19Q LOSS WILD-TYPE         1          1          0        3
D51V2, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IB                  0                  2
  STAGE II                  3                  0
  STAGE IIA                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIB                1                  1
  STAGE IIIC                1                  0
  STAGE IS                 10                  3
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  19Q LOSS MUTATED    7    10
  19Q LOSS WILD-TYPE  8     6
D51V3, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                   7                  8
  T2+T3               10                  6
[1] 2 2
[1] FALSE
D51V4, binary
                    cls
clus                 0 1
  19Q LOSS MUTATED   7 3
  19Q LOSS WILD-TYPE 6 1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      7    3
  19Q LOSS WILD-TYPE    6    1
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                7                  6
  1                3                  1
[1] 2 2
[1] FALSE
D51V5, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2 15
  19Q LOSS WILD-TYPE  1 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   15
  19Q LOSS WILD-TYPE    1   13
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               15                 13
[1] 2 2
[1] FALSE

Clustering(52) Variable = 20P LOSS MUTATION ANALYSIS
D52V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  20P LOSS MUTATED         0        1        0        2         1         0
  20P LOSS WILD-TYPE       5        0        2        1         0         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  20P LOSS MUTATED           0          1          0        3
  20P LOSS WILD-TYPE         2          1          1       10
D52V2, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  1                  0
  STAGE IB                  0                  2
  STAGE II                  2                  1
  STAGE IIA                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIB                1                  1
  STAGE IIIC                0                  1
  STAGE IS                  3                 10
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  20P LOSS MUTATED    3     5
  20P LOSS WILD-TYPE 12    11
D52V3, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                   3                 12
  T2+T3                5                 11
[1] 2 2
[1] FALSE
D52V4, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    2  2
  20P LOSS WILD-TYPE 11  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2    2
  20P LOSS WILD-TYPE   11    2
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                2                 11
  1                2                  2
[1] 2 2
[1] FALSE
D52V5, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    1  7
  20P LOSS WILD-TYPE  2 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    7
  20P LOSS WILD-TYPE    2   21
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO                7                 21
[1] 2 2
[1] FALSE

Clustering(53) Variable = 20Q LOSS MUTATION ANALYSIS
D53V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  20Q LOSS MUTATED         0        0        0        1         0         0
  20Q LOSS WILD-TYPE       5        1        2        2         1         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  20Q LOSS MUTATED           0          0          0        2
  20Q LOSS WILD-TYPE         2          2          1       11
D53V2, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IB                  0                  2
  STAGE II                  1                  2
  STAGE IIA                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIB                0                  2
  STAGE IIIC                0                  1
  STAGE IS                  2                 11
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  20Q LOSS MUTATED    0     3
  20Q LOSS WILD-TYPE 15    13
D53V3, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                   0                 15
  T2+T3                3                 13
[1] 2 2
[1] FALSE
D53V4, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    0  0
  20Q LOSS WILD-TYPE 13  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    0
  20Q LOSS WILD-TYPE   13    4
D53V5, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  2
  20Q LOSS WILD-TYPE  2 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    2
  20Q LOSS WILD-TYPE    2   26
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO                2                 26
[1] 2 2
[1] FALSE

Clustering(54) Variable = 22Q LOSS MUTATION ANALYSIS
D54V1, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  22Q LOSS MUTATED         1        1        1        2         1         0
  22Q LOSS WILD-TYPE       4        0        1        1         0         1
                    vv
clus                 STAGE III STAGE IIIB STAGE IIIC STAGE IS
  22Q LOSS MUTATED           1          0          1        7
  22Q LOSS WILD-TYPE         1          2          0        6
D54V2, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  1                  0
  STAGE IB                  1                  1
  STAGE II                  2                  1
  STAGE IIA                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIB                0                  2
  STAGE IIIC                1                  0
  STAGE IS                  7                  6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2+T3
  22Q LOSS MUTATED    6     9
  22Q LOSS WILD-TYPE  9     7
D54V3, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                   6                  9
  T2+T3                9                  7
[1] 2 2
[1] FALSE
D54V4, binary
                    cls
clus                 0 1
  22Q LOSS MUTATED   7 2
  22Q LOSS WILD-TYPE 6 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      7    2
  22Q LOSS WILD-TYPE    6    2
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0                7                  6
  1                2                  2
[1] 2 2
[1] FALSE
D54V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    2 13
  22Q LOSS WILD-TYPE  1 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2   13
  22Q LOSS WILD-TYPE    1   15
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               13                 15
[1] 2 2
[1] FALSE

Clustering(55) Variable = XQ LOSS MUTATION ANALYSIS
D55V1, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC
  XQ LOSS MUTATED         2        0        0        2         0         0
  XQ LOSS WILD-TYPE       3        1        2        1         1         1
                   vv
clus                STAGE III STAGE IIIB STAGE IIIC STAGE IS
  XQ LOSS MUTATED           0          0          0        3
  XQ LOSS WILD-TYPE         2          2          1       10
D55V2, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                 0                 1
  STAGE IB                 0                 2
  STAGE II                 2                 1
  STAGE IIA                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIB               0                 2
  STAGE IIIC               0                 1
  STAGE IS                 3                10
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2+T3
  XQ LOSS MUTATED    6     1
  XQ LOSS WILD-TYPE  9    15
D55V3, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1                  6                 9
  T2+T3               1                15
[1] 2 2
[1] FALSE
D55V4, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    3  0
  XQ LOSS WILD-TYPE 10  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    0
  XQ LOSS WILD-TYPE   10    4
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0               3                10
  1               0                 4
[1] 2 2
[1] FALSE
D55V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    1  6
  XQ LOSS WILD-TYPE  2 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    6
  XQ LOSS WILD-TYPE    2   22
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO               6                22
[1] 2 2
[1] FALSE
