[1] "ofn"        "-oTTHYM-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/THYM-TP/22541006/THYM-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THYM-TP/22571832/transformed.cor.cli.txt"

nPatients in clinical file=124, in cluster file=120, common to both=120
[1] "Reduce the number of clustering variables from 12 to 8."
[1]   8 120
[1] "GTF2I MUTATION ANALYSIS"
[1] 3
  GTF2I MUTATED GTF2I WILD-TYPE 
             49              71 
  GTF2I MUTATED GTF2I WILD-TYPE 
             49              71 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            10            110 
  HRAS MUTATED HRAS WILD-TYPE 
            10            110 
[1] "CAPNS1 MUTATION ANALYSIS"
[1] 3
  CAPNS1 MUTATED CAPNS1 WILD-TYPE 
               3              117 
  CAPNS1 MUTATED CAPNS1 WILD-TYPE 
               3              117 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             4            116 
  TP53 MUTATED TP53 WILD-TYPE 
             4            116 
[1] "ATRN MUTATION ANALYSIS"
[1] 3
  ATRN MUTATED ATRN WILD-TYPE 
             3            117 
  ATRN MUTATED ATRN WILD-TYPE 
             3            117 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             3            117 
  NRAS MUTATED NRAS WILD-TYPE 
             3            117 
[1] "PLEKHG4B MUTATION ANALYSIS"
[1] 3
  PLEKHG4B MUTATED PLEKHG4B WILD-TYPE 
                 3                117 
  PLEKHG4B MUTATED PLEKHG4B WILD-TYPE 
                 3                117 
[1] "UNC93B1 MUTATION ANALYSIS"
[1] 3
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                5               115 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                5               115 
[1] "data2feature, selection=ALL"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 120 columns.

Variable 1:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 120 columns, 0 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=8, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = GTF2I MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  GTF2I MUTATED        4     22      8     11      4
  GTF2I WILD-TYPE     31      5     11     18      6
D1V1, multiclass
        clus
vv       GTF2I MUTATED GTF2I WILD-TYPE
  CLUS_1             4              31
  CLUS_2            22               5
  CLUS_3             8              11
  CLUS_4            11              18
  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 CLUS_6 CLUS_7 CLUS_8
  GTF2I MUTATED        2     22      0      0     17      5      1      2
  GTF2I WILD-TYPE     32      1     19     10      1      3      1      4
D1V2, multiclass
        clus
vv       GTF2I MUTATED GTF2I WILD-TYPE
  CLUS_1             2              32
  CLUS_2            22               1
  CLUS_3             0              19
  CLUS_4             0              10
  CLUS_5            17               1
  CLUS_6             5               3
  CLUS_7             1               1
  CLUS_8             2               4
[1] 8 2
[1] 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
  GTF2I MUTATED       10     21      8
  GTF2I WILD-TYPE     21      4     23
D1V3, multiclass
        clus
vv       GTF2I MUTATED GTF2I WILD-TYPE
  CLUS_1            10              21
  CLUS_2            21               4
  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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GTF2I MUTATED        8     22      9      0
  GTF2I WILD-TYPE      8      1     19     20
D1V4, multiclass
        clus
vv       GTF2I MUTATED GTF2I WILD-TYPE
  CLUS_1             8               8
  CLUS_2            22               1
  CLUS_3             9              19
  CLUS_4             0              20
[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 CLUS_4
  GTF2I MUTATED        0     16     28      2
  GTF2I WILD-TYPE     42     14      2     12
D1V5, multiclass
        clus
vv       GTF2I MUTATED GTF2I WILD-TYPE
  CLUS_1             0              42
  CLUS_2            16              14
  CLUS_3            28               2
  CLUS_4             2              12
[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 CLUS_4
  GTF2I MUTATED        0     27     19      0
  GTF2I WILD-TYPE     44     15      1     10
D1V6, multiclass
        clus
vv       GTF2I MUTATED GTF2I WILD-TYPE
  CLUS_1             0              44
  CLUS_2            27              15
  CLUS_3            19               1
  CLUS_4             0              10
[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
  GTF2I MUTATED        3     46      0
  GTF2I WILD-TYPE     51     15      5
D1V7, multiclass
        clus
vv       GTF2I MUTATED GTF2I WILD-TYPE
  CLUS_1             3              51
  CLUS_2            46              15
  CLUS_3             0               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  GTF2I MUTATED        1     16      2      0     15     15
  GTF2I WILD-TYPE     25      2     24      7      1     12
D1V8, multiclass
        clus
vv       GTF2I MUTATED GTF2I WILD-TYPE
  CLUS_1             1              25
  CLUS_2            16               2
  CLUS_3             2              24
  CLUS_4             0               7
  CLUS_5            15               1
  CLUS_6            15              12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GTF2I MUTATED        0     45      4      0
  GTF2I WILD-TYPE     25      6     39      1
D1V9, multiclass
        clus
vv       GTF2I MUTATED GTF2I WILD-TYPE
  CLUS_1             0              25
  CLUS_2            45               6
  CLUS_3             4              39
  CLUS_4             0               1
[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 CLUS_4
  GTF2I MUTATED        1     30      2     16
  GTF2I WILD-TYPE     25      3     31     12
D1V10, multiclass
        clus
vv       GTF2I MUTATED GTF2I WILD-TYPE
  CLUS_1             1              25
  CLUS_2            30               3
  CLUS_3             2              31
  CLUS_4            16              12
[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"

Clustering(2) Variable = HRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HRAS MUTATED        0      7      2      0      1
  HRAS WILD-TYPE     35     20     17     29      9
D2V1, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             35
  CLUS_2            7             20
  CLUS_3            2             17
  CLUS_4            0             29
  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 CLUS_6 CLUS_7 CLUS_8
  HRAS MUTATED        0     10      0      0      0      0      0      0
  HRAS WILD-TYPE     34     13     19     10     18      8      2      6
D2V2, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             34
