[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"        "-oTLUAD-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUAD-TP/11590629/LUAD-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/10686948/transformed.cor.cli.txt"

nPatients in clinical file=519, in cluster file=229, common to both=172
[1] "Reduce the number of clustering variables from 21 to 20."
[1]  20 172
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            86             86 
  TP53 MUTATED TP53 WILD-TYPE 
            86             86 
[1] "STK11 MUTATION ANALYSIS"
[1] 3
  STK11 MUTATED STK11 WILD-TYPE 
             20             152 
  STK11 MUTATED STK11 WILD-TYPE 
             20             152 
[1] "KEAP1 MUTATION ANALYSIS"
[1] 3
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             31             141 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             31             141 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            47            125 
  KRAS MUTATED KRAS WILD-TYPE 
            47            125 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               15               157 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               15               157 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              161 
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              161 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           22           150 
  NF1 MUTATED NF1 WILD-TYPE 
           22           150 
[1] "U2AF1 MUTATION ANALYSIS"
[1] 3
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              6             166 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              6             166 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            23            149 
  EGFR MUTATED EGFR WILD-TYPE 
            23            149 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             15             157 
  SETD2 MUTATED SETD2 WILD-TYPE 
             15             157 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               8              164 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               8              164 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           11           161 
  MET MUTATED MET WILD-TYPE 
           11           161 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              8             164 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              8             164 
[1] "CHRND MUTATION ANALYSIS"
[1] 3
  CHRND MUTATED CHRND WILD-TYPE 
              9             163 
  CHRND MUTATED CHRND WILD-TYPE 
              9             163 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            16            156 
  BRAF MUTATED BRAF WILD-TYPE 
            16            156 
[1] "GEN1 MUTATION ANALYSIS"
[1] 3
  GEN1 MUTATED GEN1 WILD-TYPE 
             4            168 
  GEN1 MUTATED GEN1 WILD-TYPE 
             4            168 
[1] "STX2 MUTATION ANALYSIS"
[1] 3
  STX2 MUTATED STX2 WILD-TYPE 
             4            168 
  STX2 MUTATED STX2 WILD-TYPE 
             4            168 
[1] "MGA MUTATION ANALYSIS"
[1] 3
  MGA MUTATED MGA WILD-TYPE 
           15           157 
  MGA MUTATED MGA WILD-TYPE 
           15           157 
[1] "GALC MUTATION ANALYSIS"
[1] 3
  GALC MUTATED GALC WILD-TYPE 
             5            167 
  GALC MUTATED GALC WILD-TYPE 
             5            167 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               9              163 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               9              163 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 172 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 172 columns, 0 survival variables, and 12 non-survival variables.
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=9, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        1      6      2      6
  TP53 WILD-TYPE      4      3     10      0
D1V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              4
  CLUS_2            6              3
  CLUS_3            2             10
  CLUS_4            6              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        3      6      6
  TP53 WILD-TYPE     11      5      1
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3             11
  CLUS_2            6              5
  CLUS_3            6              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       47     20     19
  TP53 WILD-TYPE     21     48     17
D1V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           47             21
  CLUS_2           20             48
  CLUS_3           19             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        8     11     17     22
  TP53 WILD-TYPE     18     13     11     11
D1V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8             18
  CLUS_2           11             13
  CLUS_3           17             11
  CLUS_4           22             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        3     27     16
  TP53 WILD-TYPE     12     29     12
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3             12
  CLUS_2           27             29
  CLUS_3           16             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED       11      5     21      7      2
  TP53 WILD-TYPE     19     10      9      7      8
D1V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           11             19
  CLUS_2            5             10
  CLUS_3           21              9
  CLUS_4            7              7
  CLUS_5            2              8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED       40      6     11     22      6
  TP53 WILD-TYPE     18     31     18     12      7
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           40             18
  CLUS_2            6             31
  CLUS_3           11             18
  CLUS_4           22             12
  CLUS_5            6              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  TP53 MUTATED       10      4     22     21      3      7      8      1      9
  TP53 WILD-TYPE     16     16      6      6     11      8     12      3      8
D1V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           10             16
  CLUS_2            4             16
  CLUS_3           22              6
  CLUS_4           21              6
  CLUS_5            3             11
  CLUS_6            7              8
  CLUS_7            8             12
  CLUS_8            1              3
  CLUS_9            9              8
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       19     46     19
  TP53 WILD-TYPE     40     29     15
D1V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           19             40
  CLUS_2           46             29
  CLUS_3           19             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        6     31     21     26
  TP53 WILD-TYPE     13     39     23      9
D1V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            6             13
  CLUS_2           31             39
  CLUS_3           21             23
  CLUS_4           26              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       32      5     18
  TP53 WILD-TYPE     29      9     11
D1V11, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           32             29
  CLUS_2            5              9
  CLUS_3           18             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        5     34     16
  TP53 WILD-TYPE      9     25     15
D1V12, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            5              9
  CLUS_2           34             25
  CLUS_3           16             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = STK11 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STK11 MUTATED        0      0      2      1
  STK11 WILD-TYPE      5      9     10      5
D2V1, multiclass
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             0               9
  CLUS_3             2              10
  CLUS_4             1               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STK11 MUTATED        2      0      1
  STK11 WILD-TYPE     12     11      6
D2V2, multiclass
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  CLUS_1             2              12
  CLUS_2             0              11
  CLUS_3             1               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STK11 MUTATED        6     11      3
  STK11 WILD-TYPE     62     57     33
D2V3, multiclass
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  CLUS_1             6              62
  CLUS_2            11              57
  CLUS_3             3              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STK11 MUTATED        3      3      1      3
  STK11 WILD-TYPE     23     21     27     30
D2V4, multiclass
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  CLUS_1             3              23
  CLUS_2             3              21
  CLUS_3             1              27
  CLUS_4             3              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STK11 MUTATED        3      4      5
  STK11 WILD-TYPE     12     52     23
D2V5, multiclass
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  CLUS_1             3              12
  CLUS_2             4              52
  CLUS_3             5              23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  STK11 MUTATED        1      4      3      3      1
  STK11 WILD-TYPE     29     11     27     11      9
D2V6, multiclass
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  CLUS_1             1              29
  CLUS_2             4              11
  CLUS_3             3              27
  CLUS_4             3              11
  CLUS_5             1               9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  STK11 MUTATED        0      7      7      5      0
  STK11 WILD-TYPE     58     30     22     29     13
D2V7, multiclass
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  CLUS_1             0              58
  CLUS_2             7              30
  CLUS_3             7              22
  CLUS_4             5              29
  CLUS_5             0              13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  STK11 MUTATED        1      0      0      0      8      2      8      0
  STK11 WILD-TYPE     25     20     28     27      6     13     12      4
                 vv
clus              CLUS_9
  STK11 MUTATED        0
  STK11 WILD-TYPE     17
D2V8, multiclass
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             0              20
  CLUS_3             0              28
  CLUS_4             0              27
  CLUS_5             8               6
  CLUS_6             2              13
  CLUS_7             8              12
  CLUS_8             0               4
  CLUS_9             0              17
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STK11 MUTATED        7      7      4
  STK11 WILD-TYPE     52     68     30
D2V9, multiclass
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  CLUS_1             7              52
  CLUS_2             7              68
  CLUS_3             4              30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STK11 MUTATED        5      5      2      6
  STK11 WILD-TYPE     14     65     42     29
D2V10, multiclass
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  CLUS_1             5              14
  CLUS_2             5              65
  CLUS_3             2              42
  CLUS_4             6              29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STK11 MUTATED        6      1      3
  STK11 WILD-TYPE     55     13     26
D2V11, multiclass
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  CLUS_1             6              55
  CLUS_2             1              13
  CLUS_3             3              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STK11 MUTATED        3      4      3
  STK11 WILD-TYPE     11     55     28
D2V12, multiclass
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  CLUS_1             3              11
  CLUS_2             4              55
  CLUS_3             3              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = KEAP1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KEAP1 MUTATED        0      0      2      1
  KEAP1 WILD-TYPE      5      9     10      5
D3V1, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             0               9
  CLUS_3             2              10
  CLUS_4             1               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED        2      0      1
  KEAP1 WILD-TYPE     12     11      6
D3V2, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             2              12
  CLUS_2             0              11
  CLUS_3             1               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED        8     13     10
  KEAP1 WILD-TYPE     60     55     26
D3V3, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             8              60
  CLUS_2            13              55
  CLUS_3            10              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KEAP1 MUTATED        3      6      3      7
  KEAP1 WILD-TYPE     23     18     25     26
D3V4, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             3              23
  CLUS_2             6              18
  CLUS_3             3              25
  CLUS_4             7              26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED        6      5      8
  KEAP1 WILD-TYPE      9     51     20
D3V5, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             6               9
  CLUS_2             5              51
  CLUS_3             8              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KEAP1 MUTATED        2      6      3      6      2
  KEAP1 WILD-TYPE     28      9     27      8      8
D3V6, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             2              28
  CLUS_2             6               9
  CLUS_3             3              27
  CLUS_4             6               8
  CLUS_5             2               8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KEAP1 MUTATED        3      7     13      7      1
  KEAP1 WILD-TYPE     55     30     16     27     12
D3V7, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             3              55
  CLUS_2             7              30
  CLUS_3            13              16
  CLUS_4             7              27
  CLUS_5             1              12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KEAP1 MUTATED        1      0      2      6      7      2     12      0
  KEAP1 WILD-TYPE     25     20     26     21      7     13      8      4
                 vv
clus              CLUS_9
  KEAP1 MUTATED        1
  KEAP1 WILD-TYPE     16
D3V8, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             0              20
