[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"       "-oTLGG-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/LGG-TP/11590619/LGG-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/10686104/transformed.cor.cli.txt"

nPatients in clinical file=516, in cluster file=289, common to both=289
[1] "Reduce the number of clustering variables from 38 to 37."
[1]  37 289
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
           220             69 
  IDH1 MUTATED IDH1 WILD-TYPE 
           220             69 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           146            143 
  TP53 MUTATED TP53 WILD-TYPE 
           146            143 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
           118            171 
  ATRX MUTATED ATRX WILD-TYPE 
           118            171 
[1] "CIC MUTATION ANALYSIS"
[1] 3
  CIC MUTATED CIC WILD-TYPE 
           54           235 
  CIC MUTATED CIC WILD-TYPE 
           54           235 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              29              260 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              29              260 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
            12            277 
  IDH2 MUTATED IDH2 WILD-TYPE 
            12            277 
[1] "FUBP1 MUTATION ANALYSIS"
[1] 3
  FUBP1 MUTATED FUBP1 WILD-TYPE 
             26             263 
  FUBP1 MUTATED FUBP1 WILD-TYPE 
             26             263 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           19           270 
  NF1 MUTATED NF1 WILD-TYPE 
           19           270 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              13              276 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              13              276 
[1] "STK19 MUTATION ANALYSIS"
[1] 3
  STK19 MUTATED STK19 WILD-TYPE 
              8             281 
  STK19 MUTATED STK19 WILD-TYPE 
              8             281 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            13            276 
  PTEN MUTATED PTEN WILD-TYPE 
            13            276 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              25              264 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              25              264 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              277 
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              277 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            17            272 
  EGFR MUTATED EGFR WILD-TYPE 
            17            272 
[1] "GAGE2B MUTATION ANALYSIS"
[1] 3
  GAGE2B MUTATED GAGE2B WILD-TYPE 
               4              285 
  GAGE2B MUTATED GAGE2B WILD-TYPE 
               4              285 
[1] "CREBZF MUTATION ANALYSIS"
[1] 3
  CREBZF MUTATED CREBZF WILD-TYPE 
               5              284 
  CREBZF MUTATED CREBZF WILD-TYPE 
               5              284 
[1] "TCF12 MUTATION ANALYSIS"
[1] 3
  TCF12 MUTATED TCF12 WILD-TYPE 
              8             281 
  TCF12 MUTATED TCF12 WILD-TYPE 
              8             281 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               13               276 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               13               276 
[1] "VAV3 MUTATION ANALYSIS"
[1] 3
  VAV3 MUTATED VAV3 WILD-TYPE 
             8            281 
  VAV3 MUTATED VAV3 WILD-TYPE 
             8            281 
[1] "TMEM216 MUTATION ANALYSIS"
[1] 3
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                3               286 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                3               286 
[1] "ROBO3 MUTATION ANALYSIS"
[1] 3
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              4             285 
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              4             285 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
             5            284 
  IRS4 MUTATED IRS4 WILD-TYPE 
             5            284 
[1] "HTRA2 MUTATION ANALYSIS"
[1] 3
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              4             285 
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              4             285 
[1] "EIF1AX MUTATION ANALYSIS"
[1] 3
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               4              285 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               4              285 
[1] "FAM47C MUTATION ANALYSIS"
[1] 3
  FAM47C MUTATED FAM47C WILD-TYPE 
               7              282 
  FAM47C MUTATED FAM47C WILD-TYPE 
               7              282 
[1] "PLCG1 MUTATION ANALYSIS"
[1] 3
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              4             285 
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              4             285 
[1] "DDX5 MUTATION ANALYSIS"
[1] 3
  DDX5 MUTATED DDX5 WILD-TYPE 
             4            285 
  DDX5 MUTATED DDX5 WILD-TYPE 
             4            285 
[1] "ZNF709 MUTATION ANALYSIS"
[1] 3
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               3              286 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               3              286 
[1] "TRERF1 MUTATION ANALYSIS"
[1] 3
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               3              286 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               3              286 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
             9            280 
  BCOR MUTATED BCOR WILD-TYPE 
             9            280 
[1] "SRPX MUTATION ANALYSIS"
[1] 3
  SRPX MUTATED SRPX WILD-TYPE 
             3            286 
  SRPX MUTATED SRPX WILD-TYPE 
             3            286 
[1] "DOCK5 MUTATION ANALYSIS"
[1] 3
  DOCK5 MUTATED DOCK5 WILD-TYPE 
              6             283 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
              6             283 
[1] "GIGYF2 MUTATION ANALYSIS"
[1] 3
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               4              285 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               4              285 
[1] "NIPBL MUTATION ANALYSIS"
[1] 3
  NIPBL MUTATED NIPBL WILD-TYPE 
              6             283 
  NIPBL MUTATED NIPBL WILD-TYPE 
              6             283 
[1] "ZBTB20 MUTATION ANALYSIS"
[1] 3
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              13              276 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              13              276 
[1] "TRIP12 MUTATION ANALYSIS"
[1] 3
  TRIP12 MUTATED TRIP12 WILD-TYPE 
               5              284 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
               5              284 
[1] "KIAA0664 MUTATION ANALYSIS"
[1] 3
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                 5                284 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                 5                284 
[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 289 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=4,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	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=4,	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 289 columns, 0 survival variables, and 12 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = IDH1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        9      7      6
  IDH1 WILD-TYPE      0      3      1
D1V1, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            9              0
  CLUS_2            7              3
  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 CLUS_4
  IDH1 MUTATED        6      6      5      5
  IDH1 WILD-TYPE      1      1      2      0
D1V2, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            6              1
  CLUS_2            6              1
  CLUS_3            5              2
  CLUS_4            5              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
  IDH1 MUTATED       89     27    102
  IDH1 WILD-TYPE      7     42     19
D1V3, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           89              7
  CLUS_2           27             42
  CLUS_3          102             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH1 MUTATED      126      1     81     12
  IDH1 WILD-TYPE      3     41      7     18
D1V4, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1          126              3
  CLUS_2            1             41
  CLUS_3           81              7
  CLUS_4           12             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
  IDH1 MUTATED       42     31     61     57
  IDH1 WILD-TYPE     10     30      4     16
D1V5, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           42             10
  CLUS_2           31             30
  CLUS_3           61              4
  CLUS_4           57             16
[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
  IDH1 MUTATED       60     90     41
  IDH1 WILD-TYPE      6     38     16
D1V6, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           60              6
  CLUS_2           90             38
  CLUS_3           41             16
[1] 3 2
[1] 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
  IDH1 MUTATED       74     21     46     65     13
  IDH1 WILD-TYPE      1     44      5     18      1
D1V7, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           74              1
  CLUS_2           21             44
  CLUS_3           46              5
  CLUS_4           65             18
  CLUS_5           13              1
[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
  IDH1 MUTATED       77     22     53     67
  IDH1 WILD-TYPE      1     43      5     20
D1V8, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           77              1
  CLUS_2           22             43
  CLUS_3           53              5
  CLUS_4           67             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
  IDH1 MUTATED       56     41     89     34
  IDH1 WILD-TYPE     27     16     24      2
D1V9, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           56             27
  CLUS_2           41             16
  CLUS_3           89             24
  CLUS_4           34              2
[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
  IDH1 MUTATED      115     88     17
  IDH1 WILD-TYPE      9     20     40
D1V10, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1          115              9
  CLUS_2           88             20
  CLUS_3           17             40
[1] 3 2
[1] 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
  IDH1 MUTATED       76     68     75
  IDH1 WILD-TYPE     42      6     20
D1V11, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           76             42
  CLUS_2           68              6
  CLUS_3           75             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
  IDH1 MUTATED       50     60    104      5
  IDH1 WILD-TYPE      2      6     18     42
D1V12, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           50              2
  CLUS_2           60              6
  CLUS_3          104             18
  CLUS_4            5             42
[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 = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        8      4      3
  TP53 WILD-TYPE      1      6      4
D2V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8              1
  CLUS_2            4              6
  CLUS_3            3              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        5      7      1      2
  TP53 WILD-TYPE      2      0      6      3
D2V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            5              2
  CLUS_2            7              0
  CLUS_3            1              6
  CLUS_4            2              3
[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       91     28     27
  TP53 WILD-TYPE      5     41     94
D2V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           91              5
  CLUS_2           28             41
  CLUS_3           27             94
[1] 3 2
[1] 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      125      8      3     10
  TP53 WILD-TYPE      4     34     85     20
D2V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1          125              4
  CLUS_2            8             34
  CLUS_3            3             85
  CLUS_4           10             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
  TP53 MUTATED       33     30     39     29
  TP53 WILD-TYPE     19     31     26     44
D2V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           33             19
  CLUS_2           30             31
  CLUS_3           39             26
  CLUS_4           29             44
[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       37     68     26
  TP53 WILD-TYPE     29     60     31
D2V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           37             29
  CLUS_2           68             60
  CLUS_3           26             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 CLUS_5
  TP53 MUTATED       74     25      3     37      7
  TP53 WILD-TYPE      1     40     48     46      7
D2V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           74              1
  CLUS_2           25             40
  CLUS_3            3             48
  CLUS_4           37             46
  CLUS_5            7              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
  TP53 MUTATED       75     27      3     41
  TP53 WILD-TYPE      3     38     55     46
D2V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           75              3
  CLUS_2           27             38
  CLUS_3            3             55
  CLUS_4           41             46
[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       51     41     45      9
  TP53 WILD-TYPE     32     16     68     27
D2V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           51             32
  CLUS_2           41             16
  CLUS_3           45             68
  CLUS_4            9             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
  TP53 MUTATED       83     40     23
  TP53 WILD-TYPE     41     68     34
D2V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           83             41
  CLUS_2           40             68
  CLUS_3           23             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
  TP53 MUTATED       66     45     34
  TP53 WILD-TYPE     52     29     61
D2V11, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           66             52
  CLUS_2           45             29
  CLUS_3           34             61
[1] 3 2
[1] 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       48     30     56     11
  TP53 WILD-TYPE      4     36     66     36
D2V12, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           48              4