  CLUS_2           10             13
  CLUS_3            0             19
  CLUS_4            0             10
  CLUS_5            0             18
  CLUS_6            0              8
  CLUS_7            0              2
  CLUS_8            0              6
[1] 8 2
[1] 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
  HRAS MUTATED        3      5      0
  HRAS WILD-TYPE     28     20     31
D2V3, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            3             28
  CLUS_2            5             20
  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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HRAS MUTATED        0      8      0      0
  HRAS WILD-TYPE     16     15     28     20
D2V4, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             16
  CLUS_2            8             15
  CLUS_3            0             28
  CLUS_4            0             20
[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 CLUS_4
  HRAS MUTATED        0      0     10      0
  HRAS WILD-TYPE     42     30     20     14
D2V5, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             42
  CLUS_2            0             30
  CLUS_3           10             20
  CLUS_4            0             14
[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 CLUS_4
  HRAS MUTATED        0      0     10      0
  HRAS WILD-TYPE     44     42     10     10
D2V6, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             44
  CLUS_2            0             42
  CLUS_3           10             10
  CLUS_4            0             10
[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
  HRAS MUTATED        1      9      0
  HRAS WILD-TYPE     53     52      5
D2V7, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            1             53
  CLUS_2            9             52
  CLUS_3            0              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  HRAS MUTATED        0      0      1      0      8      1
  HRAS WILD-TYPE     26     18     25      7      8     26
D2V8, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             26
  CLUS_2            0             18
  CLUS_3            1             25
  CLUS_4            0              7
  CLUS_5            8              8
  CLUS_6            1             26
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HRAS MUTATED        0      9      1      0
  HRAS WILD-TYPE     25     42     42      1
D2V9, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             25
  CLUS_2            9             42
  CLUS_3            1             42
  CLUS_4            0              1
[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 CLUS_4
  HRAS MUTATED        0      8      1      1
  HRAS WILD-TYPE     26     25     32     27
D2V10, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             26
  CLUS_2            8             25
  CLUS_3            1             32
  CLUS_4            1             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"

Clustering(3) Variable = CAPNS1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CAPNS1 MUTATED        0      1      1      1      0
  CAPNS1 WILD-TYPE     35     26     18     28     10
D3V1, multiclass
        clus
vv       CAPNS1 MUTATED CAPNS1 WILD-TYPE
  CLUS_1              0               35
  CLUS_2              1               26
  CLUS_3              1               18
  CLUS_4              1               28
  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 CLUS_6 CLUS_7 CLUS_8
  CAPNS1 MUTATED        1      1      0      0      1      0      0      0
  CAPNS1 WILD-TYPE     33     22     19     10     17      8      2      6
D3V2, multiclass
        clus
vv       CAPNS1 MUTATED CAPNS1 WILD-TYPE
  CLUS_1              1               33
  CLUS_2              1               22
  CLUS_3              0               19
  CLUS_4              0               10
  CLUS_5              1               17
  CLUS_6              0                8
  CLUS_7              0                2
  CLUS_8              0                6
[1] 8 2
[1] 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
  CAPNS1 MUTATED        0      2      0
  CAPNS1 WILD-TYPE     31     23     31
D3V3, multiclass
[1] "Remove cluster labels:" "CAPNS1 MUTATED"        
clus
  CAPNS1 MUTATED CAPNS1 WILD-TYPE 
               2               85 
      TCGA-3G-AB0O       TCGA-3G-AB0Q       TCGA-3G-AB0T       TCGA-3G-AB14 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-3G-AB19       TCGA-3Q-A9WF       TCGA-3S-A8YW       TCGA-3S-AAYX 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-4V-A9QN       TCGA-4V-A9QS       TCGA-4V-A9QW       TCGA-4X-A9F9 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-4X-A9FB       TCGA-4X-A9FC       TCGA-5G-A9ZZ       TCGA-5K-AAAP 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-5U-AB0E       TCGA-5U-AB0F       TCGA-5V-A9RR       TCGA-X7-A8D6 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-X7-A8D7       TCGA-X7-A8D9       TCGA-X7-A8DB       TCGA-X7-A8DC 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-X7-A8DD       TCGA-X7-A8DE       TCGA-X7-A8DF       TCGA-X7-A8DG 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-X7-A8DI       TCGA-X7-A8DJ       TCGA-X7-A8M0       TCGA-X7-A8M1 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-X7-A8M3       TCGA-X7-A8M4       TCGA-X7-A8M5       TCGA-X7-A8M6 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-XM-A8R8       TCGA-XM-A8RB       TCGA-XM-A8RC       TCGA-XM-A8RD 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-XM-A8RE       TCGA-XM-A8RF       TCGA-XM-A8RG       TCGA-XM-A8RH 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-XM-A8RI       TCGA-XM-AAZ1       TCGA-XM-AAZ2       TCGA-XM-AAZ3 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-XU-A92Q       TCGA-XU-A92R       TCGA-XU-A92U       TCGA-XU-A92V 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-XU-A92X       TCGA-XU-A92Z       TCGA-XU-A931       TCGA-XU-A932 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-XU-A933       TCGA-XU-A936       TCGA-XU-AAY0       TCGA-XU-AAY1 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-YT-A95D       TCGA-YT-A95E       TCGA-YT-A95F       TCGA-YT-A95G 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-YT-A95H       TCGA-ZB-A961       TCGA-ZB-A962       TCGA-ZB-A963 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-ZB-A964       TCGA-ZB-A965       TCGA-ZB-A966       TCGA-ZB-A969 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-ZB-A96A       TCGA-ZB-A96B       TCGA-ZB-A96C       TCGA-ZB-A96D 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-ZB-A96I       TCGA-ZB-A96Q       TCGA-ZB-A96R       TCGA-ZB-A96V 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-ZC-AAA7       TCGA-ZC-AAAA       TCGA-ZC-AAAF       TCGA-ZC-AAAH 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-ZL-A9V6 