  CLUS_3             2              26
  CLUS_4             6              21
  CLUS_5             7               7
  CLUS_6             2              13
  CLUS_7            12               8
  CLUS_8             0               4
  CLUS_9             1              16
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED       10     13      5
  KEAP1 WILD-TYPE     49     62     29
D3V9, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1            10              49
  CLUS_2            13              62
  CLUS_3             5              29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KEAP1 MUTATED        5     11      4      8
  KEAP1 WILD-TYPE     14     59     40     27
D3V10, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             5              14
  CLUS_2            11              59
  CLUS_3             4              40
  CLUS_4             8              27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED       14      1      4
  KEAP1 WILD-TYPE     47     13     25
D3V11, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1            14              47
  CLUS_2             1              13
  CLUS_3             4              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED        3     15      1
  KEAP1 WILD-TYPE     11     44     30
D3V12, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             3              11
  CLUS_2            15              44
  CLUS_3             1              30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = KRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        2      3      3      1
  KRAS WILD-TYPE      3      6      9      5
D4V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            2              3
  CLUS_2            3              6
  CLUS_3            3              9
  CLUS_4            1              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        4      3      2
  KRAS WILD-TYPE     10      8      5
D4V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            4             10
  CLUS_2            3              8
  CLUS_3            2              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED       14     18     15
  KRAS WILD-TYPE     54     50     21
D4V3, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           14             54
  CLUS_2           18             50
  CLUS_3           15             21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        6      7      9      6
  KRAS WILD-TYPE     20     17     19     27
D4V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            6             20
  CLUS_2            7             17
  CLUS_3            9             19
  CLUS_4            6             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        8     11      5
  KRAS WILD-TYPE      7     45     23
D4V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            8              7
  CLUS_2           11             45
  CLUS_3            5             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRAS MUTATED        6      5      6      3      4
  KRAS WILD-TYPE     24     10     24     11      6
D4V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            6             24
  CLUS_2            5             10
  CLUS_3            6             24
  CLUS_4            3             11
  CLUS_5            4              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRAS MUTATED       14     12     10      8      2
  KRAS WILD-TYPE     44     25     19     26     11
D4V7, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           14             44
  CLUS_2           12             25
  CLUS_3           10             19
  CLUS_4            8             26
  CLUS_5            2             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  KRAS MUTATED        9      4      5      2      7      7      6      3      3
  KRAS WILD-TYPE     17     16     23     25      7      8     14      1     14
D4V8, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            9             17
  CLUS_2            4             16
  CLUS_3            5             23
  CLUS_4            2             25
  CLUS_5            7              7
  CLUS_6            7              8
  CLUS_7            6             14
  CLUS_8            3              1
  CLUS_9            3             14
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED       25     13      7
  KRAS WILD-TYPE     34     62     27
D4V9, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           25             34
  CLUS_2           13             62
  CLUS_3            7             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        7     17     14      7
  KRAS WILD-TYPE     12     53     30     28
D4V10, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            7             12
  CLUS_2           17             53
  CLUS_3           14             30
  CLUS_4            7             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED       15      4      7
  KRAS WILD-TYPE     46     10     22
D4V11, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           15             46
  CLUS_2            4             10
  CLUS_3            7             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        5     13      8
  KRAS WILD-TYPE      9     46     23
D4V12, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            5              9
  CLUS_2           13             46
  CLUS_3            8             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = SMARCA4 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMARCA4 MUTATED        0      1      0      2
  SMARCA4 WILD-TYPE      5      8     12      4
D5V1, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               1                 8
  CLUS_3               0                12
  CLUS_4               2                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SMARCA4 MUTATED        1      0      2
  SMARCA4 WILD-TYPE     13     11      5
D5V2, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               1                13
  CLUS_2               0                11
  CLUS_3               2                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SMARCA4 MUTATED        6      3      6
  SMARCA4 WILD-TYPE     62     65     30
D5V3, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               6                62
  CLUS_2               3                65
  CLUS_3               6                30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMARCA4 MUTATED        1      6      0      5
  SMARCA4 WILD-TYPE     25     18     28     28
D5V4, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               1                25
  CLUS_2               6                18
  CLUS_3               0                28
  CLUS_4               5                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SMARCA4 MUTATED        1      6      3
  SMARCA4 WILD-TYPE     14     50     25
D5V5, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               1                14
  CLUS_2               6                50
  CLUS_3               3                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SMARCA4 MUTATED        1      2      4      1      2
  SMARCA4 WILD-TYPE     29     13     26     13      8
D5V6, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               1                29
  CLUS_2               2                13
  CLUS_3               4                26
  CLUS_4               1                13
  CLUS_5               2                 8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SMARCA4 MUTATED        3      1      6      5      0
  SMARCA4 WILD-TYPE     55     36     23     29     13
D5V7, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               3                55
  CLUS_2               1                36
  CLUS_3               6                23
  CLUS_4               5                29
  CLUS_5               0                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SMARCA4 MUTATED        2      0      1      4      0      1      7      0
  SMARCA4 WILD-TYPE     24     20     27     23     14     14     13      4
                   vv
clus                CLUS_9
  SMARCA4 MUTATED        0
  SMARCA4 WILD-TYPE     17
D5V8, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               2                24
  CLUS_2               0                20
  CLUS_3               1                27
  CLUS_4               4                23
  CLUS_5               0                14
  CLUS_6               1                14
  CLUS_7               7                13
  CLUS_8               0                 4
  CLUS_9               0                17
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SMARCA4 MUTATED        2     10      3
  SMARCA4 WILD-TYPE     57     65     31
D5V9, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               2                57
  CLUS_2              10                65
  CLUS_3               3                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMARCA4 MUTATED        1      7      1      6
  SMARCA4 WILD-TYPE     18     63     43     29
D5V10, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               1                18
  CLUS_2               7                63
  CLUS_3               1                43
  CLUS_4               6                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SMARCA4 MUTATED        4      2      5
  SMARCA4 WILD-TYPE     57     12     24
D5V11, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               4                57
  CLUS_2               2                12
  CLUS_3               5                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SMARCA4 MUTATED        0     10      1
  SMARCA4 WILD-TYPE     14     49     30
D5V12, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               0                14
  CLUS_2              10                49
  CLUS_3               1                30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = ARID1A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        0      0      0      2
  ARID1A WILD-TYPE      5      9     12      4
D6V1, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               30 
      TCGA-05-4244       TCGA-05-4249       TCGA-05-4250       TCGA-35-3615 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-35-4122       TCGA-35-4123       TCGA-44-2655       TCGA-44-2656 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-44-2657       TCGA-44-2659       TCGA-44-2661       TCGA-44-2662 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-44-2665       TCGA-44-2666       TCGA-44-2668       TCGA-44-3398 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-44-3918       TCGA-44-3919       TCGA-44-4112       TCGA-55-1592 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-55-1594       TCGA-55-1595       TCGA-55-1596       TCGA-64-1676 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-64-1677       TCGA-64-1680       TCGA-67-3770       TCGA-67-3772 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-67-3773       TCGA-67-3774 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        0      0      2
  ARID1A WILD-TYPE     14     11      5
D6V2, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               30 
      TCGA-05-4244       TCGA-05-4249       TCGA-05-4250       TCGA-35-3615 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-35-4122       TCGA-35-4123       TCGA-44-2655       TCGA-44-2656 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-44-2657       TCGA-44-2659       TCGA-44-2661       TCGA-44-2662 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-44-2665       TCGA-44-2666       TCGA-44-2668       TCGA-44-3398 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-44-3918       TCGA-44-3919       TCGA-44-4112       TCGA-55-1592 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-55-1594       TCGA-55-1595       TCGA-55-1596       TCGA-64-1676 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-64-1677       TCGA-64-1680       TCGA-67-3770       TCGA-67-3772 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-67-3773       TCGA-67-3774 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        5      1      5
  ARID1A WILD-TYPE     63     67     31
D6V3, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              5               63
  CLUS_2              1               67
  CLUS_3              5               31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        1      3      3      1
  ARID1A WILD-TYPE     25     21     25     32
D6V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               25
  CLUS_2              3               21
  CLUS_3              3               25
  CLUS_4              1               32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        0      2      3
  ARID1A WILD-TYPE     15     54     25
D6V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0               15
  CLUS_2              2               54
  CLUS_3              3               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ARID1A MUTATED        1      1      2      1      0
  ARID1A WILD-TYPE     29     14     28     13     10
D6V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               29
  CLUS_2              1               14
  CLUS_3              2               28
  CLUS_4              1               13
  CLUS_5              0               10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ARID1A MUTATED        3      2      1      4      1
  ARID1A WILD-TYPE     55     35     28     30     12
D6V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               55
  CLUS_2              2               35
  CLUS_3              1               28
  CLUS_4              4               30
  CLUS_5              1               12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ARID1A MUTATED        1      2      1      3      0      2      1      0
  ARID1A WILD-TYPE     25     18     27     24     14     13     19      4
                  vv
clus               CLUS_9
  ARID1A MUTATED        1
  ARID1A WILD-TYPE     16
D6V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               25
  CLUS_2              2               18
  CLUS_3              1               27
  CLUS_4              3               24
  CLUS_5              0               14
  CLUS_6              2               13
  CLUS_7              1               19
  CLUS_8              0                4
  CLUS_9              1               16
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        0     10      1
  ARID1A WILD-TYPE     59     65     33
D6V9, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0               59
  CLUS_2             10               65