  CLUS_2           30             36
  CLUS_3           56             66
  CLUS_4           11             36
[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 = ATRX MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ATRX MUTATED        8      3      2
  ATRX WILD-TYPE      1      7      5
D3V1, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            8              1
  CLUS_2            3              7
  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 CLUS_4
  ATRX MUTATED        5      5      1      2
  ATRX WILD-TYPE      2      2      6      3
D3V2, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            5              2
  CLUS_2            5              2
  CLUS_3            1              6
  CLUS_4            2              3
[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
  ATRX MUTATED       75     21     22
  ATRX WILD-TYPE     21     48     99
D3V3, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           75             21
  CLUS_2           21             48
  CLUS_3           22             99
[1] 3 2
[1] 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
  ATRX MUTATED      105      2      2      9
  ATRX WILD-TYPE     24     40     86     21
D3V4, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1          105             24
  CLUS_2            2             40
  CLUS_3            2             86
  CLUS_4            9             21
[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
  ATRX MUTATED       27     23     32     26
  ATRX WILD-TYPE     25     38     33     47
D3V5, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           27             25
  CLUS_2           23             38
  CLUS_3           32             33
  CLUS_4           26             47
[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
  ATRX MUTATED       31     53     24
  ATRX WILD-TYPE     35     75     33
D3V6, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           31             35
  CLUS_2           53             75
  CLUS_3           24             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 CLUS_5
  ATRX MUTATED       65     15      1     32      5
  ATRX WILD-TYPE     10     50     50     51      9
D3V7, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           65             10
  CLUS_2           15             50
  CLUS_3            1             50
  CLUS_4           32             51
  CLUS_5            5              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
  ATRX MUTATED       65     17      1     35
  ATRX WILD-TYPE     13     48     57     52
D3V8, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           65             13
  CLUS_2           17             48
  CLUS_3            1             57
  CLUS_4           35             52
[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
  ATRX MUTATED       37     35     39      7
  ATRX WILD-TYPE     46     22     74     29
D3V9, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           37             46
  CLUS_2           35             22
  CLUS_3           39             74
  CLUS_4            7             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
  ATRX MUTATED       69     37     12
  ATRX WILD-TYPE     55     71     45
D3V10, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           69             55
  CLUS_2           37             71
  CLUS_3           12             45
[1] 3 2
[1] 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
  ATRX MUTATED       52     36     29
  ATRX WILD-TYPE     66     38     66
D3V11, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           52             66
  CLUS_2           36             38
  CLUS_3           29             66
[1] 3 2
[1] 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
  ATRX MUTATED       38     26     48      5
  ATRX WILD-TYPE     14     40     74     42
D3V12, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           38             14
  CLUS_2           26             40
  CLUS_3           48             74
  CLUS_4            5             42
[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 = CIC MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  CIC MUTATED        0      5      2
  CIC WILD-TYPE      9      5      5
D4V1, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0             9
  CLUS_2           5             5
  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 CLUS_4
  CIC MUTATED        0      0      5      2
  CIC WILD-TYPE      7      7      2      3
D4V2, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0             7
  CLUS_2           0             7
  CLUS_3           5             2
  CLUS_4           2             3
[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
  CIC MUTATED        0      3     51
  CIC WILD-TYPE     96     66     70
D4V3, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0            96
  CLUS_2           3            66
  CLUS_3          51            70
[1] 3 2
[1] 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
  CIC MUTATED        0      0     54      0
  CIC WILD-TYPE    129     42     34     30
D4V4, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0           129
  CLUS_2           0            42
  CLUS_3          54            34
  CLUS_4           0            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 CLUS_4
  CIC MUTATED        1      6     20     15
  CIC WILD-TYPE     51     55     45     58
D4V5, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           1            51
  CLUS_2           6            55
  CLUS_3          20            45
  CLUS_4          15            58
[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
  CIC MUTATED        8     24     10
  CIC WILD-TYPE     58    104     47
D4V6, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           8            58
  CLUS_2          24           104
  CLUS_3          10            47
[1] 3 2
[1] 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
  CIC MUTATED        0      1     32     19      2
  CIC WILD-TYPE     75     64     19     64     12
D4V7, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0            75
  CLUS_2           1            64
  CLUS_3          32            19
  CLUS_4          19            64
  CLUS_5           2            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
  CIC MUTATED        0      1     38     15
  CIC WILD-TYPE     78     64     20     72
D4V8, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0            78
  CLUS_2           1            64
  CLUS_3          38            20
  CLUS_4          15            72
[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
  CIC MUTATED        9      2     24     19
  CIC WILD-TYPE     74     55     89     17
D4V9, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           9            74
  CLUS_2           2            55
  CLUS_3          24            89
  CLUS_4          19            17
[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
  CIC MUTATED       28     26      0
  CIC WILD-TYPE     96     82     57
D4V10, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1          28            96
  CLUS_2          26            82
  CLUS_3           0            57
[1] 3 2
[1] 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
  CIC MUTATED        7     23     24
  CIC WILD-TYPE    111     51     71
D4V11, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           7           111
  CLUS_2          23            51
  CLUS_3          24            71
[1] 3 2
[1] 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
  CIC MUTATED        0     28     26      0
  CIC WILD-TYPE     52     38     96     47
D4V12, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0            52
  CLUS_2          28            38
  CLUS_3          26            96
  CLUS_4           0            47
[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 = NOTCH1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH1 MUTATED        0      2      1
  NOTCH1 WILD-TYPE      9      8      6
D5V1, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              2                8
  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 CLUS_4
  NOTCH1 MUTATED        0      0      2      1
  NOTCH1 WILD-TYPE      7      7      5      4
D5V2, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              0                7
  CLUS_3              2                5
  CLUS_4              1                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
  NOTCH1 MUTATED        3      4     22
  NOTCH1 WILD-TYPE     93     65     99
D5V3, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              3               93
  CLUS_2              4               65
  CLUS_3             22               99
[1] 3 2
[1] 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
  NOTCH1 MUTATED        6      0     23      0
  NOTCH1 WILD-TYPE    123     42     65     30
D5V4, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              6              123
  CLUS_2              0               42
  CLUS_3             23               65
  CLUS_4              0               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 CLUS_4
  NOTCH1 MUTATED        4      6      7      9
  NOTCH1 WILD-TYPE     48     55     58     64
D5V5, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              4               48
  CLUS_2              6               55
  CLUS_3              7               58
  CLUS_4              9               64
[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
  NOTCH1 MUTATED        6     13      7
  NOTCH1 WILD-TYPE     60    115     50
D5V6, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              6               60
  CLUS_2             13              115
  CLUS_3              7               50
[1] 3 2
[1] 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
  NOTCH1 MUTATED        1      2     15     11      0
  NOTCH1 WILD-TYPE     74     63     36     72     14
D5V7, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               74
  CLUS_2              2               63
  CLUS_3             15               36
  CLUS_4             11               72
  CLUS_5              0               14
[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
  NOTCH1 MUTATED        1      2     14     12
  NOTCH1 WILD-TYPE     77     63     44     75
D5V8, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               77
  CLUS_2              2               63
  CLUS_3             14               44
  CLUS_4             12               75
[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
  NOTCH1 MUTATED        1      2     18      8
  NOTCH1 WILD-TYPE     82     55     95     28
D5V9, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               82
  CLUS_2              2               55
  CLUS_3             18               95
  CLUS_4              8               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
  NOTCH1 MUTATED        8     20      1
  NOTCH1 WILD-TYPE    116     88     56
D5V10, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              8              116
  CLUS_2             20               88
  CLUS_3              1               56
[1] 3 2
[1] 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
  NOTCH1 MUTATED        3      7     19
  NOTCH1 WILD-TYPE    115     67     76
D5V11, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              3              115
  CLUS_2              7               67
  CLUS_3             19               76
[1] 3 2
[1] 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
  NOTCH1 MUTATED        1      8     20      0
  NOTCH1 WILD-TYPE     51     58    102     47
D5V12, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               51
  CLUS_2              8               58
  CLUS_3             20              102
  CLUS_4              0               47
[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 = IDH2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH2 MUTATED        0      2      0
  IDH2 WILD-TYPE      9      8      7
D6V1, multiclass
[1] "Remove cluster labels:" "IDH2 MUTATED"          
clus
  IDH2 MUTATED IDH2 WILD-TYPE 
             2             24 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-CS-5394     TCGA-CS-5395     TCGA-CS-5396     TCGA-DB-5273 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144     TCGA-E1-5302 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311     TCGA-E1-5322 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH2 MUTATED        0      0      2      0
  IDH2 WILD-TYPE      7      7      5      5
D6V2, multiclass
[1] "Remove cluster labels:" "IDH2 MUTATED"          
clus
  IDH2 MUTATED IDH2 WILD-TYPE 
             2             24 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-CS-5394     TCGA-CS-5395     TCGA-CS-5396     TCGA-DB-5273 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144     TCGA-E1-5302 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311     TCGA-E1-5322 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH2 MUTATED        1      1     10
  IDH2 WILD-TYPE     95     68    111
D6V3, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            1             95
  CLUS_2            1             68
  CLUS_3           10            111
[1] 3 2
[1] 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
  IDH2 MUTATED        2      0      7      3
  IDH2 WILD-TYPE    127     42     81     27
D6V4, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            2            127
  CLUS_2            0             42
  CLUS_3            7             81
  CLUS_4            3             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 CLUS_4
  IDH2 MUTATED        1      4      2      5
  IDH2 WILD-TYPE     51     57     63     68
D6V5, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            1             51
  CLUS_2            4             57
  CLUS_3            2             63
  CLUS_4            5             68
[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
  IDH2 MUTATED        1      6      5
  IDH2 WILD-TYPE     65    122     52
D6V6, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            1             65
  CLUS_2            6            122
  CLUS_3            5             52
[1] 3 2
[1] 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
  IDH2 MUTATED        0      0      5      7      0
  IDH2 WILD-TYPE     75     65     46     76     14
D6V7, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0             75
  CLUS_2            0             65
  CLUS_3            5             46
  CLUS_4            7             76
  CLUS_5            0             14
[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
  IDH2 MUTATED        0      0      5      7
  IDH2 WILD-TYPE     78     65     53     80