"CAPNS1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CAPNS1 MUTATED        1      1      0      0
  CAPNS1 WILD-TYPE     15     22     28     20
D3V4, multiclass
[1] "Remove cluster labels:" "CAPNS1 MUTATED"        
clus
  CAPNS1 MUTATED CAPNS1 WILD-TYPE 
               2               85 
      TCGA-3G-AB0O       TCGA-3G-AB0Q       TCGA-3G-AB0T       TCGA-3G-AB14 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-3G-AB19       TCGA-3Q-A9WF       TCGA-3S-A8YW       TCGA-3S-AAYX 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-4V-A9QN       TCGA-4V-A9QS       TCGA-4V-A9QW       TCGA-4X-A9F9 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-4X-A9FB       TCGA-4X-A9FC       TCGA-5G-A9ZZ       TCGA-5K-AAAP 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-5U-AB0E       TCGA-5U-AB0F       TCGA-5V-A9RR       TCGA-X7-A8D6 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-X7-A8D7       TCGA-X7-A8D9       TCGA-X7-A8DB       TCGA-X7-A8DC 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-X7-A8DD       TCGA-X7-A8DE       TCGA-X7-A8DF       TCGA-X7-A8DG 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-X7-A8DI       TCGA-X7-A8DJ       TCGA-X7-A8M0       TCGA-X7-A8M1 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-X7-A8M3       TCGA-X7-A8M4       TCGA-X7-A8M5       TCGA-X7-A8M6 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-XM-A8R8       TCGA-XM-A8RB       TCGA-XM-A8RC       TCGA-XM-A8RD 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-XM-A8RE       TCGA-XM-A8RF       TCGA-XM-A8RG       TCGA-XM-A8RH 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-XM-A8RI       TCGA-XM-AAZ1       TCGA-XM-AAZ2       TCGA-XM-AAZ3 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-XU-A92Q       TCGA-XU-A92R       TCGA-XU-A92U       TCGA-XU-A92V 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-XU-A92X       TCGA-XU-A92Z       TCGA-XU-A931       TCGA-XU-A932 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-XU-A933       TCGA-XU-A936       TCGA-XU-AAY0       TCGA-XU-AAY1 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-YT-A95D       TCGA-YT-A95E       TCGA-YT-A95F       TCGA-YT-A95G 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-YT-A95H       TCGA-ZB-A961       TCGA-ZB-A962       TCGA-ZB-A963 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-ZB-A964       TCGA-ZB-A965       TCGA-ZB-A966       TCGA-ZB-A969 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-ZB-A96A       TCGA-ZB-A96B       TCGA-ZB-A96C       TCGA-ZB-A96D 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-ZB-A96I       TCGA-ZB-A96Q       TCGA-ZB-A96R       TCGA-ZB-A96V 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-ZC-AAA7       TCGA-ZC-AAAA       TCGA-ZC-AAAF       TCGA-ZC-AAAH 
"CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" "CAPNS1 WILD-TYPE" 
      TCGA-ZL-A9V6 
"CAPNS1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CAPNS1 MUTATED        1      2      0      0
  CAPNS1 WILD-TYPE     41     28     30     14
D3V5, multiclass
        clus
vv       CAPNS1 MUTATED CAPNS1 WILD-TYPE
  CLUS_1              1               41
  CLUS_2              2               28
  CLUS_3              0               30
  CLUS_4              0               14
[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 CLUS_4
  CAPNS1 MUTATED        1      2      0      0
  CAPNS1 WILD-TYPE     43     40     20     10
D3V6, multiclass
        clus
vv       CAPNS1 MUTATED CAPNS1 WILD-TYPE
  CLUS_1              1               43
  CLUS_2              2               40
  CLUS_3              0               20
  CLUS_4              0               10
[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
  CAPNS1 MUTATED        1      2      0
  CAPNS1 WILD-TYPE     53     59      5
D3V7, multiclass
        clus
vv       CAPNS1 MUTATED CAPNS1 WILD-TYPE
  CLUS_1              1               53
  CLUS_2              2               59
  CLUS_3              0                5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CAPNS1 MUTATED        0      1      1      0      0      1
  CAPNS1 WILD-TYPE     26     17     25      7     16     26
D3V8, multiclass
        clus
vv       CAPNS1 MUTATED CAPNS1 WILD-TYPE
  CLUS_1              0               26
  CLUS_2              1               17
  CLUS_3              1               25
  CLUS_4              0                7
  CLUS_5              0               16
  CLUS_6              1               26
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CAPNS1 MUTATED        1      2      0      0
  CAPNS1 WILD-TYPE     24     49     43      1
D3V9, multiclass
        clus
vv       CAPNS1 MUTATED CAPNS1 WILD-TYPE
  CLUS_1              1               24
  CLUS_2              2               49
  CLUS_3              0               43
  CLUS_4              0                1
[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 CLUS_4
  CAPNS1 MUTATED        0      1      1      1
  CAPNS1 WILD-TYPE     26     32     32     27
D3V10, multiclass
        clus
vv       CAPNS1 MUTATED CAPNS1 WILD-TYPE
  CLUS_1              0               26
  CLUS_2              1               32
  CLUS_3              1               32
  CLUS_4              1               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"

Clustering(4) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED        1      1      1      0      1
  TP53 WILD-TYPE     34     26     18     29      9
D4V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             34
  CLUS_2            1             26
  CLUS_3            1             18
  CLUS_4            0             29
  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 CLUS_6 CLUS_7 CLUS_8
  TP53 MUTATED        1      0      1      2      0      0      0      0
  TP53 WILD-TYPE     33     23     18      8     18      8      2      6
D4V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             33
  CLUS_2            0             23
  CLUS_3            1             18
  CLUS_4            2              8
  CLUS_5            0             18
  CLUS_6            0              8
  CLUS_7            0              2
  CLUS_8            0              6
[1] 8 2
[1] 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        1      1      1
  TP53 WILD-TYPE     30     24     30
D4V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             30
  CLUS_2            1             24
  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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        1      0      0      2
  TP53 WILD-TYPE     15     23     28     18