  CLUS_3              1               33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        0      4      1      6
  ARID1A WILD-TYPE     19     66     43     29
D6V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0               19
  CLUS_2              4               66
  CLUS_3              1               43
  CLUS_4              6               29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        4      1      3
  ARID1A WILD-TYPE     57     13     26
D6V11, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4               57
  CLUS_2              1               13
  CLUS_3              3               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        0      7      1
  ARID1A WILD-TYPE     14     52     30
D6V12, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0               14
  CLUS_2              7               52
  CLUS_3              1               30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = NF1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        0      2      2      1
  NF1 WILD-TYPE      5      7     10      5
D7V1, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           0             5
  CLUS_2           2             7
  CLUS_3           2            10
  CLUS_4           1             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        3      1      1
  NF1 WILD-TYPE     11     10      6
D7V2, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           3            11
  CLUS_2           1            10
  CLUS_3           1             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED       15      5      2
  NF1 WILD-TYPE     53     63     34
D7V3, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1          15            53
  CLUS_2           5            63
  CLUS_3           2            34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        0      6      7      5
  NF1 WILD-TYPE     26     18     21     28
D7V4, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           0            26
  CLUS_2           6            18
  CLUS_3           7            21
  CLUS_4           5            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        2      8      3
  NF1 WILD-TYPE     13     48     25
D7V5, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            13
  CLUS_2           8            48
  CLUS_3           3            25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NF1 MUTATED        3      1      5      1      3
  NF1 WILD-TYPE     27     14     25     13      7
D7V6, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           3            27
  CLUS_2           1            14
  CLUS_3           5            25
  CLUS_4           1            13
  CLUS_5           3             7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NF1 MUTATED       11      2      2      4      2
  NF1 WILD-TYPE     47     35     27     30     11
D7V7, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1          11            47
  CLUS_2           2            35
  CLUS_3           2            27
  CLUS_4           4            30
  CLUS_5           2            11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  NF1 MUTATED        4      1      4      5      0      1      2      0      4
  NF1 WILD-TYPE     22     19     24     22     14     14     18      4     13
D7V8, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            22
  CLUS_2           1            19
  CLUS_3           4            24
  CLUS_4           5            22
  CLUS_5           0            14
  CLUS_6           1            14
  CLUS_7           2            18
  CLUS_8           0             4
  CLUS_9           4            13
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        4     11      7
  NF1 WILD-TYPE     55     64     27
D7V9, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            55
  CLUS_2          11            64
  CLUS_3           7            27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        2      9      5      6
  NF1 WILD-TYPE     17     61     39     29
D7V10, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            17
  CLUS_2           9            61
  CLUS_3           5            39
  CLUS_4           6            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        6      3      7
  NF1 WILD-TYPE     55     11     22
D7V11, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           6            55
  CLUS_2           3            11
  CLUS_3           7            22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        0     12      4
  NF1 WILD-TYPE     14     47     27
D7V12, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           0            14
  CLUS_2          12            47
  CLUS_3           4            27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = U2AF1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  U2AF1 MUTATED        1      0      1      0
  U2AF1 WILD-TYPE      4      9     11      6
D8V1, multiclass
[1] "Remove cluster labels:" "U2AF1 MUTATED"         
clus
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              2              30 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-35-3615 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-35-4122      TCGA-35-4123      TCGA-44-2655      TCGA-44-2656 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-44-2657      TCGA-44-2659      TCGA-44-2661      TCGA-44-2662 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-44-2665      TCGA-44-2666      TCGA-44-2668      TCGA-44-3398 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-3919      TCGA-44-4112      TCGA-55-1592 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-55-1594      TCGA-55-1596      TCGA-64-1676      TCGA-64-1677 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-64-1678      TCGA-67-3770      TCGA-67-3771      TCGA-67-3772 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-67-3773      TCGA-67-3774 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  U2AF1 MUTATED        1      0      1
  U2AF1 WILD-TYPE     13     11      6
D8V2, multiclass
[1] "Remove cluster labels:" "U2AF1 MUTATED"         
clus
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              2              30 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-35-3615 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-35-4122      TCGA-35-4123      TCGA-44-2655      TCGA-44-2656 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-44-2657      TCGA-44-2659      TCGA-44-2661      TCGA-44-2662 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-44-2665      TCGA-44-2666      TCGA-44-2668      TCGA-44-3398 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-3919      TCGA-44-4112      TCGA-55-1592 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-55-1594      TCGA-55-1596      TCGA-64-1676      TCGA-64-1677 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-64-1678      TCGA-67-3770      TCGA-67-3771      TCGA-67-3772 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-67-3773      TCGA-67-3774 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  U2AF1 MUTATED        2      3      1
  U2AF1 WILD-TYPE     66     65     35
D8V3, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             2              66
  CLUS_2             3              65
  CLUS_3             1              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  U2AF1 MUTATED        0      0      0      3
  U2AF1 WILD-TYPE     26     24     28     30
D8V4, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             0              26
  CLUS_2             0              24
  CLUS_3             0              28
  CLUS_4             3              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  U2AF1 MUTATED        2      2      0
  U2AF1 WILD-TYPE     13     54     28
D8V5, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             2              13
  CLUS_2             2              54
  CLUS_3             0              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  U2AF1 MUTATED        2      0      1      0      1
  U2AF1 WILD-TYPE     28     15     29     14      9
D8V6, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             2              28
  CLUS_2             0              15
  CLUS_3             1              29
  CLUS_4             0              14
  CLUS_5             1               9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  U2AF1 MUTATED        3      1      1      0      1
  U2AF1 WILD-TYPE     55     36     28     34     12
D8V7, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             3              55
  CLUS_2             1              36
  CLUS_3             1              28
  CLUS_4             0              34
  CLUS_5             1              12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  U2AF1 MUTATED        3      1      0      1      0      0      0      0
  U2AF1 WILD-TYPE     23     19     28     26     14     15     20      4
                 vv
clus              CLUS_9
  U2AF1 MUTATED        1
  U2AF1 WILD-TYPE     16
D8V8, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             3              23
  CLUS_2             1              19
  CLUS_3             0              28
  CLUS_4             1              26
  CLUS_5             0              14
  CLUS_6             0              15
  CLUS_7             0              20
  CLUS_8             0               4
  CLUS_9             1              16
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  U2AF1 MUTATED        5      1      0
  U2AF1 WILD-TYPE     54     74     34
D8V9, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             5              54
  CLUS_2             1              74
  CLUS_3             0              34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  U2AF1 MUTATED        1      1      3      1
  U2AF1 WILD-TYPE     18     69     41     34
D8V10, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             1              18
  CLUS_2             1              69
  CLUS_3             3              41
  CLUS_4             1              34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  U2AF1 MUTATED        3      0      0
  U2AF1 WILD-TYPE     58     14     29
D8V11, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             3              58
  CLUS_2             0              14
  CLUS_3             0              29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  U2AF1 MUTATED        0      2      1
  U2AF1 WILD-TYPE     14     57     30
D8V12, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             0              14
  CLUS_2             2              57
  CLUS_3             1              30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = EGFR MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EGFR MUTATED        0      0      3      0
  EGFR WILD-TYPE      5      9      9      6
D9V1, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0              5
  CLUS_2            0              9
  CLUS_3            3              9
  CLUS_4            0              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        3      0      0
  EGFR WILD-TYPE     11     11      7
D9V2, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            3             11
  CLUS_2            0             11
  CLUS_3            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED       13      8      2
  EGFR WILD-TYPE     55     60     34
D9V3, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           13             55
  CLUS_2            8             60
  CLUS_3            2             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EGFR MUTATED        5      2      3      3
  EGFR WILD-TYPE     21     22     25     30
D9V4, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            5             21
  CLUS_2            2             22
  CLUS_3            3             25
  CLUS_4            3             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        1     12      3
  EGFR WILD-TYPE     14     44     25
D9V5, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            1             14
  CLUS_2           12             44
  CLUS_3            3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EGFR MUTATED        9      2      3      1      1
  EGFR WILD-TYPE     21     13     27     13      9
D9V6, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            9             21
  CLUS_2            2             13
  CLUS_3            3             27
  CLUS_4            1             13
  CLUS_5            1              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EGFR MUTATED       10      8      0      2      3
  EGFR WILD-TYPE     48     29     29     32     10
D9V7, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           10             48
  CLUS_2            8             29
  CLUS_3            0             29
  CLUS_4            2             32
  CLUS_5            3             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  EGFR MUTATED        2      7      3      6      1      0      0      0      4
  EGFR WILD-TYPE     24     13     25     21     13     15     20      4     13
D9V8, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            2             24
  CLUS_2            7             13
  CLUS_3            3             25
  CLUS_4            6             21
  CLUS_5            1             13
  CLUS_6            0             15
  CLUS_7            0             20
  CLUS_8            0              4
  CLUS_9            4             13
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        7     10      6
  EGFR WILD-TYPE     52     65     28
D9V9, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            7             52
  CLUS_2           10             65
  CLUS_3            6             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EGFR MUTATED        2     11      6      4
  EGFR WILD-TYPE     17     59     38     31
D9V10, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            2             17
  CLUS_2           11             59
  CLUS_3            6             38
  CLUS_4            4             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED       10      0      3
  EGFR WILD-TYPE     51     14     26
D9V11, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           10             51
  CLUS_2            0             14
  CLUS_3            3             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        2      4      7
  EGFR WILD-TYPE     12     55     24
D9V12, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            2             12
  CLUS_2            4             55
  CLUS_3            7             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = SETD2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SETD2 MUTATED        0      0      1      0
  SETD2 WILD-TYPE      5      9     11      6