D6V8, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0             78
  CLUS_2            0             65
  CLUS_3            5             53
  CLUS_4            7             80
[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
  IDH2 MUTATED        2      0      8      2
  IDH2 WILD-TYPE     81     57    105     34
D6V9, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            2             81
  CLUS_2            0             57
  CLUS_3            8            105
  CLUS_4            2             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
  IDH2 MUTATED        3      9      0
  IDH2 WILD-TYPE    121     99     57
D6V10, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            3            121
  CLUS_2            9             99
  CLUS_3            0             57
[1] 3 2
[1] 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
  IDH2 MUTATED        0      5      7
  IDH2 WILD-TYPE    118     69     88
D6V11, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0            118
  CLUS_2            5             69
  CLUS_3            7             88
[1] 3 2
[1] 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
  IDH2 MUTATED        0      4      8      0
  IDH2 WILD-TYPE     52     62    114     47
D6V12, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0             52
  CLUS_2            4             62
  CLUS_3            8            114
  CLUS_4            0             47
[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 = FUBP1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FUBP1 MUTATED        0      4      0
  FUBP1 WILD-TYPE      9      6      7
D7V1, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             4               6
  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 CLUS_4
  FUBP1 MUTATED        0      0      4      0
  FUBP1 WILD-TYPE      7      7      3      5
D7V2, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0               7
  CLUS_2             0               7
  CLUS_3             4               3
  CLUS_4             0               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
  FUBP1 MUTATED        0      0     26
  FUBP1 WILD-TYPE     96     69     95
D7V3, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0              96
  CLUS_2             0              69
  CLUS_3            26              95
[1] 3 2
[1] 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
  FUBP1 MUTATED        0      0     26      0
  FUBP1 WILD-TYPE    129     42     62     30
D7V4, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0             129
  CLUS_2             0              42
  CLUS_3            26              62
  CLUS_4             0              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 CLUS_4
  FUBP1 MUTATED        1      2      9     10
  FUBP1 WILD-TYPE     51     59     56     63
D7V5, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             1              51
  CLUS_2             2              59
  CLUS_3             9              56
  CLUS_4            10              63
[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
  FUBP1 MUTATED        7     10      5
  FUBP1 WILD-TYPE     59    118     52
D7V6, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             7              59
  CLUS_2            10             118
  CLUS_3             5              52
[1] 3 2
[1] 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
  FUBP1 MUTATED        0      1     16      7      2
  FUBP1 WILD-TYPE     75     64     35     76     12
D7V7, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0              75
  CLUS_2             1              64
  CLUS_3            16              35
  CLUS_4             7              76
  CLUS_5             2              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
  FUBP1 MUTATED        0      1     18      7
  FUBP1 WILD-TYPE     78     64     40     80
D7V8, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0              78
  CLUS_2             1              64
  CLUS_3            18              40
  CLUS_4             7              80
[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
  FUBP1 MUTATED        4      0     12     10
  FUBP1 WILD-TYPE     79     57    101     26
D7V9, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             4              79
  CLUS_2             0              57
  CLUS_3            12             101
  CLUS_4            10              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
  FUBP1 MUTATED       14     12      0
  FUBP1 WILD-TYPE    110     96     57
D7V10, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1            14             110
  CLUS_2            12              96
  CLUS_3             0              57
[1] 3 2
[1] 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
  FUBP1 MUTATED        8      8     10
  FUBP1 WILD-TYPE    110     66     85
D7V11, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             8             110
  CLUS_2             8              66
  CLUS_3            10              85
[1] 3 2
[1] 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
  FUBP1 MUTATED        0     12     14      0
  FUBP1 WILD-TYPE     52     54    108     47
D7V12, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0              52
  CLUS_2            12              54
  CLUS_3            14             108
  CLUS_4             0              47
[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 = NF1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        0      1      0
  NF1 WILD-TYPE      9      9      7
D8V1, multiclass
[1] "Remove cluster labels:" "NF1 MUTATED"           
clus
  NF1 MUTATED NF1 WILD-TYPE 
            1            25 
   TCGA-CS-4942    TCGA-CS-4943    TCGA-CS-4944    TCGA-CS-5390    TCGA-CS-5394 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-CS-5395    TCGA-CS-5396    TCGA-DB-5273    TCGA-DB-5274    TCGA-DB-5275 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-DB-5276    TCGA-DB-5277    TCGA-DB-5278    TCGA-DB-5280    TCGA-DB-5281 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-DH-5141    TCGA-DH-5142    TCGA-DH-5143    TCGA-DH-5144    TCGA-E1-5302 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-E1-5303    TCGA-E1-5304    TCGA-E1-5311    TCGA-E1-5318    TCGA-E1-5322 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        0      1      0      0
  NF1 WILD-TYPE      7      6      7      5
D8V2, multiclass
[1] "Remove cluster labels:" "NF1 MUTATED"           
clus
  NF1 MUTATED NF1 WILD-TYPE 
            1            25 
   TCGA-CS-4942    TCGA-CS-4943    TCGA-CS-4944    TCGA-CS-5390    TCGA-CS-5394 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-CS-5395    TCGA-CS-5396    TCGA-DB-5273    TCGA-DB-5274    TCGA-DB-5275 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-DB-5276    TCGA-DB-5277    TCGA-DB-5278    TCGA-DB-5280    TCGA-DB-5281 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-DH-5141    TCGA-DH-5142    TCGA-DH-5143    TCGA-DH-5144    TCGA-E1-5302 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-E1-5303    TCGA-E1-5304    TCGA-E1-5311    TCGA-E1-5318    TCGA-E1-5322 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        4      9      6
  NF1 WILD-TYPE     92     60    115
D8V3, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            92
  CLUS_2           9            60
  CLUS_3           6           115
[1] 3 2
[1] 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        1     10      5      3
  NF1 WILD-TYPE    128     32     83     27
D8V4, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1           128
  CLUS_2          10            32
  CLUS_3           5            83
  CLUS_4           3            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 CLUS_4
  NF1 MUTATED        1      9      2      4
  NF1 WILD-TYPE     51     52     63     69
D8V5, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            51
  CLUS_2           9            52
  CLUS_3           2            63
  CLUS_4           4            69
[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        4     11      1
  NF1 WILD-TYPE     62    117     56
D8V6, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            62
  CLUS_2          11           117
  CLUS_3           1            56
[1] 3 2
[1] 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        1     10      3      4      1
  NF1 WILD-TYPE     74     55     48     79     13
D8V7, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            74
  CLUS_2          10            55
  CLUS_3           3            48
  CLUS_4           4            79
  CLUS_5           1            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
  NF1 MUTATED        1     10      4      4
  NF1 WILD-TYPE     77     55     54     83
D8V8, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            77
  CLUS_2          10            55
  CLUS_3           4            54
  CLUS_4           4            83
[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
  NF1 MUTATED        7      4      6      2
  NF1 WILD-TYPE     76     53    107     34
D8V9, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           7            76
  CLUS_2           4            53
  CLUS_3           6           107
  CLUS_4           2            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
  NF1 MUTATED        5      4     10
  NF1 WILD-TYPE    119    104     47
D8V10, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           5           119
  CLUS_2           4           104
  CLUS_3          10            47
[1] 3 2
[1] 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       12      3      4
  NF1 WILD-TYPE    106     71     91
D8V11, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1          12           106
  CLUS_2           3            71
  CLUS_3           4            91
[1] 3 2
[1] 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        1      2      5     11
  NF1 WILD-TYPE     51     64    117     36
D8V12, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            51
  CLUS_2           2            64
  CLUS_3           5           117
  CLUS_4          11            36
[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(9) Variable = PIK3R1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3R1 MUTATED        2      1      0
  PIK3R1 WILD-TYPE      7      9      7
D9V1, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              2                7
  CLUS_2              1                9
  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 CLUS_4
  PIK3R1 MUTATED        2      0      1      0
  PIK3R1 WILD-TYPE      5      7      6      5
D9V2, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              2                5
  CLUS_2              0                7
  CLUS_3              1                6
  CLUS_4              0                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
  PIK3R1 MUTATED        1      3      9
  PIK3R1 WILD-TYPE     95     66    112
D9V3, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              1               95
  CLUS_2              3               66
  CLUS_3              9              112
[1] 3 2
[1] 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
  PIK3R1 MUTATED        3      1      9      0
  PIK3R1 WILD-TYPE    126     41     79     30
D9V4, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              3              126
  CLUS_2              1               41
  CLUS_3              9               79
  CLUS_4              0               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 CLUS_4
  PIK3R1 MUTATED        3      2      4      4
  PIK3R1 WILD-TYPE     49     59     61     69
D9V5, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              3               49
  CLUS_2              2               59
  CLUS_3              4               61
  CLUS_4              4               69
[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
  PIK3R1 MUTATED        3      7      3
  PIK3R1 WILD-TYPE     63    121     54
D9V6, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              3               63
  CLUS_2              7              121
  CLUS_3              3               54
[1] 3 2
[1] 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
  PIK3R1 MUTATED        2      3      4      4      0
  PIK3R1 WILD-TYPE     73     62     47     79     14
D9V7, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              2               73
  CLUS_2              3               62
  CLUS_3              4               47
  CLUS_4              4               79
  CLUS_5              0               14
[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
  PIK3R1 MUTATED        3      2      4      4
  PIK3R1 WILD-TYPE     75     63     54     83
D9V8, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              3               75
  CLUS_2              2               63
  CLUS_3              4               54
  CLUS_4              4               83
[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
  PIK3R1 MUTATED        4      1      4      4
  PIK3R1 WILD-TYPE     79     56    109     32
D9V9, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              4               79
  CLUS_2              1               56
  CLUS_3              4              109
  CLUS_4              4               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
  PIK3R1 MUTATED        7      5      1
  PIK3R1 WILD-TYPE    117    103     56
D9V10, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              7              117
  CLUS_2              5              103
  CLUS_3              1               56
[1] 3 2
[1] 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
  PIK3R1 MUTATED        6      3      4
  PIK3R1 WILD-TYPE    112     71     91
D9V11, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              6              112
  CLUS_2              3               71
  CLUS_3              4               91
[1] 3 2
[1] 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
  PIK3R1 MUTATED        3      2      7      1
  PIK3R1 WILD-TYPE     49     64    115     46
D9V12, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              3               49
  CLUS_2              2               64
  CLUS_3              7              115
  CLUS_4              1               46
[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(10) Variable = STK19 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STK19 MUTATED        0      0      0
  STK19 WILD-TYPE      9     10      7
D10V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STK19 MUTATED        0      0      0      0
  STK19 WILD-TYPE      7      7      7      5
D10V2, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STK19 MUTATED        3      3      2