D4V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             15
  CLUS_2            0             23
  CLUS_3            0             28
  CLUS_4            2             18
[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 CLUS_4
  TP53 MUTATED        2      0      0      2
  TP53 WILD-TYPE     40     30     30     12
D4V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             40
  CLUS_2            0             30
  CLUS_3            0             30
  CLUS_4            2             12
[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 CLUS_4
  TP53 MUTATED        2      0      0      2
  TP53 WILD-TYPE     42     42     20      8
D4V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             42
  CLUS_2            0             42
  CLUS_3            0             20
  CLUS_4            2              8
[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      1      0
  TP53 WILD-TYPE     51     60      5
D4V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3             51
  CLUS_2            1             60
  CLUS_3            0              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TP53 MUTATED        1      0      0      2      1      0
  TP53 WILD-TYPE     25     18     26      5     15     27
D4V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             25
  CLUS_2            0             18
  CLUS_3            0             26
  CLUS_4            2              5
  CLUS_5            1             15
  CLUS_6            0             27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        0      0      4      0
  TP53 WILD-TYPE     25     51     39      1
D4V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             25
  CLUS_2            0             51
  CLUS_3            4             39
  CLUS_4            0              1
[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 CLUS_4
  TP53 MUTATED        1      1      2      0
  TP53 WILD-TYPE     25     32     31     28
D4V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             25
  CLUS_2            1             32
  CLUS_3            2             31
  CLUS_4            0             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"

Clustering(5) Variable = ATRN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ATRN MUTATED        1      0      1      1      0
  ATRN WILD-TYPE     34     27     18     28     10
D5V1, multiclass
        clus
vv       ATRN MUTATED ATRN WILD-TYPE
  CLUS_1            1             34
  CLUS_2            0             27
  CLUS_3            1             18
  CLUS_4            1             28
  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 CLUS_6 CLUS_7 CLUS_8
  ATRN MUTATED        0      2      0      0      1      0      0      0
  ATRN WILD-TYPE     34     21     19     10     17      8      2      6
D5V2, multiclass
        clus
vv       ATRN MUTATED ATRN WILD-TYPE
  CLUS_1            0             34
  CLUS_2            2             21
  CLUS_3            0             19
  CLUS_4            0             10
  CLUS_5            1             17
  CLUS_6            0              8
  CLUS_7            0              2
  CLUS_8            0              6
[1] 8 2
[1] 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
  ATRN MUTATED        0      1      1
  ATRN WILD-TYPE     31     24     30
D5V3, multiclass
[1] "Remove cluster labels:" "ATRN MUTATED"          
clus
  ATRN MUTATED ATRN WILD-TYPE 
             2             85 
    TCGA-3G-AB0O     TCGA-3G-AB0Q     TCGA-3G-AB0T     TCGA-3G-AB14 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-3G-AB19     TCGA-3Q-A9WF     TCGA-3S-A8YW     TCGA-3S-AAYX 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-4V-A9QL     TCGA-4V-A9QN     TCGA-4V-A9QS     TCGA-4V-A9QW 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-4V-A9QX     TCGA-4X-A9F9     TCGA-4X-A9FB     TCGA-4X-A9FC 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-5G-A9ZZ     TCGA-5K-AAAP     TCGA-5U-AB0E     TCGA-5U-AB0F 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-5V-A9RR     TCGA-X7-A8D6     TCGA-X7-A8D7     TCGA-X7-A8D9 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-X7-A8DB     TCGA-X7-A8DC     TCGA-X7-A8DD     TCGA-X7-A8DE 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-X7-A8DG     TCGA-X7-A8DI     TCGA-X7-A8DJ     TCGA-X7-A8M0 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-X7-A8M1     TCGA-X7-A8M3     TCGA-X7-A8M4     TCGA-X7-A8M5 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-X7-A8M6     TCGA-XM-A8R8     TCGA-XM-A8RB     TCGA-XM-A8RC 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-XM-A8RD     TCGA-XM-A8RE     TCGA-XM-A8RF     TCGA-XM-A8RG 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-XM-A8RH     TCGA-XM-A8RI     TCGA-XM-AAZ1     TCGA-XM-AAZ2 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-XM-AAZ3     TCGA-XU-A92Q     TCGA-XU-A92R     TCGA-XU-A92U 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-XU-A92V     TCGA-XU-A92X     TCGA-XU-A92Z     TCGA-XU-A931 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-XU-A932     TCGA-XU-A933     TCGA-XU-A936     TCGA-XU-AAY0 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-XU-AAY1     TCGA-YT-A95D     TCGA-YT-A95E     TCGA-YT-A95F 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-YT-A95G     TCGA-YT-A95H     TCGA-ZB-A961     TCGA-ZB-A962 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-ZB-A963     TCGA-ZB-A964     TCGA-ZB-A965     TCGA-ZB-A966 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-ZB-A96A     TCGA-ZB-A96B     TCGA-ZB-A96C     TCGA-ZB-A96D 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-ZB-A96I     TCGA-ZB-A96Q     TCGA-ZB-A96R     TCGA-ZB-A96V 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-ZC-AAA7     TCGA-ZC-AAAA     TCGA-ZC-AAAF     TCGA-ZC-AAAH 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-ZL-A9V6 
"ATRN WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATRN MUTATED        0      1      1      0
  ATRN WILD-TYPE     16     22     27     20
D5V4, multiclass
[1] "Remove cluster labels:" "ATRN MUTATED"          
clus
  ATRN MUTATED ATRN WILD-TYPE 
             2             85 