D10V1, multiclass
[1] "Remove cluster labels:" "SETD2 MUTATED"         
clus
  SETD2 MUTATED SETD2 WILD-TYPE 
              1              31 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-35-3615 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-35-4122      TCGA-35-4123      TCGA-44-2655      TCGA-44-2656 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-44-2657      TCGA-44-2659      TCGA-44-2661      TCGA-44-2662 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-44-2665      TCGA-44-2668      TCGA-44-3398      TCGA-44-3918 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-44-3919      TCGA-44-4112      TCGA-55-1592      TCGA-55-1594 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-55-1595      TCGA-55-1596      TCGA-64-1676      TCGA-64-1677 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-64-1678      TCGA-64-1680      TCGA-67-3770      TCGA-67-3771 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-67-3772      TCGA-67-3773      TCGA-67-3774 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED        1      0      0
  SETD2 WILD-TYPE     13     11      7
D10V2, multiclass
[1] "Remove cluster labels:" "SETD2 MUTATED"         
clus
  SETD2 MUTATED SETD2 WILD-TYPE 
              1              31 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-35-3615 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-35-4122      TCGA-35-4123      TCGA-44-2655      TCGA-44-2656 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-44-2657      TCGA-44-2659      TCGA-44-2661      TCGA-44-2662 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-44-2665      TCGA-44-2668      TCGA-44-3398      TCGA-44-3918 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-44-3919      TCGA-44-4112      TCGA-55-1592      TCGA-55-1594 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-55-1595      TCGA-55-1596      TCGA-64-1676      TCGA-64-1677 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-64-1678      TCGA-64-1680      TCGA-67-3770      TCGA-67-3771 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-67-3772      TCGA-67-3773      TCGA-67-3774 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED        4      8      3
  SETD2 WILD-TYPE     64     60     33
D10V3, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             4              64
  CLUS_2             8              60
  CLUS_3             3              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SETD2 MUTATED        3      1      6      4
  SETD2 WILD-TYPE     23     23     22     29
D10V4, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             3              23
  CLUS_2             1              23
  CLUS_3             6              22
  CLUS_4             4              29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED        2      4      2
  SETD2 WILD-TYPE     13     52     26
D10V5, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             2              13
  CLUS_2             4              52
  CLUS_3             2              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SETD2 MUTATED        2      1      2      0      3
  SETD2 WILD-TYPE     28     14     28     14      7
D10V6, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             2              28
  CLUS_2             1              14
  CLUS_3             2              28
  CLUS_4             0              14
  CLUS_5             3               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SETD2 MUTATED        6      5      1      2      1
  SETD2 WILD-TYPE     52     32     28     32     12
D10V7, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             6              52
  CLUS_2             5              32
  CLUS_3             1              28
  CLUS_4             2              32
  CLUS_5             1              12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SETD2 MUTATED        4      4      3      1      1      0      1      0
  SETD2 WILD-TYPE     22     16     25     26     13     15     19      4
                 vv
clus              CLUS_9
  SETD2 MUTATED        1
  SETD2 WILD-TYPE     16
D10V8, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             4              22
  CLUS_2             4              16
  CLUS_3             3              25
  CLUS_4             1              26
  CLUS_5             1              13
  CLUS_6             0              15
  CLUS_7             1              19
  CLUS_8             0               4
  CLUS_9             1              16
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED        8      4      2
  SETD2 WILD-TYPE     51     71     32
D10V9, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             8              51
  CLUS_2             4              71
  CLUS_3             2              32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SETD2 MUTATED        1      6      5      2
  SETD2 WILD-TYPE     18     64     39     33
D10V10, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             1              18
  CLUS_2             6              64
  CLUS_3             5              39
  CLUS_4             2              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED       10      0      3
  SETD2 WILD-TYPE     51     14     26
D10V11, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1            10              51
  CLUS_2             0              14
  CLUS_3             3              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED        2      6      5
  SETD2 WILD-TYPE     12     53     26
D10V12, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             2              12
  CLUS_2             6              53
  CLUS_3             5              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = CDKN2A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDKN2A MUTATED        0      0      0      2
  CDKN2A WILD-TYPE      5      9     12      4
D11V1, multiclass
[1] "Remove cluster labels:" "CDKN2A MUTATED"        
clus
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               2               30 
      TCGA-05-4244       TCGA-05-4249       TCGA-05-4250       TCGA-35-3615 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-35-4122       TCGA-35-4123       TCGA-44-2655       TCGA-44-2656 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-44-2657       TCGA-44-2659       TCGA-44-2661       TCGA-44-2662 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-44-2665       TCGA-44-2666       TCGA-44-2668       TCGA-44-3398 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-44-3918       TCGA-44-3919       TCGA-44-4112       TCGA-55-1592 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-55-1595       TCGA-55-1596       TCGA-64-1676       TCGA-64-1677 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-64-1678       TCGA-64-1680       TCGA-67-3770       TCGA-67-3772 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-67-3773       TCGA-67-3774 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        0      0      2
  CDKN2A WILD-TYPE     14     11      5
D11V2, multiclass
[1] "Remove cluster labels:" "CDKN2A MUTATED"        
clus
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               2               30 
      TCGA-05-4244       TCGA-05-4249       TCGA-05-4250       TCGA-35-3615 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-35-4122       TCGA-35-4123       TCGA-44-2655       TCGA-44-2656 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-44-2657       TCGA-44-2659       TCGA-44-2661       TCGA-44-2662 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-44-2665       TCGA-44-2666       TCGA-44-2668       TCGA-44-3398 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-44-3918       TCGA-44-3919       TCGA-44-4112       TCGA-55-1592 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-55-1595       TCGA-55-1596       TCGA-64-1676       TCGA-64-1677 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-64-1678       TCGA-64-1680       TCGA-67-3770       TCGA-67-3772 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-67-3773       TCGA-67-3774 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        3      3      2
  CDKN2A WILD-TYPE     65     65     34
D11V3, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              3               65
  CLUS_2              3               65
  CLUS_3              2               34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDKN2A MUTATED        1      0      1      1
  CDKN2A WILD-TYPE     25     24     27     32
D11V4, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              1               25
  CLUS_2              0               24
  CLUS_3              1               27
  CLUS_4              1               32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        1      3      2
  CDKN2A WILD-TYPE     14     53     26
D11V5, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              1               14
  CLUS_2              3               53
  CLUS_3              2               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDKN2A MUTATED        2      1      1      1      1
  CDKN2A WILD-TYPE     28     14     29     13      9
D11V6, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              2               28
  CLUS_2              1               14
  CLUS_3              1               29
  CLUS_4              1               13
  CLUS_5              1                9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDKN2A MUTATED        3      0      2      2      1
  CDKN2A WILD-TYPE     55     37     27     32     12
D11V7, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              3               55
  CLUS_2              0               37
  CLUS_3              2               27
  CLUS_4              2               32
  CLUS_5              1               12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CDKN2A MUTATED        2      0      2      1      0      1      0      1
  CDKN2A WILD-TYPE     24     20     26     26     14     14     20      3
                  vv
clus               CLUS_9
  CDKN2A MUTATED        1
  CDKN2A WILD-TYPE     16
D11V8, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              2               24
  CLUS_2              0               20
  CLUS_3              2               26
  CLUS_4              1               26
  CLUS_5              0               14
  CLUS_6              1               14
  CLUS_7              0               20
  CLUS_8              1                3
  CLUS_9              1               16
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        3      4      1
  CDKN2A WILD-TYPE     56     71     33
D11V9, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              3               56
  CLUS_2              4               71
  CLUS_3              1               33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDKN2A MUTATED        0      1      5      2
  CDKN2A WILD-TYPE     19     69     39     33
D11V10, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              0               19
  CLUS_2              1               69
  CLUS_3              5               39
  CLUS_4              2               33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        2      0      1
  CDKN2A WILD-TYPE     59     14     28
D11V11, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              2               59
  CLUS_2              0               14
  CLUS_3              1               28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        2      0      1
  CDKN2A WILD-TYPE     12     59     30
D11V12, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              2               12
  CLUS_2              0               59
  CLUS_3              1               30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MET MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MET MUTATED        0      0      1      0
  MET WILD-TYPE      5      9     11      6
D12V1, multiclass
[1] "Remove cluster labels:" "MET MUTATED"           
clus
  MET MUTATED MET WILD-TYPE 
            1            31 
   TCGA-05-4244    TCGA-05-4249    TCGA-05-4250    TCGA-35-3615    TCGA-35-4122 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-35-4123    TCGA-44-2655    TCGA-44-2656    TCGA-44-2659    TCGA-44-2661 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-44-2662    TCGA-44-2665    TCGA-44-2666    TCGA-44-2668    TCGA-44-3398 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-44-3918    TCGA-44-3919    TCGA-44-4112    TCGA-55-1592    TCGA-55-1594 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-55-1595    TCGA-55-1596    TCGA-64-1676    TCGA-64-1677    TCGA-64-1678 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-64-1680    TCGA-67-3770    TCGA-67-3771    TCGA-67-3772    TCGA-67-3773 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-67-3774 
"MET WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MET MUTATED        1      0      0
  MET WILD-TYPE     13     11      7
D12V2, multiclass
[1] "Remove cluster labels:" "MET MUTATED"           
clus
  MET MUTATED MET WILD-TYPE 
            1            31 
   TCGA-05-4244    TCGA-05-4249    TCGA-05-4250    TCGA-35-3615    TCGA-35-4122 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-35-4123    TCGA-44-2655    TCGA-44-2656    TCGA-44-2659    TCGA-44-2661 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-44-2662    TCGA-44-2665    TCGA-44-2666    TCGA-44-2668    TCGA-44-3398 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-44-3918    TCGA-44-3919    TCGA-44-4112    TCGA-55-1592    TCGA-55-1594 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-55-1595    TCGA-55-1596    TCGA-64-1676    TCGA-64-1677    TCGA-64-1678 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-64-1680    TCGA-67-3770    TCGA-67-3771    TCGA-67-3772    TCGA-67-3773 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-67-3774 
"MET WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MET MUTATED        4      7      0
  MET WILD-TYPE     64     61     36
D12V3, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           4            64
  CLUS_2           7            61
  CLUS_3           0            36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MET MUTATED        0      0      5      3
  MET WILD-TYPE     26     24     23     30
D12V4, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           0            26
  CLUS_2           0            24
  CLUS_3           5            23
  CLUS_4           3            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MET MUTATED        1      7      2
  MET WILD-TYPE     14     49     26
D12V5, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           1            14
  CLUS_2           7            49
  CLUS_3           2            26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MET MUTATED        1      1      5      2      1