  STK19 WILD-TYPE     93     66    119
D10V3, multiclass
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  CLUS_1             3              93
  CLUS_2             3              66
  CLUS_3             2             119
[1] 3 2
[1] 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
  STK19 MUTATED        4      2      0      2
  STK19 WILD-TYPE    125     40     88     28
D10V4, multiclass
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  CLUS_1             4             125
  CLUS_2             2              40
  CLUS_3             0              88
  CLUS_4             2              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 CLUS_4
  STK19 MUTATED        4      0      0      2
  STK19 WILD-TYPE     48     61     65     71
D10V5, multiclass
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  CLUS_1             4              48
  CLUS_2             0              61
  CLUS_3             0              65
  CLUS_4             2              71
[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
  STK19 MUTATED        3      1      2
  STK19 WILD-TYPE     63    127     55
D10V6, multiclass
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  CLUS_1             3              63
  CLUS_2             1             127
  CLUS_3             2              55
[1] 3 2
[1] 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
  STK19 MUTATED        2      2      0      4      0
  STK19 WILD-TYPE     73     63     51     79     14
D10V7, multiclass
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  CLUS_1             2              73
  CLUS_2             2              63
  CLUS_3             0              51
  CLUS_4             4              79
  CLUS_5             0              14
[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
  STK19 MUTATED        2      2      0      4
  STK19 WILD-TYPE     76     63     58     83
D10V8, multiclass
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  CLUS_1             2              76
  CLUS_2             2              63
  CLUS_3             0              58
  CLUS_4             4              83
[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
  STK19 MUTATED        1      3      4      0
  STK19 WILD-TYPE     82     54    109     36
D10V9, multiclass
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  CLUS_1             1              82
  CLUS_2             3              54
  CLUS_3             4             109
  CLUS_4             0              36
[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
  STK19 MUTATED        3      3      2
  STK19 WILD-TYPE    121    105     55
D10V10, multiclass
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  CLUS_1             3             121
  CLUS_2             3             105
  CLUS_3             2              55
[1] 3 2
[1] 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
  STK19 MUTATED        3      4      1
  STK19 WILD-TYPE    115     70     94
D10V11, multiclass
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  CLUS_1             3             115
  CLUS_2             4              70
  CLUS_3             1              94
[1] 3 2
[1] 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
  STK19 MUTATED        1      2      3      2
  STK19 WILD-TYPE     51     64    119     45
D10V12, multiclass
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  CLUS_1             1              51
  CLUS_2             2              64
  CLUS_3             3             119
  CLUS_4             2              45
[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(11) Variable = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        0      0      1
  PTEN WILD-TYPE      9     10      6
D11V1, multiclass
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             1             25 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CS-5394     TCGA-CS-5396     TCGA-DB-5273     TCGA-DB-5274 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277     TCGA-DB-5278 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140     TCGA-DH-5141 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144     TCGA-E1-5302 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311     TCGA-E1-5318 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-E1-5322 
"PTEN WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        1      0      0      0
  PTEN WILD-TYPE      6      7      7      5
D11V2, multiclass
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             1             25 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CS-5394     TCGA-CS-5396     TCGA-DB-5273     TCGA-DB-5274 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277     TCGA-DB-5278 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140     TCGA-DH-5141 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144     TCGA-E1-5302 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311     TCGA-E1-5318 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-E1-5322 
"PTEN WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        0     13      0
  PTEN WILD-TYPE     96     56    121
D11V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             96
  CLUS_2           13             56
  CLUS_3            0            121
[1] 3 2
[1] 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
  PTEN MUTATED        0     13      0      0
  PTEN WILD-TYPE    129     29     88     30
D11V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0            129
  CLUS_2           13             29
  CLUS_3            0             88
  CLUS_4            0             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 CLUS_4
  PTEN MUTATED        1      8      1      0
  PTEN WILD-TYPE     51     53     64     73
D11V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             51
  CLUS_2            8             53
  CLUS_3            1             64
  CLUS_4            0             73
[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
  PTEN MUTATED        0     10      0
  PTEN WILD-TYPE     66    118     57
D11V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             66
  CLUS_2           10            118
  CLUS_3            0             57
[1] 3 2
[1] 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
  PTEN MUTATED        0     13      0      0      0
  PTEN WILD-TYPE     75     52     51     83     14
D11V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             75
  CLUS_2           13             52
  CLUS_3            0             51
  CLUS_4            0             83
  CLUS_5            0             14
[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
  PTEN MUTATED        0     12      0      1
  PTEN WILD-TYPE     78     53     58     86
D11V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             78
  CLUS_2           12             53
  CLUS_3            0             58
  CLUS_4            1             86
[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
  PTEN MUTATED        8      3      2      0
  PTEN WILD-TYPE     75     54    111     36
D11V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            8             75
  CLUS_2            3             54
  CLUS_3            2            111
  CLUS_4            0             36
[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
  PTEN MUTATED        0      0     13
  PTEN WILD-TYPE    124    108     44
D11V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0            124
  CLUS_2            0            108
  CLUS_3           13             44
[1] 3 2
[1] 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
  PTEN MUTATED       12      0      1
  PTEN WILD-TYPE    106     74     94
D11V11, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           12            106
  CLUS_2            0             74
  CLUS_3            1             94
[1] 3 2
[1] 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
  PTEN MUTATED        0      0      0     13
  PTEN WILD-TYPE     52     66    122     34
D11V12, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             52
  CLUS_2            0             66
  CLUS_3            0            122
  CLUS_4           13             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"

Clustering(12) Variable = PIK3CA MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        0      0      0
  PIK3CA WILD-TYPE      9     10      7
D12V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        0      0      0      0
  PIK3CA WILD-TYPE      7      7      7      5
D12V2, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        1      7     17
  PIK3CA WILD-TYPE     95     62    104
D12V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1               95
  CLUS_2              7               62
  CLUS_3             17              104
[1] 3 2
[1] 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
  PIK3CA MUTATED        1      5     17      2
  PIK3CA WILD-TYPE    128     37     71     28
D12V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1              128
  CLUS_2              5               37
  CLUS_3             17               71
  CLUS_4              2               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 CLUS_4
  PIK3CA MUTATED        3      7      4      8
  PIK3CA WILD-TYPE     49     54     61     65
D12V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               49
  CLUS_2              7               54
  CLUS_3              4               61
  CLUS_4              8               65
[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
  PIK3CA MUTATED        7     10      5
  PIK3CA WILD-TYPE     59    118     52
D12V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              7               59
  CLUS_2             10              118
  CLUS_3              5               52
[1] 3 2
[1] 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
  PIK3CA MUTATED        1      5      9      7      3
  PIK3CA WILD-TYPE     74     60     42     76     11
D12V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1               74
  CLUS_2              5               60
  CLUS_3              9               42
  CLUS_4              7               76
  CLUS_5              3               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
  PIK3CA MUTATED        0      6     10      9
  PIK3CA WILD-TYPE     78     59     48     78
D12V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              0               78
  CLUS_2              6               59
  CLUS_3             10               48
  CLUS_4              9               78
[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
  PIK3CA MUTATED        4      5     11      5
  PIK3CA WILD-TYPE     79     52    102     31
D12V9, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4               79
  CLUS_2              5               52
  CLUS_3             11              102
  CLUS_4              5               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
  PIK3CA MUTATED        7     12      6
  PIK3CA WILD-TYPE    117     96     51
D12V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              7              117
  CLUS_2             12               96
  CLUS_3              6               51
[1] 3 2
[1] 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
  PIK3CA MUTATED        8      5     12
  PIK3CA WILD-TYPE    110     69     83
D12V11, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              8              110
  CLUS_2              5               69
  CLUS_3             12               83
[1] 3 2
[1] 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
  PIK3CA MUTATED        0      7     13      5
  PIK3CA WILD-TYPE     52     59    109     42
D12V12, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              0               52
  CLUS_2              7               59
  CLUS_3             13              109
  CLUS_4              5               42
[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(13) Variable = ARID1A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        0      1      0
  ARID1A WILD-TYPE      9      9      7
D13V1, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               25 
      TCGA-CS-4942       TCGA-CS-4943       TCGA-CS-4944       TCGA-CS-5390 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-CS-5394       TCGA-CS-5395       TCGA-CS-5396       TCGA-DB-5273 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DB-5274       TCGA-DB-5276       TCGA-DB-5277       TCGA-DB-5278 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DB-5280       TCGA-DB-5281       TCGA-DH-5140       TCGA-DH-5141 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144       TCGA-E1-5302 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5311       TCGA-E1-5318 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-E1-5322 
"ARID1A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        0      1      0      0
  ARID1A WILD-TYPE      7      6      7      5
D13V2, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               25 
      TCGA-CS-4942       TCGA-CS-4943       TCGA-CS-4944       TCGA-CS-5390 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-CS-5394       TCGA-CS-5395       TCGA-CS-5396       TCGA-DB-5273 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DB-5274       TCGA-DB-5276       TCGA-DB-5277       TCGA-DB-5278 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DB-5280       TCGA-DB-5281       TCGA-DH-5140       TCGA-DH-5141 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144       TCGA-E1-5302 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5311       TCGA-E1-5318 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-E1-5322 
"ARID1A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        5      2      4
  ARID1A WILD-TYPE     91     67    117
D13V3, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              5               91
  CLUS_2              2               67
  CLUS_3              4              117
[1] 3 2
[1] 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        5      1      6      0
  ARID1A WILD-TYPE    124     41     82     30
D13V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              5              124
  CLUS_2              1               41
  CLUS_3              6               82
  CLUS_4              0               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 CLUS_4
  ARID1A MUTATED        2      1      5      4
  ARID1A WILD-TYPE     50     60     60     69
D13V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2               50
  CLUS_2              1               60
  CLUS_3              5               60
  CLUS_4              4               69
[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        2      7      3