    TCGA-3G-AB0O     TCGA-3G-AB0Q     TCGA-3G-AB0T     TCGA-3G-AB14 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-3G-AB19     TCGA-3Q-A9WF     TCGA-3S-A8YW     TCGA-3S-AAYX 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-4V-A9QL     TCGA-4V-A9QN     TCGA-4V-A9QS     TCGA-4V-A9QW 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-4V-A9QX     TCGA-4X-A9F9     TCGA-4X-A9FB     TCGA-4X-A9FC 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-5G-A9ZZ     TCGA-5K-AAAP     TCGA-5U-AB0E     TCGA-5U-AB0F 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-5V-A9RR     TCGA-X7-A8D6     TCGA-X7-A8D7     TCGA-X7-A8D9 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-X7-A8DB     TCGA-X7-A8DC     TCGA-X7-A8DD     TCGA-X7-A8DE 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-X7-A8DG     TCGA-X7-A8DI     TCGA-X7-A8DJ     TCGA-X7-A8M0 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-X7-A8M1     TCGA-X7-A8M3     TCGA-X7-A8M4     TCGA-X7-A8M5 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-X7-A8M6     TCGA-XM-A8R8     TCGA-XM-A8RB     TCGA-XM-A8RC 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-XM-A8RD     TCGA-XM-A8RE     TCGA-XM-A8RF     TCGA-XM-A8RG 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-XM-A8RH     TCGA-XM-A8RI     TCGA-XM-AAZ1     TCGA-XM-AAZ2 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-XM-AAZ3     TCGA-XU-A92Q     TCGA-XU-A92R     TCGA-XU-A92U 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-XU-A92V     TCGA-XU-A92X     TCGA-XU-A92Z     TCGA-XU-A931 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-XU-A932     TCGA-XU-A933     TCGA-XU-A936     TCGA-XU-AAY0 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-XU-AAY1     TCGA-YT-A95D     TCGA-YT-A95E     TCGA-YT-A95F 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-YT-A95G     TCGA-YT-A95H     TCGA-ZB-A961     TCGA-ZB-A962 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-ZB-A963     TCGA-ZB-A964     TCGA-ZB-A965     TCGA-ZB-A966 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-ZB-A96A     TCGA-ZB-A96B     TCGA-ZB-A96C     TCGA-ZB-A96D 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-ZB-A96I     TCGA-ZB-A96Q     TCGA-ZB-A96R     TCGA-ZB-A96V 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-ZC-AAA7     TCGA-ZC-AAAA     TCGA-ZC-AAAF     TCGA-ZC-AAAH 
"ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" "ATRN WILD-TYPE" 
    TCGA-ZL-A9V6 
"ATRN WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATRN MUTATED        0      2      1      0
  ATRN WILD-TYPE     42     28     29     14
D5V5, multiclass
        clus
vv       ATRN MUTATED ATRN WILD-TYPE
  CLUS_1            0             42
  CLUS_2            2             28
  CLUS_3            1             29
  CLUS_4            0             14
[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 CLUS_4
  ATRN MUTATED        0      1      2      0
  ATRN WILD-TYPE     44     41     18     10
D5V6, multiclass
        clus
vv       ATRN MUTATED ATRN WILD-TYPE
  CLUS_1            0             44
  CLUS_2            1             41
  CLUS_3            2             18
  CLUS_4            0             10
[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
  ATRN MUTATED        0      3      0
  ATRN WILD-TYPE     54     58      5
D5V7, multiclass
        clus
vv       ATRN MUTATED ATRN WILD-TYPE
  CLUS_1            0             54
  CLUS_2            3             58
  CLUS_3            0              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ATRN MUTATED        0      0      0      0      2      1
  ATRN WILD-TYPE     26     18     26      7     14     26
D5V8, multiclass
        clus
vv       ATRN MUTATED ATRN WILD-TYPE
  CLUS_1            0             26
  CLUS_2            0             18
  CLUS_3            0             26
  CLUS_4            0              7
  CLUS_5            2             14
  CLUS_6            1             26
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATRN MUTATED        0      3      0      0
  ATRN WILD-TYPE     25     48     43      1
D5V9, multiclass
        clus
vv       ATRN MUTATED ATRN WILD-TYPE
  CLUS_1            0             25
  CLUS_2            3             48
  CLUS_3            0             43
  CLUS_4            0              1
[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 CLUS_4
  ATRN MUTATED        0      2      0      1
  ATRN WILD-TYPE     26     31     33     27
D5V10, multiclass
        clus
vv       ATRN MUTATED ATRN WILD-TYPE
  CLUS_1            0             26
  CLUS_2            2             31
  CLUS_3            0             33
  CLUS_4            1             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"

Clustering(6) Variable = NRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NRAS MUTATED        1      0      1      1      0
  NRAS WILD-TYPE     34     27     18     28     10
D6V1, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1             34
  CLUS_2            0             27
  CLUS_3            1             18
  CLUS_4            1             28
  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 CLUS_6 CLUS_7 CLUS_8
  NRAS MUTATED        0      1      1      1      0      0      0      0
  NRAS WILD-TYPE     34     22     18      9     18      8      2      6
D6V2, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0             34
  CLUS_2            1             22
  CLUS_3            1             18
  CLUS_4            1              9
  CLUS_5            0             18
  CLUS_6            0              8
  CLUS_7            0              2
  CLUS_8            0              6
[1] 8 2
[1] 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
  NRAS MUTATED        2      0      0
  NRAS WILD-TYPE     29     25     31
D6V3, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2             85 
    TCGA-3G-AB0O     TCGA-3G-AB0Q     TCGA-3G-AB0T     TCGA-3G-AB14 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-3G-AB19     TCGA-3Q-A9WF     TCGA-3S-A8YW     TCGA-3S-AAYX 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-4V-A9QL     TCGA-4V-A9QN     TCGA-4V-A9QS     TCGA-4V-A9QW 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-4V-A9QX     TCGA-4X-A9F9     TCGA-4X-A9FB     TCGA-4X-A9FC 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-5G-A9ZZ     TCGA-5K-AAAP     TCGA-5U-AB0E     TCGA-5U-AB0F 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-5V-A9RR     TCGA-X7-A8D6     TCGA-X7-A8D7     TCGA-X7-A8D9 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-X7-A8DB     TCGA-X7-A8DC     TCGA-X7-A8DD     TCGA-X7-A8DE 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-X7-A8DF     TCGA-X7-A8DG     TCGA-X7-A8DI     TCGA-X7-A8DJ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-X7-A8M0     TCGA-X7-A8M1     TCGA-X7-A8M3     TCGA-X7-A8M4 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-X7-A8M5     TCGA-X7-A8M6     TCGA-XM-A8R8     TCGA-XM-A8RB 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XM-A8RC     TCGA-XM-A8RD     TCGA-XM-A8RE     TCGA-XM-A8RF 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XM-A8RG     TCGA-XM-A8RH     TCGA-XM-A8RI     TCGA-XM-AAZ2 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XM-AAZ3     TCGA-XU-A92Q     TCGA-XU-A92R     TCGA-XU-A92U 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XU-A92V     TCGA-XU-A92X     TCGA-XU-A931     TCGA-XU-A932 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XU-A933     TCGA-XU-A936     TCGA-XU-AAY0     TCGA-XU-AAY1 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-YT-A95D     TCGA-YT-A95E     TCGA-YT-A95F     TCGA-YT-A95G 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-YT-A95H     TCGA-ZB-A961     TCGA-ZB-A962     TCGA-ZB-A963 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-ZB-A964     TCGA-ZB-A965     TCGA-ZB-A966     TCGA-ZB-A969 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-ZB-A96A     TCGA-ZB-A96B     TCGA-ZB-A96C     TCGA-ZB-A96D 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-ZB-A96I     TCGA-ZB-A96Q     TCGA-ZB-A96R     TCGA-ZB-A96V 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-ZC-AAA7     TCGA-ZC-AAAA     TCGA-ZC-AAAF     TCGA-ZC-AAAH 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-ZL-A9V6 