  MET WILD-TYPE     29     14     25     12      9
D12V6, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           1            29
  CLUS_2           1            14
  CLUS_3           5            25
  CLUS_4           2            12
  CLUS_5           1             9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MET MUTATED        5      2      3      1      0
  MET WILD-TYPE     53     35     26     33     13
D12V7, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           5            53
  CLUS_2           2            35
  CLUS_3           3            26
  CLUS_4           1            33
  CLUS_5           0            13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  MET MUTATED        0      1      5      0      1      0      2      1      1
  MET WILD-TYPE     26     19     23     27     13     15     18      3     16
D12V8, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           0            26
  CLUS_2           1            19
  CLUS_3           5            23
  CLUS_4           0            27
  CLUS_5           1            13
  CLUS_6           0            15
  CLUS_7           2            18
  CLUS_8           1             3
  CLUS_9           1            16
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MET MUTATED        4      4      3
  MET WILD-TYPE     55     71     31
D12V9, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           4            55
  CLUS_2           4            71
  CLUS_3           3            31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MET MUTATED        0      5      6      0
  MET WILD-TYPE     19     65     38     35
D12V10, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           0            19
  CLUS_2           5            65
  CLUS_3           6            38
  CLUS_4           0            35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MET MUTATED        6      0      2
  MET WILD-TYPE     55     14     27
D12V11, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           6            55
  CLUS_2           0            14
  CLUS_3           2            27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MET MUTATED        1      3      4
  MET WILD-TYPE     13     56     27
D12V12, multiclass
        clus
vv       MET MUTATED MET WILD-TYPE
  CLUS_1           1            13
  CLUS_2           3            56
  CLUS_3           4            27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = ERBB2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ERBB2 MUTATED        1      1      0      0
  ERBB2 WILD-TYPE      4      8     12      6
D13V1, multiclass
[1] "Remove cluster labels:" "ERBB2 MUTATED"         
clus
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              2              30 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-35-3615 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-35-4122      TCGA-35-4123      TCGA-44-2655      TCGA-44-2657 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-44-2659      TCGA-44-2661      TCGA-44-2662      TCGA-44-2665 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-44-2666      TCGA-44-2668      TCGA-44-3398      TCGA-44-3918 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-44-4112      TCGA-55-1592      TCGA-55-1594      TCGA-55-1595 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-55-1596      TCGA-64-1676      TCGA-64-1677      TCGA-64-1678 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-64-1680      TCGA-67-3770      TCGA-67-3771      TCGA-67-3772 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-67-3773      TCGA-67-3774 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERBB2 MUTATED        1      1      0
  ERBB2 WILD-TYPE     13     10      7
D13V2, multiclass
[1] "Remove cluster labels:" "ERBB2 MUTATED"         
clus
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              2              30 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-35-3615 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-35-4122      TCGA-35-4123      TCGA-44-2655      TCGA-44-2657 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-44-2659      TCGA-44-2661      TCGA-44-2662      TCGA-44-2665 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-44-2666      TCGA-44-2668      TCGA-44-3398      TCGA-44-3918 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-44-4112      TCGA-55-1592      TCGA-55-1594      TCGA-55-1595 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-55-1596      TCGA-64-1676      TCGA-64-1677      TCGA-64-1678 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-64-1680      TCGA-67-3770      TCGA-67-3771      TCGA-67-3772 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-67-3773      TCGA-67-3774 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERBB2 MUTATED        5      3      0
  ERBB2 WILD-TYPE     63     65     36
D13V3, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             5              63
  CLUS_2             3              65
  CLUS_3             0              36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ERBB2 MUTATED        2      1      1      1
  ERBB2 WILD-TYPE     24     23     27     32
D13V4, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             2              24
  CLUS_2             1              23
  CLUS_3             1              27
  CLUS_4             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERBB2 MUTATED        1      3      1
  ERBB2 WILD-TYPE     14     53     27
D13V5, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             3              53
  CLUS_3             1              27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ERBB2 MUTATED        3      1      1      0      0
  ERBB2 WILD-TYPE     27     14     29     14     10
D13V6, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             3              27
  CLUS_2             1              14
  CLUS_3             1              29
  CLUS_4             0              14
  CLUS_5             0              10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ERBB2 MUTATED        5      2      0      0      1
  ERBB2 WILD-TYPE     53     35     29     34     12
D13V7, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             5              53
  CLUS_2             2              35
  CLUS_3             0              29
  CLUS_4             0              34
  CLUS_5             1              12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ERBB2 MUTATED        4      1      1      1      1      0      0      0
  ERBB2 WILD-TYPE     22     19     27     26     13     15     20      4
                 vv
clus              CLUS_9
  ERBB2 MUTATED        0
  ERBB2 WILD-TYPE     17
D13V8, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             4              22
  CLUS_2             1              19
  CLUS_3             1              27
  CLUS_4             1              26
  CLUS_5             1              13
  CLUS_6             0              15
  CLUS_7             0              20
  CLUS_8             0               4
  CLUS_9             0              17
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERBB2 MUTATED        4      3      1
  ERBB2 WILD-TYPE     55     72     33
D13V9, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             4              55
  CLUS_2             3              72
  CLUS_3             1              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ERBB2 MUTATED        4      3      1      0
  ERBB2 WILD-TYPE     15     67     43     35
D13V10, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             4              15
  CLUS_2             3              67
  CLUS_3             1              43
  CLUS_4             0              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERBB2 MUTATED        2      1      1
  ERBB2 WILD-TYPE     59     13     28
D13V11, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             2              59
  CLUS_2             1              13
  CLUS_3             1              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERBB2 MUTATED        1      2      1
  ERBB2 WILD-TYPE     13     57     30
D13V12, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             1              13
  CLUS_2             2              57
  CLUS_3             1              30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = CHRND MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CHRND MUTATED        0      1      0      0
  CHRND WILD-TYPE      5      8     12      6
D14V1, multiclass
[1] "Remove cluster labels:" "CHRND MUTATED"         
clus
  CHRND MUTATED CHRND WILD-TYPE 
              1              31 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-35-3615 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-35-4122      TCGA-35-4123      TCGA-44-2655      TCGA-44-2656 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-44-2657      TCGA-44-2659      TCGA-44-2661      TCGA-44-2662 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-44-2665      TCGA-44-2666      TCGA-44-2668      TCGA-44-3398 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-44-3919      TCGA-44-4112      TCGA-55-1592      TCGA-55-1594 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-55-1595      TCGA-55-1596      TCGA-64-1676      TCGA-64-1677 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-64-1678      TCGA-64-1680      TCGA-67-3770      TCGA-67-3771 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-67-3772      TCGA-67-3773      TCGA-67-3774 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CHRND MUTATED        0      1      0
  CHRND WILD-TYPE     14     10      7
D14V2, multiclass
[1] "Remove cluster labels:" "CHRND MUTATED"         
clus
  CHRND MUTATED CHRND WILD-TYPE 
              1              31 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-35-3615 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-35-4122      TCGA-35-4123      TCGA-44-2655      TCGA-44-2656 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-44-2657      TCGA-44-2659      TCGA-44-2661      TCGA-44-2662 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-44-2665      TCGA-44-2666      TCGA-44-2668      TCGA-44-3398 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-44-3919      TCGA-44-4112      TCGA-55-1592      TCGA-55-1594 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-55-1595      TCGA-55-1596      TCGA-64-1676      TCGA-64-1677 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-64-1678      TCGA-64-1680      TCGA-67-3770      TCGA-67-3771 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-67-3772      TCGA-67-3773      TCGA-67-3774 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CHRND MUTATED        4      2      3
  CHRND WILD-TYPE     64     66     33
D14V3, multiclass
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  CLUS_1             4              64
  CLUS_2             2              66
  CLUS_3             3              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CHRND MUTATED        1      0      4      1
  CHRND WILD-TYPE     25     24     24     32
D14V4, multiclass
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  CLUS_1             1              25
  CLUS_2             0              24
  CLUS_3             4              24
  CLUS_4             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CHRND MUTATED        0      3      3
  CHRND WILD-TYPE     15     53     25
D14V5, multiclass
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  CLUS_1             0              15
  CLUS_2             3              53
  CLUS_3             3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CHRND MUTATED        0      3      2      1      0
  CHRND WILD-TYPE     30     12     28     13     10
D14V6, multiclass
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  CLUS_1             0              30
  CLUS_2             3              12
  CLUS_3             2              28
  CLUS_4             1              13
  CLUS_5             0              10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CHRND MUTATED        4      0      1      4      0
  CHRND WILD-TYPE     54     37     28     30     13
D14V7, multiclass
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  CLUS_1             4              54
  CLUS_2             0              37
  CLUS_3             1              28
  CLUS_4             4              30
  CLUS_5             0              13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CHRND MUTATED        1      0      1      0      1      3      1      0
  CHRND WILD-TYPE     25     20     27     27     13     12     19      4
                 vv
clus              CLUS_9
  CHRND MUTATED        2
  CHRND WILD-TYPE     15
D14V8, multiclass
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  CLUS_1             1              25
  CLUS_2             0              20
  CLUS_3             1              27
  CLUS_4             0              27
  CLUS_5             1              13
  CLUS_6             3              12
  CLUS_7             1              19
  CLUS_8             0               4
  CLUS_9             2              15
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CHRND MUTATED        1      8      0
  CHRND WILD-TYPE     58     67     34
D14V9, multiclass
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  CLUS_1             1              58
  CLUS_2             8              67
  CLUS_3             0              34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CHRND MUTATED        0      4      1      4
  CHRND WILD-TYPE     19     66     43     31
D14V10, multiclass
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  CLUS_1             0              19
  CLUS_2             4              66
  CLUS_3             1              43
  CLUS_4             4              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CHRND MUTATED        2      1      2
  CHRND WILD-TYPE     59     13     27
D14V11, multiclass
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  CLUS_1             2              59
  CLUS_2             1              13
  CLUS_3             2              27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CHRND MUTATED        1      4      0
  CHRND WILD-TYPE     13     55     31
D14V12, multiclass
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  CLUS_1             1              13
  CLUS_2             4              55
  CLUS_3             0              31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = BRAF MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRAF MUTATED        0      3      1      0
  BRAF WILD-TYPE      5      6     11      6
D15V1, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            0              5
  CLUS_2            3              6
  CLUS_3            1             11
  CLUS_4            0              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        1      3      0