  ARID1A WILD-TYPE     64    121     54
D13V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2               64
  CLUS_2              7              121
  CLUS_3              3               54
[1] 3 2
[1] 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      0      4      5      0
  ARID1A WILD-TYPE     72     65     47     78     14
D13V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               72
  CLUS_2              0               65
  CLUS_3              4               47
  CLUS_4              5               78
  CLUS_5              0               14
[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
  ARID1A MUTATED        3      0      4      5
  ARID1A WILD-TYPE     75     65     54     82
D13V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               75
  CLUS_2              0               65
  CLUS_3              4               54
  CLUS_4              5               82
[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
  ARID1A MUTATED        3      1      6      2
  ARID1A WILD-TYPE     80     56    107     34
D13V9, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               80
  CLUS_2              1               56
  CLUS_3              6              107
  CLUS_4              2               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
  ARID1A MUTATED        6      5      1
  ARID1A WILD-TYPE    118    103     56
D13V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              6              118
  CLUS_2              5              103
  CLUS_3              1               56
[1] 3 2
[1] 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        2      4      6
  ARID1A WILD-TYPE    116     70     89
D13V11, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2              116
  CLUS_2              4               70
  CLUS_3              6               89
[1] 3 2
[1] 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      5      5      1
  ARID1A WILD-TYPE     51     61    117     46
D13V12, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               51
  CLUS_2              5               61
  CLUS_3              5              117
  CLUS_4              1               46
[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(14) Variable = EGFR MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        0      0      0
  EGFR WILD-TYPE      9     10      7
D14V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EGFR MUTATED        0      0      0      0
  EGFR WILD-TYPE      7      7      7      5
D14V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        0     16      1
  EGFR WILD-TYPE     96     53    120
D14V3, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0             96
  CLUS_2           16             53
  CLUS_3            1            120
[1] 3 2
[1] 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        0     14      1      2
  EGFR WILD-TYPE    129     28     87     28
D14V4, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0            129
  CLUS_2           14             28
  CLUS_3            1             87
  CLUS_4            2             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 CLUS_4
  EGFR MUTATED        1      9      1      3
  EGFR WILD-TYPE     51     52     64     70
D14V5, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            1             51
  CLUS_2            9             52
  CLUS_3            1             64
  CLUS_4            3             70
[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        0     11      3
  EGFR WILD-TYPE     66    117     54
D14V6, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0             66
  CLUS_2           11            117
  CLUS_3            3             54
[1] 3 2
[1] 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        0     13      1      3      0
  EGFR WILD-TYPE     75     52     50     80     14
D14V7, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0             75
  CLUS_2           13             52
  CLUS_3            1             50
  CLUS_4            3             80
  CLUS_5            0             14
[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
  EGFR MUTATED        0     13      1      3
  EGFR WILD-TYPE     78     52     57     84
D14V8, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0             78
  CLUS_2           13             52
  CLUS_3            1             57
  CLUS_4            3             84
[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
  EGFR MUTATED        6      4      7      0
  EGFR WILD-TYPE     77     53    106     36
D14V9, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            6             77
  CLUS_2            4             53
  CLUS_3            7            106
  CLUS_4            0             36
[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        0      4     13
  EGFR WILD-TYPE    124    104     44
D14V10, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0            124
  CLUS_2            4            104
  CLUS_3           13             44
[1] 3 2
[1] 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       12      0      5
  EGFR WILD-TYPE    106     74     90
D14V11, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           12            106
  CLUS_2            0             74
  CLUS_3            5             90
[1] 3 2
[1] 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        0      0      3     14
  EGFR WILD-TYPE     52     66    119     33
D14V12, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0             52
  CLUS_2            0             66
  CLUS_3            3            119
  CLUS_4           14             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"

Clustering(15) Variable = GAGE2B MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GAGE2B MUTATED        1      0      0
  GAGE2B WILD-TYPE      8     10      7
D15V1, multiclass
[1] "Remove cluster labels:" "GAGE2B MUTATED"        
clus
  GAGE2B MUTATED GAGE2B WILD-TYPE 
               1               25 
      TCGA-CS-4942       TCGA-CS-4943       TCGA-CS-4944       TCGA-CS-5390 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-CS-5394       TCGA-CS-5395       TCGA-CS-5396       TCGA-DB-5273 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DB-5274       TCGA-DB-5275       TCGA-DB-5276       TCGA-DB-5277 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DB-5278       TCGA-DB-5280       TCGA-DB-5281       TCGA-DH-5140 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DH-5141       TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-E1-5302       TCGA-E1-5304       TCGA-E1-5311       TCGA-E1-5318 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-E1-5322 
"GAGE2B WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GAGE2B MUTATED        1      0      0      0
  GAGE2B WILD-TYPE      6      7      7      5
D15V2, multiclass
[1] "Remove cluster labels:" "GAGE2B MUTATED"        
clus
  GAGE2B MUTATED GAGE2B WILD-TYPE 
               1               25 
      TCGA-CS-4942       TCGA-CS-4943       TCGA-CS-4944       TCGA-CS-5390 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-CS-5394       TCGA-CS-5395       TCGA-CS-5396       TCGA-DB-5273 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DB-5274       TCGA-DB-5275       TCGA-DB-5276       TCGA-DB-5277 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DB-5278       TCGA-DB-5280       TCGA-DB-5281       TCGA-DH-5140 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DH-5141       TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-E1-5302       TCGA-E1-5304       TCGA-E1-5311       TCGA-E1-5318 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-E1-5322 
"GAGE2B WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GAGE2B MUTATED        2      0      2
  GAGE2B WILD-TYPE     94     69    119
D15V3, multiclass
        clus
vv       GAGE2B MUTATED GAGE2B WILD-TYPE
  CLUS_1              2               94
  CLUS_2              0               69
  CLUS_3              2              119
[1] 3 2
[1] 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
  GAGE2B MUTATED        2      0      2      0
  GAGE2B WILD-TYPE    127     42     86     30
D15V4, multiclass
        clus
vv       GAGE2B MUTATED GAGE2B WILD-TYPE
  CLUS_1              2              127
  CLUS_2              0               42
  CLUS_3              2               86
  CLUS_4              0               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 CLUS_4
  GAGE2B MUTATED        0      0      2      2
  GAGE2B WILD-TYPE     52     61     63     71
D15V5, multiclass
        clus
vv       GAGE2B MUTATED GAGE2B WILD-TYPE
  CLUS_1              0               52
  CLUS_2              0               61
  CLUS_3              2               63
  CLUS_4              2               71
[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
  GAGE2B MUTATED        1      2      1
  GAGE2B WILD-TYPE     65    126     56
D15V6, multiclass
        clus
vv       GAGE2B MUTATED GAGE2B WILD-TYPE
  CLUS_1              1               65
  CLUS_2              2              126
  CLUS_3              1               56
[1] 3 2
[1] 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
  GAGE2B MUTATED        2      0      1      1      0
  GAGE2B WILD-TYPE     73     65     50     82     14
D15V7, multiclass
        clus
vv       GAGE2B MUTATED GAGE2B WILD-TYPE
  CLUS_1              2               73
  CLUS_2              0               65
  CLUS_3              1               50
  CLUS_4              1               82
  CLUS_5              0               14
[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
  GAGE2B MUTATED        2      0      0      2
  GAGE2B WILD-TYPE     76     65     58     85
D15V8, multiclass
        clus
vv       GAGE2B MUTATED GAGE2B WILD-TYPE
  CLUS_1              2               76
  CLUS_2              0               65
  CLUS_3              0               58
  CLUS_4              2               85
[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
  GAGE2B MUTATED        1      1      2      0
  GAGE2B WILD-TYPE     82     56    111     36
D15V9, multiclass
        clus
vv       GAGE2B MUTATED GAGE2B WILD-TYPE
  CLUS_1              1               82
  CLUS_2              1               56
  CLUS_3              2              111
  CLUS_4              0               36
[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
  GAGE2B MUTATED        2      2      0
  GAGE2B WILD-TYPE    122    106     57
D15V10, multiclass
        clus
vv       GAGE2B MUTATED GAGE2B WILD-TYPE
  CLUS_1              2              122
  CLUS_2              2              106
  CLUS_3              0               57
[1] 3 2
[1] 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
  GAGE2B MUTATED        0      2      2
  GAGE2B WILD-TYPE    118     72     93
D15V11, multiclass
        clus
vv       GAGE2B MUTATED GAGE2B WILD-TYPE
  CLUS_1              0              118
  CLUS_2              2               72
  CLUS_3              2               93
[1] 3 2
[1] 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
  GAGE2B MUTATED        2      0      2      0
  GAGE2B WILD-TYPE     50     66    120     47
D15V12, multiclass
        clus
vv       GAGE2B MUTATED GAGE2B WILD-TYPE
  CLUS_1              2               50
  CLUS_2              0               66
  CLUS_3              2              120
  CLUS_4              0               47
[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(16) Variable = CREBZF MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CREBZF MUTATED        0      0      0
  CREBZF WILD-TYPE      9     10      7
D16V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CREBZF MUTATED        0      0      0      0
  CREBZF WILD-TYPE      7      7      7      5
D16V2, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CREBZF MUTATED        0      1      4
  CREBZF WILD-TYPE     96     68    117
D16V3, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               96
  CLUS_2              1               68
  CLUS_3              4              117
[1] 3 2
[1] 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
  CREBZF MUTATED        0      0      4      1
  CREBZF WILD-TYPE    129     42     84     29
D16V4, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0              129
  CLUS_2              0               42
  CLUS_3              4               84
  CLUS_4              1               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 CLUS_4
  CREBZF MUTATED        0      1      0      4
  CREBZF WILD-TYPE     52     60     65     69
D16V5, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               52
  CLUS_2              1               60
  CLUS_3              0               65
  CLUS_4              4               69
[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
  CREBZF MUTATED        1      0      4
  CREBZF WILD-TYPE     65    128     53
D16V6, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              1               65
  CLUS_2              0              128
  CLUS_3              4               53
[1] 3 2
[1] 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
  CREBZF MUTATED        0      1      1      3      0
  CREBZF WILD-TYPE     75     64     50     80     14
D16V7, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               75
  CLUS_2              1               64
  CLUS_3              1               50
  CLUS_4              3               80
  CLUS_5              0               14
[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
  CREBZF MUTATED        0      1      1      3
  CREBZF WILD-TYPE     78     64     57     84
D16V8, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               78
  CLUS_2              1               64
  CLUS_3              1               57
  CLUS_4              3               84
[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
  CREBZF MUTATED        0      1      3      1
  CREBZF WILD-TYPE     83     56    110     35
D16V9, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               83
  CLUS_2              1               56
  CLUS_3              3              110
  CLUS_4              1               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
  CREBZF MUTATED        0      4      1
  CREBZF WILD-TYPE    124    104     56
D16V10, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0              124
  CLUS_2              4              104
  CLUS_3              1               56
[1] 3 2
[1] 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
  CREBZF MUTATED        1      0      4
  CREBZF WILD-TYPE    117     74     91
D16V11, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              1              117
  CLUS_2              0               74
  CLUS_3              4               91