"NRAS WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NRAS MUTATED        0      0      0      2
  NRAS WILD-TYPE     16     23     28     18
D6V4, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2             85 
    TCGA-3G-AB0O     TCGA-3G-AB0Q     TCGA-3G-AB0T     TCGA-3G-AB14 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-3G-AB19     TCGA-3Q-A9WF     TCGA-3S-A8YW     TCGA-3S-AAYX 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-4V-A9QL     TCGA-4V-A9QN     TCGA-4V-A9QS     TCGA-4V-A9QW 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-4V-A9QX     TCGA-4X-A9F9     TCGA-4X-A9FB     TCGA-4X-A9FC 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-5G-A9ZZ     TCGA-5K-AAAP     TCGA-5U-AB0E     TCGA-5U-AB0F 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-5V-A9RR     TCGA-X7-A8D6     TCGA-X7-A8D7     TCGA-X7-A8D9 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-X7-A8DB     TCGA-X7-A8DC     TCGA-X7-A8DD     TCGA-X7-A8DE 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-X7-A8DF     TCGA-X7-A8DG     TCGA-X7-A8DI     TCGA-X7-A8DJ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-X7-A8M0     TCGA-X7-A8M1     TCGA-X7-A8M3     TCGA-X7-A8M4 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-X7-A8M5     TCGA-X7-A8M6     TCGA-XM-A8R8     TCGA-XM-A8RB 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XM-A8RC     TCGA-XM-A8RD     TCGA-XM-A8RE     TCGA-XM-A8RF 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XM-A8RG     TCGA-XM-A8RH     TCGA-XM-A8RI     TCGA-XM-AAZ2 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XM-AAZ3     TCGA-XU-A92Q     TCGA-XU-A92R     TCGA-XU-A92U 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XU-A92V     TCGA-XU-A92X     TCGA-XU-A931     TCGA-XU-A932 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XU-A933     TCGA-XU-A936     TCGA-XU-AAY0     TCGA-XU-AAY1 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-YT-A95D     TCGA-YT-A95E     TCGA-YT-A95F     TCGA-YT-A95G 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-YT-A95H     TCGA-ZB-A961     TCGA-ZB-A962     TCGA-ZB-A963 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-ZB-A964     TCGA-ZB-A965     TCGA-ZB-A966     TCGA-ZB-A969 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-ZB-A96A     TCGA-ZB-A96B     TCGA-ZB-A96C     TCGA-ZB-A96D 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-ZB-A96I     TCGA-ZB-A96Q     TCGA-ZB-A96R     TCGA-ZB-A96V 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-ZC-AAA7     TCGA-ZC-AAAA     TCGA-ZC-AAAF     TCGA-ZC-AAAH 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-ZL-A9V6 
"NRAS WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NRAS MUTATED        1      1      1      0
  NRAS WILD-TYPE     41     29     29     14
D6V5, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1             41
  CLUS_2            1             29
  CLUS_3            1             29
  CLUS_4            0             14
[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 CLUS_4
  NRAS MUTATED        1      0      1      1
  NRAS WILD-TYPE     43     42     19      9
D6V6, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1             43
  CLUS_2            0             42
  CLUS_3            1             19
  CLUS_4            1              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
  NRAS MUTATED        2      1      0
  NRAS WILD-TYPE     52     60      5
D6V7, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            2             52
  CLUS_2            1             60
  CLUS_3            0              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NRAS MUTATED        1      0      1      0      1      0
  NRAS WILD-TYPE     25     18     25      7     15     27
D6V8, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1             25
  CLUS_2            0             18
  CLUS_3            1             25
  CLUS_4            0              7
  CLUS_5            1             15
  CLUS_6            0             27
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NRAS MUTATED        0      1      2      0
  NRAS WILD-TYPE     25     50     41      1
D6V9, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0             25
  CLUS_2            1             50
  CLUS_3            2             41
  CLUS_4            0              1
[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 CLUS_4
  NRAS MUTATED        1      1      1      0
  NRAS WILD-TYPE     25     32     32     28
D6V10, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1             25
  CLUS_2            1             32
  CLUS_3            1             32
  CLUS_4            0             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"

Clustering(7) Variable = PLEKHG4B MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PLEKHG4B MUTATED        0      0      0      1      2
  PLEKHG4B WILD-TYPE     35     27     19     28      8
D7V1, multiclass
        clus
vv       PLEKHG4B MUTATED PLEKHG4B WILD-TYPE
  CLUS_1                0                 35
  CLUS_2                0                 27
  CLUS_3                0                 19
  CLUS_4                1                 28
  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 CLUS_6 CLUS_7 CLUS_8
  PLEKHG4B MUTATED        0      1      0      1      0      0      0      1
  PLEKHG4B WILD-TYPE     34     22     19      9     18      8      2      5
D7V2, multiclass
        clus
vv       PLEKHG4B MUTATED PLEKHG4B WILD-TYPE
  CLUS_1                0                 34
  CLUS_2                1                 22
  CLUS_3                0                 19
  CLUS_4                1                  9
  CLUS_5                0                 18
  CLUS_6                0                  8
  CLUS_7                0                  2