  BRAF WILD-TYPE     13      8      7
D15V2, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             13
  CLUS_2            3              8
  CLUS_3            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        6      7      3
  BRAF WILD-TYPE     62     61     33
D15V3, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            6             62
  CLUS_2            7             61
  CLUS_3            3             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRAF MUTATED        4      1      4      3
  BRAF WILD-TYPE     22     23     24     30
D15V4, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            4             22
  CLUS_2            1             23
  CLUS_3            4             24
  CLUS_4            3             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        1      3      3
  BRAF WILD-TYPE     14     53     25
D15V5, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             14
  CLUS_2            3             53
  CLUS_3            3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BRAF MUTATED        3      0      3      1      0
  BRAF WILD-TYPE     27     15     27     13     10
D15V6, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3             27
  CLUS_2            0             15
  CLUS_3            3             27
  CLUS_4            1             13
  CLUS_5            0             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BRAF MUTATED        7      4      1      3      1
  BRAF WILD-TYPE     51     33     28     31     12
D15V7, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            7             51
  CLUS_2            4             33
  CLUS_3            1             28
  CLUS_4            3             31
  CLUS_5            1             12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  BRAF MUTATED        2      2      5      3      1      1      0      0      2
  BRAF WILD-TYPE     24     18     23     24     13     14     20      4     15
D15V8, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2             24
  CLUS_2            2             18
  CLUS_3            5             23
  CLUS_4            3             24
  CLUS_5            1             13
  CLUS_6            1             14
  CLUS_7            0             20
  CLUS_8            0              4
  CLUS_9            2             15
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        5      5      6
  BRAF WILD-TYPE     54     70     28
D15V9, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            5             54
  CLUS_2            5             70
  CLUS_3            6             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRAF MUTATED        2      8      4      2
  BRAF WILD-TYPE     17     62     40     33
D15V10, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2             17
  CLUS_2            8             62
  CLUS_3            4             40
  CLUS_4            2             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        5      1      4
  BRAF WILD-TYPE     56     13     25
D15V11, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            5             56
  CLUS_2            1             13
  CLUS_3            4             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        2      3      5
  BRAF WILD-TYPE     12     56     26
D15V12, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2             12
  CLUS_2            3             56
  CLUS_3            5             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = GEN1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GEN1 MUTATED        0      0      0      0
  GEN1 WILD-TYPE      5      9     12      6
D16V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GEN1 MUTATED        0      0      0
  GEN1 WILD-TYPE     14     11      7
D16V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GEN1 MUTATED        2      1      1
  GEN1 WILD-TYPE     66     67     35
D16V3, multiclass
        clus
vv       GEN1 MUTATED GEN1 WILD-TYPE
  CLUS_1            2             66
  CLUS_2            1             67
  CLUS_3            1             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GEN1 MUTATED        0      0      2      1
  GEN1 WILD-TYPE     26     24     26     32
D16V4, multiclass
        clus
vv       GEN1 MUTATED GEN1 WILD-TYPE
  CLUS_1            0             26
  CLUS_2            0             24
  CLUS_3            2             26
  CLUS_4            1             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GEN1 MUTATED        0      2      0
  GEN1 WILD-TYPE     15     54     28
D16V5, multiclass
[1] "Remove cluster labels:" "GEN1 MUTATED"          
clus
  GEN1 MUTATED GEN1 WILD-TYPE 
             2             97 
    TCGA-05-4249     TCGA-05-4384     TCGA-05-4398     TCGA-05-4402 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-05-4405     TCGA-05-4410     TCGA-05-4417     TCGA-05-4418 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-05-4420     TCGA-05-4422     TCGA-05-4426     TCGA-05-4430 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-05-5420     TCGA-05-5423     TCGA-05-5429     TCGA-05-5715 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-35-3615     TCGA-38-4626     TCGA-38-4627     TCGA-38-6178 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-44-2656     TCGA-44-2657     TCGA-44-2661     TCGA-44-2665 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3919     TCGA-44-4112     TCGA-44-5645 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-44-6145     TCGA-44-6146     TCGA-44-6147     TCGA-44-6774 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-6776     TCGA-44-6777     TCGA-44-6779 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4487     TCGA-49-4488     TCGA-49-4494 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-49-4501     TCGA-49-4505     TCGA-49-4506     TCGA-49-4507 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-49-4510     TCGA-49-4512     TCGA-49-4514     TCGA-49-6742 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-49-6744     TCGA-49-6745     TCGA-49-6767     TCGA-50-5044 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-50-5049     TCGA-50-5051     TCGA-50-5068     TCGA-50-5072 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-50-5931     TCGA-50-5932     TCGA-50-5933     TCGA-50-5936 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-50-5939     TCGA-50-5942     TCGA-50-5944     TCGA-50-6593 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-50-6595     TCGA-50-6597     TCGA-55-1592     TCGA-55-1594 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-55-1596     TCGA-55-6543     TCGA-55-6712     TCGA-64-1676 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1678     TCGA-64-1680     TCGA-64-5774 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-64-5778     TCGA-64-5781     TCGA-67-3771     TCGA-67-6215 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-67-6216     TCGA-67-6217     TCGA-71-6725     TCGA-73-4658 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4675     TCGA-73-4676     TCGA-75-5122 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-75-6203     TCGA-75-6205     TCGA-75-6207     TCGA-75-6211 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-75-6212     TCGA-86-6562     TCGA-91-6828     TCGA-91-6829 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-91-6835 
"GEN1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GEN1 MUTATED        0      1      1      0      0
  GEN1 WILD-TYPE     30     14     29     14     10
D16V6, multiclass
[1] "Remove cluster labels:" "GEN1 MUTATED"          
clus
  GEN1 MUTATED GEN1 WILD-TYPE 
             2             97 
    TCGA-05-4249     TCGA-05-4384     TCGA-05-4398     TCGA-05-4402 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-05-4405     TCGA-05-4410     TCGA-05-4417     TCGA-05-4418 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-05-4420     TCGA-05-4422     TCGA-05-4426     TCGA-05-4430 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-05-5420     TCGA-05-5423     TCGA-05-5429     TCGA-05-5715 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-35-3615     TCGA-38-4626     TCGA-38-4627     TCGA-38-6178 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-44-2656     TCGA-44-2657     TCGA-44-2661     TCGA-44-2665 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3919     TCGA-44-4112     TCGA-44-5645 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-44-6145     TCGA-44-6146     TCGA-44-6147     TCGA-44-6774 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-6776     TCGA-44-6777     TCGA-44-6779 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4487     TCGA-49-4488     TCGA-49-4494 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-49-4501     TCGA-49-4505     TCGA-49-4506     TCGA-49-4507 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-49-4510     TCGA-49-4512     TCGA-49-4514     TCGA-49-6742 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-49-6744     TCGA-49-6745     TCGA-49-6767     TCGA-50-5044 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-50-5049     TCGA-50-5051     TCGA-50-5068     TCGA-50-5072 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-50-5931     TCGA-50-5932     TCGA-50-5933     TCGA-50-5936 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-50-5939     TCGA-50-5942     TCGA-50-5944     TCGA-50-6593 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-50-6595     TCGA-50-6597     TCGA-55-1592     TCGA-55-1594 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-55-1596     TCGA-55-6543     TCGA-55-6712     TCGA-64-1676 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1678     TCGA-64-1680     TCGA-64-5774 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-64-5778     TCGA-64-5781     TCGA-67-3771     TCGA-67-6215 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-67-6216     TCGA-67-6217     TCGA-71-6725     TCGA-73-4658 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4675     TCGA-73-4676     TCGA-75-5122 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-75-6203     TCGA-75-6205     TCGA-75-6207     TCGA-75-6211 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-75-6212     TCGA-86-6562     TCGA-91-6828     TCGA-91-6829 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-91-6835 
"GEN1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GEN1 MUTATED        3      0      0      1      0
  GEN1 WILD-TYPE     55     37     29     33     13
D16V7, multiclass
        clus
vv       GEN1 MUTATED GEN1 WILD-TYPE
  CLUS_1            3             55
  CLUS_2            0             37
  CLUS_3            0             29
  CLUS_4            1             33
  CLUS_5            0             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  GEN1 MUTATED        3      0      0      0      1      0      0      0      0
  GEN1 WILD-TYPE     23     20     28     27     13     15     20      4     17
D16V8, multiclass
        clus
vv       GEN1 MUTATED GEN1 WILD-TYPE
  CLUS_1            3             23
  CLUS_2            0             20
  CLUS_3            0             28
  CLUS_4            0             27
  CLUS_5            1             13
  CLUS_6            0             15
  CLUS_7            0             20
  CLUS_8            0              4
  CLUS_9            0             17
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GEN1 MUTATED        1      2      0
  GEN1 WILD-TYPE     58     73     34
D16V9, multiclass
        clus
vv       GEN1 MUTATED GEN1 WILD-TYPE
  CLUS_1            1             58
  CLUS_2            2             73
  CLUS_3            0             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GEN1 MUTATED        0      2      0      1
  GEN1 WILD-TYPE     19     68     44     34
D16V10, multiclass
        clus
vv       GEN1 MUTATED GEN1 WILD-TYPE
  CLUS_1            0             19
  CLUS_2            2             68
  CLUS_3            0             44
  CLUS_4            1             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GEN1 MUTATED        3      0      0
  GEN1 WILD-TYPE     58     14     29
D16V11, multiclass
        clus
vv       GEN1 MUTATED GEN1 WILD-TYPE
  CLUS_1            3             58
  CLUS_2            0             14
  CLUS_3            0             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GEN1 MUTATED        1      1      1
  GEN1 WILD-TYPE     13     58     30
D16V12, multiclass
        clus
vv       GEN1 MUTATED GEN1 WILD-TYPE
  CLUS_1            1             13
  CLUS_2            1             58
  CLUS_3            1             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = STX2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STX2 MUTATED        1      0      0      0
  STX2 WILD-TYPE      4      9     12      6
D17V1, multiclass
[1] "Remove cluster labels:" "STX2 MUTATED"          
clus
  STX2 MUTATED STX2 WILD-TYPE 
             1             31 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-35-3615 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-35-4122     TCGA-44-2655     TCGA-44-2656     TCGA-44-2657 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-44-2659     TCGA-44-2661     TCGA-44-2662     TCGA-44-2665 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-44-2666     TCGA-44-2668     TCGA-44-3398     TCGA-44-3918 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-44-3919     TCGA-44-4112     TCGA-55-1592     TCGA-55-1594 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-55-1595     TCGA-55-1596     TCGA-64-1676     TCGA-64-1677 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-64-1678     TCGA-64-1680     TCGA-67-3770     TCGA-67-3771 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-67-3772     TCGA-67-3773     TCGA-67-3774 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  STX2 MUTATED        0      1      0
  STX2 WILD-TYPE     14     10      7
D17V2, multiclass
[1] "Remove cluster labels:" "STX2 MUTATED"          
clus
  STX2 MUTATED STX2 WILD-TYPE 
             1             31 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-35-3615 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-35-4122     TCGA-44-2655     TCGA-44-2656     TCGA-44-2657 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-44-2659     TCGA-44-2661     TCGA-44-2662     TCGA-44-2665 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-44-2666     TCGA-44-2668     TCGA-44-3398     TCGA-44-3918 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-44-3919     TCGA-44-4112     TCGA-55-1592     TCGA-55-1594 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-55-1595     TCGA-55-1596     TCGA-64-1676     TCGA-64-1677 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-64-1678     TCGA-64-1680     TCGA-67-3770     TCGA-67-3771 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-67-3772     TCGA-67-3773     TCGA-67-3774 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  STX2 MUTATED        1      3      0