[1] 3 2
[1] 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
  CREBZF MUTATED        0      0      4      1
  CREBZF WILD-TYPE     52     66    118     46
D16V12, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               52
  CLUS_2              0               66
  CLUS_3              4              118
  CLUS_4              1               46
[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(17) Variable = TCF12 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TCF12 MUTATED        0      0      0
  TCF12 WILD-TYPE      9     10      7
D17V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TCF12 MUTATED        0      0      0      0
  TCF12 WILD-TYPE      7      7      7      5
D17V2, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TCF12 MUTATED        2      1      5
  TCF12 WILD-TYPE     94     68    116
D17V3, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             2              94
  CLUS_2             1              68
  CLUS_3             5             116
[1] 3 2
[1] 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
  TCF12 MUTATED        2      1      4      1
  TCF12 WILD-TYPE    127     41     84     29
D17V4, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             2             127
  CLUS_2             1              41
  CLUS_3             4              84
  CLUS_4             1              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 CLUS_4
  TCF12 MUTATED        1      1      5      1
  TCF12 WILD-TYPE     51     60     60     72
D17V5, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             1              51
  CLUS_2             1              60
  CLUS_3             5              60
  CLUS_4             1              72
[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
  TCF12 MUTATED        1      6      1
  TCF12 WILD-TYPE     65    122     56
D17V6, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             1              65
  CLUS_2             6             122
  CLUS_3             1              56
[1] 3 2
[1] 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
  TCF12 MUTATED        1      2      4      1      0
  TCF12 WILD-TYPE     74     63     47     82     14
D17V7, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             1              74
  CLUS_2             2              63
  CLUS_3             4              47
  CLUS_4             1              82
  CLUS_5             0              14
[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
  TCF12 MUTATED        1      2      3      2
  TCF12 WILD-TYPE     77     63     55     85
D17V8, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             1              77
  CLUS_2             2              63
  CLUS_3             3              55
  CLUS_4             2              85
[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
  TCF12 MUTATED        3      0      3      2
  TCF12 WILD-TYPE     80     57    110     34
D17V9, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             3              80
  CLUS_2             0              57
  CLUS_3             3             110
  CLUS_4             2              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
  TCF12 MUTATED        4      3      1
  TCF12 WILD-TYPE    120    105     56
D17V10, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             4             120
  CLUS_2             3             105
  CLUS_3             1              56
[1] 3 2
[1] 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
  TCF12 MUTATED        3      2      3
  TCF12 WILD-TYPE    115     72     92
D17V11, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             3             115
  CLUS_2             2              72
  CLUS_3             3              92
[1] 3 2
[1] 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
  TCF12 MUTATED        1      2      4      1
  TCF12 WILD-TYPE     51     64    118     46
D17V12, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             1              51
  CLUS_2             2              64
  CLUS_3             4             118
  CLUS_4             1              46
[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(18) Variable = SMARCA4 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SMARCA4 MUTATED        0      0      0
  SMARCA4 WILD-TYPE      9     10      7
D18V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMARCA4 MUTATED        0      0      0      0
  SMARCA4 WILD-TYPE      7      7      7      5
D18V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SMARCA4 MUTATED        8      2      3
  SMARCA4 WILD-TYPE     88     67    118
D18V3, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               8                88
  CLUS_2               2                67
  CLUS_3               3               118
[1] 3 2
[1] 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        9      0      4      0
  SMARCA4 WILD-TYPE    120     42     84     30
D18V4, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               9               120
  CLUS_2               0                42
  CLUS_3               4                84
  CLUS_4               0                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 CLUS_4
  SMARCA4 MUTATED        0      3      4      4
  SMARCA4 WILD-TYPE     52     58     61     69
D18V5, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               0                52
  CLUS_2               3                58
  CLUS_3               4                61
  CLUS_4               4                69
[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        2      6      3
  SMARCA4 WILD-TYPE     64    122     54
D18V6, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               2                64
  CLUS_2               6               122
  CLUS_3               3                54
[1] 3 2
[1] 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      0      4      5      1
  SMARCA4 WILD-TYPE     72     65     47     78     13
D18V7, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               3                72
  CLUS_2               0                65
  CLUS_3               4                47
  CLUS_4               5                78
  CLUS_5               1                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
  SMARCA4 MUTATED        5      1      3      4
  SMARCA4 WILD-TYPE     73     64     55     83
D18V8, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               5                73
  CLUS_2               1                64
  CLUS_3               3                55
  CLUS_4               4                83
[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
  SMARCA4 MUTATED        3      0      6      4
  SMARCA4 WILD-TYPE     80     57    107     32
D18V9, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               3                80
  CLUS_2               0                57
  CLUS_3               6               107
  CLUS_4               4                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
  SMARCA4 MUTATED        8      5      0
  SMARCA4 WILD-TYPE    116    103     57
D18V10, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               8               116
  CLUS_2               5               103
  CLUS_3               0                57
[1] 3 2
[1] 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      3      6
  SMARCA4 WILD-TYPE    114     71     89
D18V11, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               4               114
  CLUS_2               3                71
  CLUS_3               6                89
[1] 3 2
[1] 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        3      2      8      0
  SMARCA4 WILD-TYPE     49     64    114     47
D18V12, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               3                49
  CLUS_2               2                64
  CLUS_3               8               114
  CLUS_4               0                47
[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(19) Variable = VAV3 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  VAV3 MUTATED        0      0      0
  VAV3 WILD-TYPE      9     10      7
D19V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  VAV3 MUTATED        0      0      0      0
  VAV3 WILD-TYPE      7      7      7      5
D19V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  VAV3 MUTATED        3      3      2
  VAV3 WILD-TYPE     93     66    119
D19V3, multiclass
        clus
vv       VAV3 MUTATED VAV3 WILD-TYPE
  CLUS_1            3             93
  CLUS_2            3             66
  CLUS_3            2            119
[1] 3 2
[1] 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
  VAV3 MUTATED        3      1      2      2
  VAV3 WILD-TYPE    126     41     86     28
D19V4, multiclass
        clus
vv       VAV3 MUTATED VAV3 WILD-TYPE
  CLUS_1            3            126
  CLUS_2            1             41
  CLUS_3            2             86
  CLUS_4            2             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 CLUS_4
  VAV3 MUTATED        1      2      2      3
  VAV3 WILD-TYPE     51     59     63     70
D19V5, multiclass
        clus
vv       VAV3 MUTATED VAV3 WILD-TYPE
  CLUS_1            1             51
  CLUS_2            2             59
  CLUS_3            2             63
  CLUS_4            3             70
[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
  VAV3 MUTATED        2      3      3
  VAV3 WILD-TYPE     64    125     54
D19V6, multiclass
        clus
vv       VAV3 MUTATED VAV3 WILD-TYPE
  CLUS_1            2             64
  CLUS_2            3            125
  CLUS_3            3             54
[1] 3 2
[1] 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
  VAV3 MUTATED        0      3      1      2      2
  VAV3 WILD-TYPE     75     62     50     81     12
D19V7, multiclass
        clus
vv       VAV3 MUTATED VAV3 WILD-TYPE
  CLUS_1            0             75
  CLUS_2            3             62
  CLUS_3            1             50
  CLUS_4            2             81
  CLUS_5            2             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
  VAV3 MUTATED        2      2      0      4
  VAV3 WILD-TYPE     76     63     58     83
D19V8, multiclass
        clus
vv       VAV3 MUTATED VAV3 WILD-TYPE
  CLUS_1            2             76
  CLUS_2            2             63
  CLUS_3            0             58
  CLUS_4            4             83
[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
  VAV3 MUTATED        2      1      5      0
  VAV3 WILD-TYPE     81     56    108     36
D19V9, multiclass
        clus
vv       VAV3 MUTATED VAV3 WILD-TYPE
  CLUS_1            2             81
  CLUS_2            1             56
  CLUS_3            5            108
  CLUS_4            0             36
[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
  VAV3 MUTATED        2      5      1
  VAV3 WILD-TYPE    122    103     56
D19V10, multiclass
        clus
vv       VAV3 MUTATED VAV3 WILD-TYPE
  CLUS_1            2            122
  CLUS_2            5            103
  CLUS_3            1             56
[1] 3 2
[1] 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
  VAV3 MUTATED        2      2      4
  VAV3 WILD-TYPE    116     72     91
D19V11, multiclass
        clus
vv       VAV3 MUTATED VAV3 WILD-TYPE
  CLUS_1            2            116
  CLUS_2            2             72
  CLUS_3            4             91
[1] 3 2
[1] 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
  VAV3 MUTATED        2      0      4      2
  VAV3 WILD-TYPE     50     66    118     45
D19V12, multiclass
        clus
vv       VAV3 MUTATED VAV3 WILD-TYPE
  CLUS_1            2             50
  CLUS_2            0             66
  CLUS_3            4            118
  CLUS_4            2             45
[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(20) Variable = TMEM216 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TMEM216 MUTATED        0      0      0
  TMEM216 WILD-TYPE      9     10      7
D20V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMEM216 MUTATED        0      0      0      0
  TMEM216 WILD-TYPE      7      7      7      5
D20V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TMEM216 MUTATED        2      1      0
  TMEM216 WILD-TYPE     94     68    121
D20V3, multiclass
        clus
vv       TMEM216 MUTATED TMEM216 WILD-TYPE
  CLUS_1               2                94
  CLUS_2               1                68
  CLUS_3               0               121
[1] 3 2
[1] 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
  TMEM216 MUTATED        2      0      1      0
  TMEM216 WILD-TYPE    127     42     87     30
D20V4, multiclass
        clus
vv       TMEM216 MUTATED TMEM216 WILD-TYPE
  CLUS_1               2               127
  CLUS_2               0                42
  CLUS_3               1                87
  CLUS_4               0                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 CLUS_4
  TMEM216 MUTATED        1      1      0      1
  TMEM216 WILD-TYPE     51     60     65     72
D20V5, multiclass
        clus
vv       TMEM216 MUTATED TMEM216 WILD-TYPE
  CLUS_1               1                51
  CLUS_2               1                60
  CLUS_3               0                65
  CLUS_4               1                72
[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
  TMEM216 MUTATED        1      1      1
  TMEM216 WILD-TYPE     65    127     56
D20V6, multiclass
        clus
vv       TMEM216 MUTATED TMEM216 WILD-TYPE
  CLUS_1               1                65
  CLUS_2               1               127
  CLUS_3               1                56
[1] 3 2
[1] 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
  TMEM216 MUTATED        1      0      1      1      0
  TMEM216 WILD-TYPE     74     65     50     82     14
D20V7, multiclass
        clus
vv       TMEM216 MUTATED TMEM216 WILD-TYPE
  CLUS_1               1                74
  CLUS_2               0                65
  CLUS_3               1                50
  CLUS_4               1                82
  CLUS_5               0                14
[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
  TMEM216 MUTATED        1      0      1      1
  TMEM216 WILD-TYPE     77     65     57     86
D20V8, multiclass
        clus
vv       TMEM216 MUTATED TMEM216 WILD-TYPE
  CLUS_1               1                77
  CLUS_2               0                65
  CLUS_3               1                57
  CLUS_4               1                86
[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
  TMEM216 MUTATED        0      1      1      1
  TMEM216 WILD-TYPE     83     56    112     35
D20V9, multiclass
        clus
vv       TMEM216 MUTATED TMEM216 WILD-TYPE
  CLUS_1               0                83