  CLUS_8                1                  5
[1] 8 2
[1] 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
  PLEKHG4B MUTATED        2      0      0
  PLEKHG4B WILD-TYPE     29     25     31
D7V3, multiclass
[1] "Remove cluster labels:" "PLEKHG4B MUTATED"      
clus
  PLEKHG4B MUTATED PLEKHG4B WILD-TYPE 
                 2                 85 
        TCGA-3G-AB0O         TCGA-3G-AB0Q         TCGA-3G-AB0T 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-3G-AB14         TCGA-3G-AB19         TCGA-3Q-A9WF 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-3S-A8YW         TCGA-3S-AAYX         TCGA-4V-A9QL 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-4V-A9QN         TCGA-4V-A9QS         TCGA-4V-A9QW 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-4V-A9QX         TCGA-4X-A9F9         TCGA-4X-A9FB 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-4X-A9FC         TCGA-5G-A9ZZ         TCGA-5K-AAAP 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-5U-AB0E         TCGA-5U-AB0F         TCGA-5V-A9RR 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8D6         TCGA-X7-A8D7         TCGA-X7-A8D9 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8DB         TCGA-X7-A8DC         TCGA-X7-A8DD 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8DE         TCGA-X7-A8DF         TCGA-X7-A8DG 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8DI         TCGA-X7-A8DJ         TCGA-X7-A8M0 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8M1         TCGA-X7-A8M3         TCGA-X7-A8M4 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8M5         TCGA-X7-A8M6         TCGA-XM-A8R8 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XM-A8RB         TCGA-XM-A8RC         TCGA-XM-A8RD 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XM-A8RE         TCGA-XM-A8RF         TCGA-XM-A8RG 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XM-A8RH         TCGA-XM-AAZ1         TCGA-XM-AAZ2 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XM-AAZ3         TCGA-XU-A92Q         TCGA-XU-A92R 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-A92U         TCGA-XU-A92V         TCGA-XU-A92X 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-A92Z         TCGA-XU-A931         TCGA-XU-A932 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-A933         TCGA-XU-A936         TCGA-XU-AAY0 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-AAY1         TCGA-YT-A95D         TCGA-YT-A95E 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-YT-A95F         TCGA-YT-A95G         TCGA-YT-A95H 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A961         TCGA-ZB-A962         TCGA-ZB-A963 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A964         TCGA-ZB-A965         TCGA-ZB-A969 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A96A         TCGA-ZB-A96B         TCGA-ZB-A96C 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A96D         TCGA-ZB-A96I         TCGA-ZB-A96Q 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A96R         TCGA-ZB-A96V         TCGA-ZC-AAA7 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZC-AAAA         TCGA-ZC-AAAF         TCGA-ZC-AAAH 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZL-A9V6 
"PLEKHG4B WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PLEKHG4B MUTATED        0      0      0      2
  PLEKHG4B WILD-TYPE     16     23     28     18
D7V4, multiclass
[1] "Remove cluster labels:" "PLEKHG4B MUTATED"      
clus
  PLEKHG4B MUTATED PLEKHG4B WILD-TYPE 
                 2                 85 
        TCGA-3G-AB0O         TCGA-3G-AB0Q         TCGA-3G-AB0T 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-3G-AB14         TCGA-3G-AB19         TCGA-3Q-A9WF 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-3S-A8YW         TCGA-3S-AAYX         TCGA-4V-A9QL 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-4V-A9QN         TCGA-4V-A9QS         TCGA-4V-A9QW 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-4V-A9QX         TCGA-4X-A9F9         TCGA-4X-A9FB 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-4X-A9FC         TCGA-5G-A9ZZ         TCGA-5K-AAAP 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-5U-AB0E         TCGA-5U-AB0F         TCGA-5V-A9RR 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8D6         TCGA-X7-A8D7         TCGA-X7-A8D9 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8DB         TCGA-X7-A8DC         TCGA-X7-A8DD 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8DE         TCGA-X7-A8DF         TCGA-X7-A8DG 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8DI         TCGA-X7-A8DJ         TCGA-X7-A8M0 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8M1         TCGA-X7-A8M3         TCGA-X7-A8M4 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8M5         TCGA-X7-A8M6         TCGA-XM-A8R8 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XM-A8RB         TCGA-XM-A8RC         TCGA-XM-A8RD 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XM-A8RE         TCGA-XM-A8RF         TCGA-XM-A8RG 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XM-A8RH         TCGA-XM-AAZ1         TCGA-XM-AAZ2 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XM-AAZ3         TCGA-XU-A92Q         TCGA-XU-A92R 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-A92U         TCGA-XU-A92V         TCGA-XU-A92X 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-A92Z         TCGA-XU-A931         TCGA-XU-A932 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-A933         TCGA-XU-A936         TCGA-XU-AAY0 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-AAY1         TCGA-YT-A95D         TCGA-YT-A95E 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-YT-A95F         TCGA-YT-A95G         TCGA-YT-A95H 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A961         TCGA-ZB-A962         TCGA-ZB-A963 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A964         TCGA-ZB-A965         TCGA-ZB-A969 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A96A         TCGA-ZB-A96B         TCGA-ZB-A96C 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A96D         TCGA-ZB-A96I         TCGA-ZB-A96Q 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A96R         TCGA-ZB-A96V         TCGA-ZC-AAA7 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZC-AAAA         TCGA-ZC-AAAF         TCGA-ZC-AAAH 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZL-A9V6 
"PLEKHG4B WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PLEKHG4B MUTATED        1      0      1      1
  PLEKHG4B WILD-TYPE     41     30     29     13
D7V5, multiclass
        clus
vv       PLEKHG4B MUTATED PLEKHG4B WILD-TYPE
  CLUS_1                1                 41
  CLUS_2                0                 30