  STX2 WILD-TYPE     67     65     36
D17V3, multiclass
        clus
vv       STX2 MUTATED STX2 WILD-TYPE
  CLUS_1            1             67
  CLUS_2            3             65
  CLUS_3            0             36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STX2 MUTATED        0      0      1      2
  STX2 WILD-TYPE     26     24     27     31
D17V4, multiclass
        clus
vv       STX2 MUTATED STX2 WILD-TYPE
  CLUS_1            0             26
  CLUS_2            0             24
  CLUS_3            1             27
  CLUS_4            2             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  STX2 MUTATED        0      1      1
  STX2 WILD-TYPE     15     55     27
D17V5, multiclass
[1] "Remove cluster labels:" "STX2 MUTATED"          
clus
  STX2 MUTATED STX2 WILD-TYPE 
             2             97 
    TCGA-05-4249     TCGA-05-4384     TCGA-05-4398     TCGA-05-4402 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-05-4405     TCGA-05-4410     TCGA-05-4417     TCGA-05-4418 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-05-4420     TCGA-05-4422     TCGA-05-4426     TCGA-05-4430 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-05-5420     TCGA-05-5423     TCGA-05-5429     TCGA-05-5715 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-35-3615     TCGA-38-4626     TCGA-38-4627     TCGA-38-6178 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-44-2656     TCGA-44-2657     TCGA-44-2661     TCGA-44-2665 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3919     TCGA-44-4112     TCGA-44-5645 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-44-6145     TCGA-44-6146     TCGA-44-6147     TCGA-44-6775 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-44-6776     TCGA-44-6777     TCGA-44-6779     TCGA-49-4486 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-49-4487     TCGA-49-4488     TCGA-49-4494     TCGA-49-4501 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-49-4505     TCGA-49-4506     TCGA-49-4507     TCGA-49-4510 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-49-4512     TCGA-49-4514     TCGA-49-6742     TCGA-49-6744 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-49-6745     TCGA-49-6767     TCGA-50-5044     TCGA-50-5049 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-50-5051     TCGA-50-5068     TCGA-50-5072     TCGA-50-5931 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-50-5932     TCGA-50-5933     TCGA-50-5936     TCGA-50-5939 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-50-5941     TCGA-50-5942     TCGA-50-5944     TCGA-50-6593 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-50-6595     TCGA-50-6597     TCGA-55-1592     TCGA-55-1594 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-55-1596     TCGA-55-6543     TCGA-55-6712     TCGA-64-1676 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1678     TCGA-64-1680     TCGA-64-5774 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-64-5778     TCGA-64-5781     TCGA-67-3771     TCGA-67-6215 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-67-6216     TCGA-67-6217     TCGA-71-6725     TCGA-73-4658 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4675     TCGA-73-4676     TCGA-75-5122 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-75-6203     TCGA-75-6205     TCGA-75-6207     TCGA-75-6211 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-75-6212     TCGA-86-6562     TCGA-91-6828     TCGA-91-6829 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-91-6835 
"STX2 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  STX2 MUTATED        0      1      0      1      0
  STX2 WILD-TYPE     30     14     30     13     10
D17V6, multiclass
[1] "Remove cluster labels:" "STX2 MUTATED"          
clus
  STX2 MUTATED STX2 WILD-TYPE 
             2             97 
    TCGA-05-4249     TCGA-05-4384     TCGA-05-4398     TCGA-05-4402 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-05-4405     TCGA-05-4410     TCGA-05-4417     TCGA-05-4418 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-05-4420     TCGA-05-4422     TCGA-05-4426     TCGA-05-4430 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-05-5420     TCGA-05-5423     TCGA-05-5429     TCGA-05-5715 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-35-3615     TCGA-38-4626     TCGA-38-4627     TCGA-38-6178 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-44-2656     TCGA-44-2657     TCGA-44-2661     TCGA-44-2665 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3919     TCGA-44-4112     TCGA-44-5645 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-44-6145     TCGA-44-6146     TCGA-44-6147     TCGA-44-6775 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-44-6776     TCGA-44-6777     TCGA-44-6779     TCGA-49-4486 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-49-4487     TCGA-49-4488     TCGA-49-4494     TCGA-49-4501 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-49-4505     TCGA-49-4506     TCGA-49-4507     TCGA-49-4510 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-49-4512     TCGA-49-4514     TCGA-49-6742     TCGA-49-6744 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-49-6745     TCGA-49-6767     TCGA-50-5044     TCGA-50-5049 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-50-5051     TCGA-50-5068     TCGA-50-5072     TCGA-50-5931 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-50-5932     TCGA-50-5933     TCGA-50-5936     TCGA-50-5939 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-50-5941     TCGA-50-5942     TCGA-50-5944     TCGA-50-6593 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-50-6595     TCGA-50-6597     TCGA-55-1592     TCGA-55-1594 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-55-1596     TCGA-55-6543     TCGA-55-6712     TCGA-64-1676 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1678     TCGA-64-1680     TCGA-64-5774 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-64-5778     TCGA-64-5781     TCGA-67-3771     TCGA-67-6215 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-67-6216     TCGA-67-6217     TCGA-71-6725     TCGA-73-4658 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4675     TCGA-73-4676     TCGA-75-5122 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-75-6203     TCGA-75-6205     TCGA-75-6207     TCGA-75-6211 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-75-6212     TCGA-86-6562     TCGA-91-6828     TCGA-91-6829 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-91-6835 
"STX2 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  STX2 MUTATED        2      0      0      2      0
  STX2 WILD-TYPE     56     37     29     32     13
D17V7, multiclass
        clus
vv       STX2 MUTATED STX2 WILD-TYPE
  CLUS_1            2             56
  CLUS_2            0             37
  CLUS_3            0             29
  CLUS_4            2             32
  CLUS_5            0             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  STX2 MUTATED        0      0      2      0      1      1      0      0      0
  STX2 WILD-TYPE     26     20     26     27     13     14     20      4     17
D17V8, multiclass
        clus
vv       STX2 MUTATED STX2 WILD-TYPE
  CLUS_1            0             26
  CLUS_2            0             20
  CLUS_3            2             26
  CLUS_4            0             27
  CLUS_5            1             13
  CLUS_6            1             14
  CLUS_7            0             20
  CLUS_8            0              4
  CLUS_9            0             17
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  STX2 MUTATED        0      3      1
  STX2 WILD-TYPE     59     72     33
D17V9, multiclass
        clus
vv       STX2 MUTATED STX2 WILD-TYPE
  CLUS_1            0             59
  CLUS_2            3             72
  CLUS_3            1             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STX2 MUTATED        0      3      1      0
  STX2 WILD-TYPE     19     67     43     35
D17V10, multiclass
        clus
vv       STX2 MUTATED STX2 WILD-TYPE
  CLUS_1            0             19
  CLUS_2            3             67
  CLUS_3            1             43
  CLUS_4            0             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  STX2 MUTATED        1      0      2
  STX2 WILD-TYPE     60     14     27
D17V11, multiclass
        clus
vv       STX2 MUTATED STX2 WILD-TYPE
  CLUS_1            1             60
  CLUS_2            0             14
  CLUS_3            2             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  STX2 MUTATED        1      1      1
  STX2 WILD-TYPE     13     58     30
D17V12, multiclass
        clus
vv       STX2 MUTATED STX2 WILD-TYPE
  CLUS_1            1             13
  CLUS_2            1             58
  CLUS_3            1             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = MGA MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MGA MUTATED        0      0      0      0
  MGA WILD-TYPE      5      9     12      6
D18V1, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MGA MUTATED        0      0      0
  MGA WILD-TYPE     14     11      7
D18V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MGA MUTATED        7      4      4
  MGA WILD-TYPE     61     64     32
D18V3, multiclass
        clus
vv       MGA MUTATED MGA WILD-TYPE
  CLUS_1           7            61
  CLUS_2           4            64
  CLUS_3           4            32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MGA MUTATED        1      4      5      1
  MGA WILD-TYPE     25     20     23     32
D18V4, multiclass
        clus
vv       MGA MUTATED MGA WILD-TYPE
  CLUS_1           1            25
  CLUS_2           4            20
  CLUS_3           5            23
  CLUS_4           1            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MGA MUTATED        0      5      4
  MGA WILD-TYPE     15     51     24
D18V5, multiclass
        clus
vv       MGA MUTATED MGA WILD-TYPE
  CLUS_1           0            15
  CLUS_2           5            51
  CLUS_3           4            24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MGA MUTATED        1      2      5      1      0
  MGA WILD-TYPE     29     13     25     13     10
D18V6, multiclass
        clus
vv       MGA MUTATED MGA WILD-TYPE
  CLUS_1           1            29
  CLUS_2           2            13
  CLUS_3           5            25
  CLUS_4           1            13
  CLUS_5           0            10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MGA MUTATED        8      1      2      4      0
  MGA WILD-TYPE     50     36     27     30     13
D18V7, multiclass
        clus
vv       MGA MUTATED MGA WILD-TYPE
  CLUS_1           8            50
  CLUS_2           1            36
  CLUS_3           2            27
  CLUS_4           4            30
  CLUS_5           0            13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  MGA MUTATED        5      1      2      4      1      1      1      0      0
  MGA WILD-TYPE     21     19     26     23     13     14     19      4     17
D18V8, multiclass
        clus
vv       MGA MUTATED MGA WILD-TYPE
  CLUS_1           5            21
  CLUS_2           1            19
  CLUS_3           2            26
  CLUS_4           4            23
  CLUS_5           1            13
  CLUS_6           1            14
  CLUS_7           1            19
  CLUS_8           0             4
  CLUS_9           0            17
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MGA MUTATED        2     10      2
  MGA WILD-TYPE     57     65     32
D18V9, multiclass
        clus
vv       MGA MUTATED MGA WILD-TYPE
  CLUS_1           2            57
  CLUS_2          10            65
  CLUS_3           2            32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MGA MUTATED        0      6      3      5
  MGA WILD-TYPE     19     64     41     30
D18V10, multiclass
        clus
vv       MGA MUTATED MGA WILD-TYPE
  CLUS_1           0            19
  CLUS_2           6            64
  CLUS_3           3            41
  CLUS_4           5            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MGA MUTATED        7      4      0
  MGA WILD-TYPE     54     10     29
D18V11, multiclass
        clus
vv       MGA MUTATED MGA WILD-TYPE
  CLUS_1           7            54
  CLUS_2           4            10
  CLUS_3           0            29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  MGA MUTATED        1      7      3
  MGA WILD-TYPE     13     52     28
D18V12, multiclass
        clus
vv       MGA MUTATED MGA WILD-TYPE
  CLUS_1           1            13
  CLUS_2           7            52
  CLUS_3           3            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = GALC MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GALC MUTATED        0      1      0      0
  GALC WILD-TYPE      5      8     12      6
D19V1, multiclass
[1] "Remove cluster labels:" "GALC MUTATED"          
clus
  GALC MUTATED GALC WILD-TYPE 
             1             31 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-35-3615 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-35-4122     TCGA-35-4123     TCGA-44-2655     TCGA-44-2657 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-44-2659     TCGA-44-2661     TCGA-44-2662     TCGA-44-2665 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-44-2666     TCGA-44-2668     TCGA-44-3398     TCGA-44-3918 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-44-3919     TCGA-44-4112     TCGA-55-1592     TCGA-55-1594 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-55-1595     TCGA-55-1596     TCGA-64-1676     TCGA-64-1677 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-64-1678     TCGA-64-1680     TCGA-67-3770     TCGA-67-3771 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-67-3772     TCGA-67-3773     TCGA-67-3774 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GALC MUTATED        1      0      0
  GALC WILD-TYPE     13     11      7
D19V2, multiclass
[1] "Remove cluster labels:" "GALC MUTATED"          
clus
  GALC MUTATED GALC WILD-TYPE 
             1             31 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-35-3615 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-35-4122     TCGA-35-4123     TCGA-44-2655     TCGA-44-2657 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-44-2659     TCGA-44-2661     TCGA-44-2662     TCGA-44-2665 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-44-2666     TCGA-44-2668     TCGA-44-3398     TCGA-44-3918 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-44-3919     TCGA-44-4112     TCGA-55-1592     TCGA-55-1594 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-55-1595     TCGA-55-1596     TCGA-64-1676     TCGA-64-1677 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-64-1678     TCGA-64-1680     TCGA-67-3770     TCGA-67-3771 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-67-3772     TCGA-67-3773     TCGA-67-3774 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GALC MUTATED        3      1      1