  CLUS_2               1                56
  CLUS_3               1               112
  CLUS_4               1                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
  TMEM216 MUTATED        1      2      0
  TMEM216 WILD-TYPE    123    106     57
D20V10, multiclass
        clus
vv       TMEM216 MUTATED TMEM216 WILD-TYPE
  CLUS_1               1               123
  CLUS_2               2               106
  CLUS_3               0                57
[1] 3 2
[1] 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
  TMEM216 MUTATED        0      2      1
  TMEM216 WILD-TYPE    118     72     94
D20V11, multiclass
        clus
vv       TMEM216 MUTATED TMEM216 WILD-TYPE
  CLUS_1               0               118
  CLUS_2               2                72
  CLUS_3               1                94
[1] 3 2
[1] 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
  TMEM216 MUTATED        0      2      1      0
  TMEM216 WILD-TYPE     52     64    121     47
D20V12, multiclass
        clus
vv       TMEM216 MUTATED TMEM216 WILD-TYPE
  CLUS_1               0                52
  CLUS_2               2                64
  CLUS_3               1               121
  CLUS_4               0                47
[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(21) Variable = ROBO3 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ROBO3 MUTATED        0      0      0
  ROBO3 WILD-TYPE      9     10      7
D21V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ROBO3 MUTATED        0      0      0      0
  ROBO3 WILD-TYPE      7      7      7      5
D21V2, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ROBO3 MUTATED        2      0      2
  ROBO3 WILD-TYPE     94     69    119
D21V3, multiclass
        clus
vv       ROBO3 MUTATED ROBO3 WILD-TYPE
  CLUS_1             2              94
  CLUS_2             0              69
  CLUS_3             2             119
[1] 3 2
[1] 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
  ROBO3 MUTATED        3      0      1      0
  ROBO3 WILD-TYPE    126     42     87     30
D21V4, multiclass
        clus
vv       ROBO3 MUTATED ROBO3 WILD-TYPE
  CLUS_1             3             126
  CLUS_2             0              42
  CLUS_3             1              87
  CLUS_4             0              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 CLUS_4
  ROBO3 MUTATED        2      0      0      0
  ROBO3 WILD-TYPE     50     61     65     73
D21V5, multiclass
[1] "Remove cluster labels:" "ROBO3 MUTATED"         
clus
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              2             249 
     TCGA-CS-4938      TCGA-CS-4942      TCGA-CS-4943      TCGA-CS-4944 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5394      TCGA-CS-5396 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188      TCGA-CS-6665 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-CS-6666      TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5273 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DB-5274      TCGA-DB-5275      TCGA-DB-5276      TCGA-DB-5277 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DB-5278      TCGA-DB-5279      TCGA-DB-5280      TCGA-DB-5281 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DB-A4X9      TCGA-DB-A4XA      TCGA-DB-A4XB      TCGA-DB-A4XC 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DB-A4XD      TCGA-DB-A4XE      TCGA-DB-A4XF      TCGA-DB-A4XG 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DB-A4XH      TCGA-DH-5140      TCGA-DH-5141      TCGA-DH-5142 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DU-5847      TCGA-DU-5849 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853      TCGA-DU-5854 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871      TCGA-DU-5872 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6393      TCGA-DU-6394      TCGA-DU-6395 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-6396      TCGA-DU-6397      TCGA-DU-6399      TCGA-DU-6400 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-6401      TCGA-DU-6402      TCGA-DU-6403      TCGA-DU-6404 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-6542      TCGA-DU-7006      TCGA-DU-7007      TCGA-DU-7008 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-7009      TCGA-DU-7010      TCGA-DU-7012      TCGA-DU-7013 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-7015      TCGA-DU-7018      TCGA-DU-7019      TCGA-DU-7290 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-7292      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7300 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304      TCGA-DU-7306 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161      TCGA-DU-8162 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-8163      TCGA-DU-8164      TCGA-DU-8165      TCGA-DU-8166 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-8167      TCGA-DU-8168      TCGA-DU-A5TP      TCGA-DU-A5TR 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-A5TS      TCGA-DU-A5TT      TCGA-DU-A5TU      TCGA-DU-A5TW 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-A5TY      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-EZ-7264      TCGA-FG-5962 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-FG-5963      TCGA-FG-5964      TCGA-FG-5965      TCGA-FG-6688 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691      TCGA-FG-7634 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-FG-7636      TCGA-FG-7637      TCGA-FG-7638      TCGA-FG-7641 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-FG-7643      TCGA-FG-8181      TCGA-FG-8182      TCGA-FG-8185 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-FG-8191      TCGA-FG-A4MT      TCGA-FG-A4MU      TCGA-FG-A4MW 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-FG-A4MX      TCGA-FG-A4MY      TCGA-FG-A60J      TCGA-HT-7467 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7468      TCGA-HT-7469      TCGA-HT-7470      TCGA-HT-7471 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7472      TCGA-HT-7473      TCGA-HT-7474      TCGA-HT-7475 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7476      TCGA-HT-7477      TCGA-HT-7478      TCGA-HT-7479 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7480      TCGA-HT-7481      TCGA-HT-7482      TCGA-HT-7483 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7485      TCGA-HT-7601      TCGA-HT-7602      TCGA-HT-7603 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7604      TCGA-HT-7605      TCGA-HT-7606      TCGA-HT-7607 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7608      TCGA-HT-7609      TCGA-HT-7610      TCGA-HT-7611 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7616      TCGA-HT-7620      TCGA-HT-7677      TCGA-HT-7680 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7681      TCGA-HT-7684      TCGA-HT-7686      TCGA-HT-7687 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7688      TCGA-HT-7689      TCGA-HT-7690      TCGA-HT-7691 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7692      TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7695 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7854      TCGA-HT-7855      TCGA-HT-7856      TCGA-HT-7857 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7858      TCGA-HT-7860      TCGA-HT-7873      TCGA-HT-7874 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7875      TCGA-HT-7877      TCGA-HT-7879      TCGA-HT-7880 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7881      TCGA-HT-7882      TCGA-HT-7884      TCGA-HT-7902 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-8010      TCGA-HT-8011      TCGA-HT-8012      TCGA-HT-8013 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-8015      TCGA-HT-8018      TCGA-HT-8019      TCGA-HT-8104 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-8105      TCGA-HT-8106      TCGA-HT-8107      TCGA-HT-8109 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-8110      TCGA-HT-8111      TCGA-HT-8113      TCGA-HT-8114 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-8558      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R5 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-A5R7      TCGA-HT-A5R9      TCGA-HT-A5RB      TCGA-HW-7486 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HW-7487      TCGA-HW-7489      TCGA-HW-7490      TCGA-HW-7491 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HW-7495      TCGA-HW-8319      TCGA-HW-8320      TCGA-HW-8321 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HW-8322      TCGA-HW-A5KJ      TCGA-HW-A5KK      TCGA-HW-A5KM 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-IK-7675      TCGA-IK-8125      TCGA-P5-A5ET      TCGA-P5-A5EU 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX      TCGA-P5-A5EY 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-P5-A5EZ      TCGA-P5-A5F0      TCGA-P5-A5F1      TCGA-P5-A5F4 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-P5-A5F6 
"ROBO3 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ROBO3 MUTATED        1      1      0
  ROBO3 WILD-TYPE     65    127     57
D21V6, multiclass
[1] "Remove cluster labels:" "ROBO3 MUTATED"         
clus
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              2             249 
     TCGA-CS-4938      TCGA-CS-4942      TCGA-CS-4943      TCGA-CS-4944 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5394      TCGA-CS-5396 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188      TCGA-CS-6665 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-CS-6666      TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5273 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DB-5274      TCGA-DB-5275      TCGA-DB-5276      TCGA-DB-5277 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DB-5278      TCGA-DB-5279      TCGA-DB-5280      TCGA-DB-5281 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DB-A4X9      TCGA-DB-A4XA      TCGA-DB-A4XB      TCGA-DB-A4XC 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DB-A4XD      TCGA-DB-A4XE      TCGA-DB-A4XF      TCGA-DB-A4XG 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DB-A4XH      TCGA-DH-5140      TCGA-DH-5141      TCGA-DH-5142 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DU-5847      TCGA-DU-5849 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853      TCGA-DU-5854 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871      TCGA-DU-5872 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6393      TCGA-DU-6394      TCGA-DU-6395 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-6396      TCGA-DU-6397      TCGA-DU-6399      TCGA-DU-6400 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-6401      TCGA-DU-6402      TCGA-DU-6403      TCGA-DU-6404 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-6542      TCGA-DU-7006      TCGA-DU-7007      TCGA-DU-7008 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-7009      TCGA-DU-7010      TCGA-DU-7012      TCGA-DU-7013 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-7015      TCGA-DU-7018      TCGA-DU-7019      TCGA-DU-7290 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-7292      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7300 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304      TCGA-DU-7306 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161      TCGA-DU-8162 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-8163      TCGA-DU-8164      TCGA-DU-8165      TCGA-DU-8166 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-8167      TCGA-DU-8168      TCGA-DU-A5TP      TCGA-DU-A5TR 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-A5TS      TCGA-DU-A5TT      TCGA-DU-A5TU      TCGA-DU-A5TW 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-DU-A5TY      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-EZ-7264      TCGA-FG-5962 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-FG-5963      TCGA-FG-5964      TCGA-FG-5965      TCGA-FG-6688 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691      TCGA-FG-7634 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-FG-7636      TCGA-FG-7637      TCGA-FG-7638      TCGA-FG-7641 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-FG-7643      TCGA-FG-8181      TCGA-FG-8182      TCGA-FG-8185 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-FG-8191      TCGA-FG-A4MT      TCGA-FG-A4MU      TCGA-FG-A4MW 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-FG-A4MX      TCGA-FG-A4MY      TCGA-FG-A60J      TCGA-HT-7467 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7468      TCGA-HT-7469      TCGA-HT-7470      TCGA-HT-7471 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7472      TCGA-HT-7473      TCGA-HT-7474      TCGA-HT-7475 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7476      TCGA-HT-7477      TCGA-HT-7478      TCGA-HT-7479 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7480      TCGA-HT-7481      TCGA-HT-7482      TCGA-HT-7483 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7485      TCGA-HT-7601      TCGA-HT-7602      TCGA-HT-7603 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7604      TCGA-HT-7605      TCGA-HT-7606      TCGA-HT-7607 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7608      TCGA-HT-7609      TCGA-HT-7610      TCGA-HT-7611 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7616      TCGA-HT-7620      TCGA-HT-7677      TCGA-HT-7680 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7681      TCGA-HT-7684      TCGA-HT-7686      TCGA-HT-7687 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7688      TCGA-HT-7689      TCGA-HT-7690      TCGA-HT-7691 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7692      TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7695 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7854      TCGA-HT-7855      TCGA-HT-7856      TCGA-HT-7857 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7858      TCGA-HT-7860      TCGA-HT-7873      TCGA-HT-7874 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7875      TCGA-HT-7877      TCGA-HT-7879      TCGA-HT-7880 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-7881      TCGA-HT-7882      TCGA-HT-7884      TCGA-HT-7902 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-8010      TCGA-HT-8011      TCGA-HT-8012      TCGA-HT-8013 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-8015      TCGA-HT-8018      TCGA-HT-8019      TCGA-HT-8104 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-8105      TCGA-HT-8106      TCGA-HT-8107      TCGA-HT-8109 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-8110      TCGA-HT-8111      TCGA-HT-8113      TCGA-HT-8114 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-8558      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R5 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HT-A5R7      TCGA-HT-A5R9      TCGA-HT-A5RB      TCGA-HW-7486 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HW-7487      TCGA-HW-7489      TCGA-HW-7490      TCGA-HW-7491 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HW-7495      TCGA-HW-8319      TCGA-HW-8320      TCGA-HW-8321 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-HW-8322      TCGA-HW-A5KJ      TCGA-HW-A5KK      TCGA-HW-A5KM 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-IK-7675      TCGA-IK-8125      TCGA-P5-A5ET      TCGA-P5-A5EU 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX      TCGA-P5-A5EY 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-P5-A5EZ      TCGA-P5-A5F0      TCGA-P5-A5F1      TCGA-P5-A5F4 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-P5-A5F6 