  CLUS_3                1                 29
  CLUS_4                1                 13
[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 CLUS_4
  PLEKHG4B MUTATED        1      0      1      1
  PLEKHG4B WILD-TYPE     43     42     19      9
D7V6, multiclass
        clus
vv       PLEKHG4B MUTATED PLEKHG4B WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                0                 42
  CLUS_3                1                 19
  CLUS_4                1                  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
  PLEKHG4B MUTATED        2      1      0
  PLEKHG4B WILD-TYPE     52     60      5
D7V7, multiclass
        clus
vv       PLEKHG4B MUTATED PLEKHG4B WILD-TYPE
  CLUS_1                2                 52
  CLUS_2                1                 60
  CLUS_3                0                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PLEKHG4B MUTATED        1      0      0      1      0      1
  PLEKHG4B WILD-TYPE     25     18     26      6     16     26
D7V8, multiclass
        clus
vv       PLEKHG4B MUTATED PLEKHG4B WILD-TYPE
  CLUS_1                1                 25
  CLUS_2                0                 18
  CLUS_3                0                 26
  CLUS_4                1                  6
  CLUS_5                0                 16
  CLUS_6                1                 26
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PLEKHG4B MUTATED        0      1      2      0
  PLEKHG4B WILD-TYPE     25     50     41      1
D7V9, multiclass
        clus
vv       PLEKHG4B MUTATED PLEKHG4B WILD-TYPE
  CLUS_1                0                 25
  CLUS_2                1                 50
  CLUS_3                2                 41
  CLUS_4                0                  1
[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 CLUS_4
  PLEKHG4B MUTATED        1      0      1      1
  PLEKHG4B WILD-TYPE     25     33     32     27
D7V10, multiclass
        clus
vv       PLEKHG4B MUTATED PLEKHG4B WILD-TYPE
  CLUS_1                1                 25
  CLUS_2                0                 33
  CLUS_3                1                 32
  CLUS_4                1                 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"

Clustering(8) Variable = UNC93B1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  UNC93B1 MUTATED        0      4      0      1      0
  UNC93B1 WILD-TYPE     35     23     19     28     10
D8V1, multiclass
        clus
vv       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  CLUS_1               0                35
  CLUS_2               4                23
  CLUS_3               0                19
  CLUS_4               1                28
  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 CLUS_6 CLUS_7 CLUS_8
  UNC93B1 MUTATED        0      3      0      0      1      1      0      0
  UNC93B1 WILD-TYPE     34     20     19     10     17      7      2      6
D8V2, multiclass
        clus
vv       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  CLUS_1               0                34
  CLUS_2               3                20
  CLUS_3               0                19
  CLUS_4               0                10
  CLUS_5               1                17
  CLUS_6               1                 7
  CLUS_7               0                 2
  CLUS_8               0                 6
[1] 8 2
[1] 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
  UNC93B1 MUTATED        1      2      1
  UNC93B1 WILD-TYPE     30     23     30
D8V3, multiclass
        clus
vv       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  CLUS_1               1                30
  CLUS_2               2                23
  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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  UNC93B1 MUTATED        0      3      1      0
  UNC93B1 WILD-TYPE     16     20     27     20
D8V4, multiclass
        clus
vv       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  CLUS_1               0                16
  CLUS_2               3                20
  CLUS_3               1                27
  CLUS_4               0                20
[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 CLUS_4
  UNC93B1 MUTATED        0      2      3      0
  UNC93B1 WILD-TYPE     42     28     27     14
D8V5, multiclass
        clus
vv       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  CLUS_1               0                42
  CLUS_2               2                28
  CLUS_3               3                27
  CLUS_4               0                14
[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 CLUS_4
  UNC93B1 MUTATED        0      3      2      0
  UNC93B1 WILD-TYPE     44     39     18     10
D8V6, multiclass
        clus
vv       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  CLUS_1               0                44
  CLUS_2               3                39
  CLUS_3               2                18
  CLUS_4               0                10
[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
  UNC93B1 MUTATED        0      5      0
  UNC93B1 WILD-TYPE     54     56      5
D8V7, multiclass
        clus
vv       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  CLUS_1               0                54
  CLUS_2               5                56
  CLUS_3               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  UNC93B1 MUTATED        0      2      0      0      2      1
  UNC93B1 WILD-TYPE     26     16     26      7     14     26
D8V8, multiclass
        clus
vv       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  CLUS_1               0                26
  CLUS_2               2                16
  CLUS_3               0                26
  CLUS_4               0                 7
  CLUS_5               2                14
  CLUS_6               1                26
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  UNC93B1 MUTATED        0      5      0      0
  UNC93B1 WILD-TYPE     25     46     43      1
D8V9, multiclass
        clus
vv       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  CLUS_1               0                25
  CLUS_2               5                46
  CLUS_3               0                43
  CLUS_4               0                 1
[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 CLUS_4
  UNC93B1 MUTATED        0      4      0      1
  UNC93B1 WILD-TYPE     26     29     33     27
D8V10, multiclass
        clus
vv       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  CLUS_1               0                26
  CLUS_2               4                29
  CLUS_3               0                33
  CLUS_4               1                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"