  GALC WILD-TYPE     65     67     35
D19V3, multiclass
        clus
vv       GALC MUTATED GALC WILD-TYPE
  CLUS_1            3             65
  CLUS_2            1             67
  CLUS_3            1             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GALC MUTATED        0      2      1      2
  GALC WILD-TYPE     26     22     27     31
D19V4, multiclass
        clus
vv       GALC MUTATED GALC WILD-TYPE
  CLUS_1            0             26
  CLUS_2            2             22
  CLUS_3            1             27
  CLUS_4            2             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GALC MUTATED        0      2      0
  GALC WILD-TYPE     15     54     28
D19V5, multiclass
[1] "Remove cluster labels:" "GALC MUTATED"          
clus
  GALC MUTATED GALC WILD-TYPE 
             2             97 
    TCGA-05-4249     TCGA-05-4384     TCGA-05-4396     TCGA-05-4398 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-05-4402     TCGA-05-4405     TCGA-05-4410     TCGA-05-4417 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-05-4418     TCGA-05-4420     TCGA-05-4422     TCGA-05-4426 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-05-4430     TCGA-05-5420     TCGA-05-5423     TCGA-05-5429 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-05-5715     TCGA-35-3615     TCGA-38-4626     TCGA-38-4627 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-38-6178     TCGA-44-2657     TCGA-44-2661     TCGA-44-2665 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3919     TCGA-44-4112     TCGA-44-5645 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-44-6145     TCGA-44-6146     TCGA-44-6147     TCGA-44-6774 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-44-6775     TCGA-44-6776     TCGA-44-6777     TCGA-44-6779 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4487     TCGA-49-4488     TCGA-49-4494 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-49-4501     TCGA-49-4505     TCGA-49-4506     TCGA-49-4507 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-49-4510     TCGA-49-4512     TCGA-49-4514     TCGA-49-6742 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-49-6744     TCGA-49-6745     TCGA-50-5044     TCGA-50-5049 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-50-5051     TCGA-50-5068     TCGA-50-5072     TCGA-50-5931 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-50-5932     TCGA-50-5933     TCGA-50-5936     TCGA-50-5939 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-50-5941     TCGA-50-5942     TCGA-50-5944     TCGA-50-6593 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-50-6595     TCGA-50-6597     TCGA-55-1592     TCGA-55-1594 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-55-1596     TCGA-55-6543     TCGA-55-6712     TCGA-64-1676 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1678     TCGA-64-1680     TCGA-64-5774 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-64-5778     TCGA-64-5781     TCGA-67-3771     TCGA-67-6215 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-67-6216     TCGA-67-6217     TCGA-71-6725     TCGA-73-4658 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4675     TCGA-73-4676     TCGA-75-5122 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-75-6203     TCGA-75-6205     TCGA-75-6207     TCGA-75-6211 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-75-6212     TCGA-86-6562     TCGA-91-6828     TCGA-91-6829 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-91-6835 
"GALC WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GALC MUTATED        1      0      1      0      0
  GALC WILD-TYPE     29     15     29     14     10
D19V6, multiclass
[1] "Remove cluster labels:" "GALC MUTATED"          
clus
  GALC MUTATED GALC WILD-TYPE 
             2             97 
    TCGA-05-4249     TCGA-05-4384     TCGA-05-4396     TCGA-05-4398 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-05-4402     TCGA-05-4405     TCGA-05-4410     TCGA-05-4417 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-05-4418     TCGA-05-4420     TCGA-05-4422     TCGA-05-4426 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-05-4430     TCGA-05-5420     TCGA-05-5423     TCGA-05-5429 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-05-5715     TCGA-35-3615     TCGA-38-4626     TCGA-38-4627 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-38-6178     TCGA-44-2657     TCGA-44-2661     TCGA-44-2665 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3919     TCGA-44-4112     TCGA-44-5645 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-44-6145     TCGA-44-6146     TCGA-44-6147     TCGA-44-6774 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-44-6775     TCGA-44-6776     TCGA-44-6777     TCGA-44-6779 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4487     TCGA-49-4488     TCGA-49-4494 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-49-4501     TCGA-49-4505     TCGA-49-4506     TCGA-49-4507 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-49-4510     TCGA-49-4512     TCGA-49-4514     TCGA-49-6742 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-49-6744     TCGA-49-6745     TCGA-50-5044     TCGA-50-5049 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-50-5051     TCGA-50-5068     TCGA-50-5072     TCGA-50-5931 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-50-5932     TCGA-50-5933     TCGA-50-5936     TCGA-50-5939 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-50-5941     TCGA-50-5942     TCGA-50-5944     TCGA-50-6593 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-50-6595     TCGA-50-6597     TCGA-55-1592     TCGA-55-1594 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-55-1596     TCGA-55-6543     TCGA-55-6712     TCGA-64-1676 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1678     TCGA-64-1680     TCGA-64-5774 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-64-5778     TCGA-64-5781     TCGA-67-3771     TCGA-67-6215 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-67-6216     TCGA-67-6217     TCGA-71-6725     TCGA-73-4658 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4675     TCGA-73-4676     TCGA-75-5122 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-75-6203     TCGA-75-6205     TCGA-75-6207     TCGA-75-6211 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-75-6212     TCGA-86-6562     TCGA-91-6828     TCGA-91-6829 
"GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" "GALC WILD-TYPE" 
    TCGA-91-6835 
"GALC WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GALC MUTATED        3      0      0      2      0
  GALC WILD-TYPE     55     37     29     32     13
D19V7, multiclass
        clus
vv       GALC MUTATED GALC WILD-TYPE
  CLUS_1            3             55
  CLUS_2            0             37
  CLUS_3            0             29
  CLUS_4            2             32
  CLUS_5            0             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  GALC MUTATED        2      0      1      1      0      1      0      0      0
  GALC WILD-TYPE     24     20     27     26     14     14     20      4     17
D19V8, multiclass
        clus
vv       GALC MUTATED GALC WILD-TYPE
  CLUS_1            2             24
  CLUS_2            0             20
  CLUS_3            1             27
  CLUS_4            1             26
  CLUS_5            0             14
  CLUS_6            1             14
  CLUS_7            0             20
  CLUS_8            0              4
  CLUS_9            0             17
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GALC MUTATED        0      4      1
  GALC WILD-TYPE     59     71     33
D19V9, multiclass
        clus
vv       GALC MUTATED GALC WILD-TYPE
  CLUS_1            0             59
  CLUS_2            4             71
  CLUS_3            1             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GALC MUTATED        1      2      0      2
  GALC WILD-TYPE     18     68     44     33
D19V10, multiclass
        clus
vv       GALC MUTATED GALC WILD-TYPE
  CLUS_1            1             18
  CLUS_2            2             68
  CLUS_3            0             44
  CLUS_4            2             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GALC MUTATED        1      0      3
  GALC WILD-TYPE     60     14     26
D19V11, multiclass
        clus
vv       GALC MUTATED GALC WILD-TYPE
  CLUS_1            1             60
  CLUS_2            0             14
  CLUS_3            3             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GALC MUTATED        0      2      2
  GALC WILD-TYPE     14     57     29
D19V12, multiclass
        clus
vv       GALC MUTATED GALC WILD-TYPE
  CLUS_1            0             14
  CLUS_2            2             57
  CLUS_3            2             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = CTNNB1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CTNNB1 MUTATED        0      0      1      1
  CTNNB1 WILD-TYPE      5      9     11      5
D20V1, multiclass
[1] "Remove cluster labels:" "CTNNB1 MUTATED"        
clus
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               2               30 
      TCGA-05-4244       TCGA-05-4249       TCGA-05-4250       TCGA-35-3615 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-35-4122       TCGA-35-4123       TCGA-44-2655       TCGA-44-2656 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-44-2657       TCGA-44-2659       TCGA-44-2661       TCGA-44-2662 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-44-2665       TCGA-44-2666       TCGA-44-2668       TCGA-44-3398 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-44-3918       TCGA-44-3919       TCGA-55-1592       TCGA-55-1594 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-55-1595       TCGA-55-1596       TCGA-64-1676       TCGA-64-1677 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-64-1678       TCGA-64-1680       TCGA-67-3770       TCGA-67-3772 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-67-3773       TCGA-67-3774 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        1      0      1
  CTNNB1 WILD-TYPE     13     11      6
D20V2, multiclass
[1] "Remove cluster labels:" "CTNNB1 MUTATED"        
clus
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               2               30 
      TCGA-05-4244       TCGA-05-4249       TCGA-05-4250       TCGA-35-3615 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-35-4122       TCGA-35-4123       TCGA-44-2655       TCGA-44-2656 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-44-2657       TCGA-44-2659       TCGA-44-2661       TCGA-44-2662 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-44-2665       TCGA-44-2666       TCGA-44-2668       TCGA-44-3398 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-44-3918       TCGA-44-3919       TCGA-55-1592       TCGA-55-1594 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-55-1595       TCGA-55-1596       TCGA-64-1676       TCGA-64-1677 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-64-1678       TCGA-64-1680       TCGA-67-3770       TCGA-67-3772 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-67-3773       TCGA-67-3774 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        2      5      2
  CTNNB1 WILD-TYPE     66     63     34
D20V3, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              2               66
  CLUS_2              5               63
  CLUS_3              2               34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CTNNB1 MUTATED        2      0      3      1
  CTNNB1 WILD-TYPE     24     24     25     32
D20V4, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              2               24
  CLUS_2              0               24
  CLUS_3              3               25
  CLUS_4              1               32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        1      2      3
  CTNNB1 WILD-TYPE     14     54     25
D20V5, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              1               14
  CLUS_2              2               54
  CLUS_3              3               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CTNNB1 MUTATED        0      4      1      1      0
  CTNNB1 WILD-TYPE     30     11     29     13     10
D20V6, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               30
  CLUS_2              4               11
  CLUS_3              1               29
  CLUS_4              1               13
  CLUS_5              0               10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CTNNB1 MUTATED        1      3      1      4      0
  CTNNB1 WILD-TYPE     57     34     28     30     13
D20V7, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              1               57
  CLUS_2              3               34
  CLUS_3              1               28
  CLUS_4              4               30
  CLUS_5              0               13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CTNNB1 MUTATED        1      1      0      2      3      0      1      0
  CTNNB1 WILD-TYPE     25     19     28     25     11     15     19      4
                  vv
clus               CLUS_9
  CTNNB1 MUTATED        1
  CTNNB1 WILD-TYPE     16
D20V8, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              1               25
  CLUS_2              1               19
  CLUS_3              0               28
  CLUS_4              2               25
  CLUS_5              3               11
  CLUS_6              0               15
  CLUS_7              1               19
  CLUS_8              0                4
  CLUS_9              1               16
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        3      5      1
  CTNNB1 WILD-TYPE     56     70     33
D20V9, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               56
  CLUS_2              5               70
  CLUS_3              1               33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CTNNB1 MUTATED        2      3      2      2
  CTNNB1 WILD-TYPE     17     67     42     33
D20V10, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              2               17
  CLUS_2              3               67
  CLUS_3              2               42
  CLUS_4              2               33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        4      0      0
  CTNNB1 WILD-TYPE     57     14     29
D20V11, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              4               57
  CLUS_2              0               14
  CLUS_3              0               29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        2      1      1
  CTNNB1 WILD-TYPE     12     58     30
D20V12, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              2               12
  CLUS_2              1               58
  CLUS_3              1               30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