"ROBO3 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ROBO3 MUTATED        2      0      0      2      0
  ROBO3 WILD-TYPE     73     65     51     81     14
D21V7, multiclass
        clus
vv       ROBO3 MUTATED ROBO3 WILD-TYPE
  CLUS_1             2              73
  CLUS_2             0              65
  CLUS_3             0              51
  CLUS_4             2              81
  CLUS_5             0              14
[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
  ROBO3 MUTATED        2      0      1      1
  ROBO3 WILD-TYPE     76     65     57     86
D21V8, multiclass
        clus
vv       ROBO3 MUTATED ROBO3 WILD-TYPE
  CLUS_1             2              76
  CLUS_2             0              65
  CLUS_3             1              57
  CLUS_4             1              86
[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
  ROBO3 MUTATED        1      0      2      1
  ROBO3 WILD-TYPE     82     57    111     35
D21V9, multiclass
        clus
vv       ROBO3 MUTATED ROBO3 WILD-TYPE
  CLUS_1             1              82
  CLUS_2             0              57
  CLUS_3             2             111
  CLUS_4             1              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
  ROBO3 MUTATED        3      1      0
  ROBO3 WILD-TYPE    121    107     57
D21V10, multiclass
        clus
vv       ROBO3 MUTATED ROBO3 WILD-TYPE
  CLUS_1             3             121
  CLUS_2             1             107
  CLUS_3             0              57
[1] 3 2
[1] 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
  ROBO3 MUTATED        2      1      1
  ROBO3 WILD-TYPE    116     73     94
D21V11, multiclass
        clus
vv       ROBO3 MUTATED ROBO3 WILD-TYPE
  CLUS_1             2             116
  CLUS_2             1              73
  CLUS_3             1              94
[1] 3 2
[1] 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
  ROBO3 MUTATED        1      1      2      0
  ROBO3 WILD-TYPE     51     65    120     47
D21V12, multiclass
        clus
vv       ROBO3 MUTATED ROBO3 WILD-TYPE
  CLUS_1             1              51
  CLUS_2             1              65
  CLUS_3             2             120
  CLUS_4             0              47
[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(22) Variable = IRS4 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IRS4 MUTATED        0      1      0
  IRS4 WILD-TYPE      9      9      7
D22V1, multiclass
[1] "Remove cluster labels:" "IRS4 MUTATED"          
clus
  IRS4 MUTATED IRS4 WILD-TYPE 
             1             25 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-CS-5394     TCGA-CS-5395     TCGA-CS-5396     TCGA-DB-5273 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-DH-5141     TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5311     TCGA-E1-5318 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-E1-5322 
"IRS4 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IRS4 MUTATED        0      1      0      0
  IRS4 WILD-TYPE      7      6      7      5
D22V2, multiclass
[1] "Remove cluster labels:" "IRS4 MUTATED"          
clus
  IRS4 MUTATED IRS4 WILD-TYPE 
             1             25 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-CS-5394     TCGA-CS-5395     TCGA-CS-5396     TCGA-DB-5273 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-DH-5141     TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5311     TCGA-E1-5318 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-E1-5322 
"IRS4 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IRS4 MUTATED        1      3      1
  IRS4 WILD-TYPE     95     66    120
D22V3, multiclass
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  CLUS_1            1             95
  CLUS_2            3             66
  CLUS_3            1            120
[1] 3 2
[1] 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
  IRS4 MUTATED        3      1      1      0
  IRS4 WILD-TYPE    126     41     87     30
D22V4, multiclass
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  CLUS_1            3            126
  CLUS_2            1             41
  CLUS_3            1             87
  CLUS_4            0             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 CLUS_4
  IRS4 MUTATED        0      1      1      1
  IRS4 WILD-TYPE     52     60     64     72
D22V5, multiclass
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  CLUS_1            0             52
  CLUS_2            1             60
  CLUS_3            1             64
  CLUS_4            1             72
[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
  IRS4 MUTATED        0      1      2
  IRS4 WILD-TYPE     66    127     55
D22V6, multiclass
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  CLUS_1            0             66
  CLUS_2            1            127
  CLUS_3            2             55
[1] 3 2
[1] 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
  IRS4 MUTATED        2      1      0      2      0
  IRS4 WILD-TYPE     73     64     51     81     14
D22V7, multiclass
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  CLUS_1            2             73
  CLUS_2            1             64
  CLUS_3            0             51
  CLUS_4            2             81
  CLUS_5            0             14
[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
  IRS4 MUTATED        2      1      1      1
  IRS4 WILD-TYPE     76     64     57     86
D22V8, multiclass
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  CLUS_1            2             76
  CLUS_2            1             64
  CLUS_3            1             57
  CLUS_4            1             86
[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
  IRS4 MUTATED        1      1      3      0
  IRS4 WILD-TYPE     82     56    110     36
D22V9, multiclass
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  CLUS_1            1             82
  CLUS_2            1             56
  CLUS_3            3            110
  CLUS_4            0             36
[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
  IRS4 MUTATED        2      2      1
  IRS4 WILD-TYPE    122    106     56
D22V10, multiclass
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  CLUS_1            2            122
  CLUS_2            2            106
  CLUS_3            1             56
[1] 3 2
[1] 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
  IRS4 MUTATED        0      2      3
  IRS4 WILD-TYPE    118     72     92
D22V11, multiclass
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  CLUS_1            0            118
  CLUS_2            2             72
  CLUS_3            3             92
[1] 3 2
[1] 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
  IRS4 MUTATED        1      1      2      1
  IRS4 WILD-TYPE     51     65    120     46
D22V12, multiclass
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  CLUS_1            1             51
  CLUS_2            1             65
  CLUS_3            2            120
  CLUS_4            1             46
[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(23) Variable = HTRA2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HTRA2 MUTATED        0      0      0
  HTRA2 WILD-TYPE      9     10      7
D23V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HTRA2 MUTATED        0      0      0      0
  HTRA2 WILD-TYPE      7      7      7      5
D23V2, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HTRA2 MUTATED        3      1      0
  HTRA2 WILD-TYPE     93     68    121
D23V3, multiclass
        clus
vv       HTRA2 MUTATED HTRA2 WILD-TYPE
  CLUS_1             3              93
  CLUS_2             1              68
  CLUS_3             0             121
[1] 3 2
[1] 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
  HTRA2 MUTATED        2      0      1      1
  HTRA2 WILD-TYPE    127     42     87     29
D23V4, multiclass
        clus
vv       HTRA2 MUTATED HTRA2 WILD-TYPE
  CLUS_1             2             127
  CLUS_2             0              42
  CLUS_3             1              87
  CLUS_4             1              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 CLUS_4
  HTRA2 MUTATED        2      1      0      1
  HTRA2 WILD-TYPE     50     60     65     72
D23V5, multiclass
        clus
vv       HTRA2 MUTATED HTRA2 WILD-TYPE
  CLUS_1             2              50
  CLUS_2             1              60
  CLUS_3             0              65
  CLUS_4             1              72
[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
  HTRA2 MUTATED        1      2      1
  HTRA2 WILD-TYPE     65    126     56
D23V6, multiclass
        clus
vv       HTRA2 MUTATED HTRA2 WILD-TYPE
  CLUS_1             1              65
  CLUS_2             2             126
  CLUS_3             1              56
[1] 3 2
[1] 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
  HTRA2 MUTATED        1      1      1      1      0
  HTRA2 WILD-TYPE     74     64     50     82     14
D23V7, multiclass
        clus
vv       HTRA2 MUTATED HTRA2 WILD-TYPE
  CLUS_1             1              74
  CLUS_2             1              64
  CLUS_3             1              50
  CLUS_4             1              82
  CLUS_5             0              14
[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
  HTRA2 MUTATED        1      1      1      1
  HTRA2 WILD-TYPE     77     64     57     86
D23V8, multiclass
        clus
vv       HTRA2 MUTATED HTRA2 WILD-TYPE
  CLUS_1             1              77
  CLUS_2             1              64
  CLUS_3             1              57
  CLUS_4             1              86
[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
  HTRA2 MUTATED        2      0      1      1
  HTRA2 WILD-TYPE     81     57    112     35
D23V9, multiclass
        clus
vv       HTRA2 MUTATED HTRA2 WILD-TYPE
  CLUS_1             2              81
  CLUS_2             0              57
  CLUS_3             1             112
  CLUS_4             1              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
  HTRA2 MUTATED        2      2      0
  HTRA2 WILD-TYPE    122    106     57
D23V10, multiclass
        clus
vv       HTRA2 MUTATED HTRA2 WILD-TYPE
  CLUS_1             2             122
  CLUS_2             2             106
  CLUS_3             0              57
[1] 3 2
[1] 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
  HTRA2 MUTATED        1      2      0
  HTRA2 WILD-TYPE    117     72     95
D23V11, multiclass
        clus
vv       HTRA2 MUTATED HTRA2 WILD-TYPE
  CLUS_1             1             117
  CLUS_2             2              72
  CLUS_3             0              95
[1] 3 2
[1] 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
  HTRA2 MUTATED        1      1      1      0
  HTRA2 WILD-TYPE     51     65    121     47
D23V12, multiclass
        clus
vv       HTRA2 MUTATED HTRA2 WILD-TYPE
  CLUS_1             1              51
  CLUS_2             1              65
  CLUS_3             1             121
  CLUS_4             0              47
[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(24) Variable = EIF1AX MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  EIF1AX MUTATED        0      0      0
  EIF1AX WILD-TYPE      9     10      7
D24V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EIF1AX MUTATED        0      0      0      0
  EIF1AX WILD-TYPE      7      7      7      5
D24V2, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  EIF1AX MUTATED        0      1      3
  EIF1AX WILD-TYPE     96     68    118
D24V3, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               96
  CLUS_2              1               68
  CLUS_3              3              118
[1] 3 2
[1] 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
  EIF1AX MUTATED        4      0      0      0
  EIF1AX WILD-TYPE    125     42     88     30
D24V4, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              4              125
  CLUS_2              0               42
  CLUS_3              0               88
  CLUS_4              0               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 CLUS_4
  EIF1AX MUTATED        0      0      2      2
  EIF1AX WILD-TYPE     52     61     63     71
D24V5, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               52
  CLUS_2              0               61
  CLUS_3              2               63
  CLUS_4              2               71
[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
  EIF1AX MUTATED        0      2      2
  EIF1AX WILD-TYPE     66    126     55
D24V6, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               66
  CLUS_2              2              126
  CLUS_3              2               55
[1] 3 2
[1] 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
  EIF1AX MUTATED        2      1      0      1      0
  EIF1AX WILD-TYPE     73     64     51     82     14
D24V7, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              2               73
  CLUS_2              1               64
  CLUS_3              0               51
  CLUS_4              1               82
  CLUS_5              0               14
[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
  EIF1AX MUTATED        2      1      0      1
  EIF1AX WILD-TYPE     76     64     58     86
D24V8, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              2               76
  CLUS_2              1               64
  CLUS_3              0               58
  CLUS_4              1               86
[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
  EIF1AX MUTATED        2      1      1      0
  EIF1AX WILD-TYPE     81     56    112     36
D24V9, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              2               81
  CLUS_2              1               56
  CLUS_3              1              112
  CLUS_4              0               36
[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
  EIF1AX MUTATED        3      0      1
  EIF1AX WILD-TYPE    121    108     56
D24V10, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              3              121
  CLUS_2              0              108
  CLUS_3              1               56
[1] 3 2
[1] 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
  EIF1AX MUTATED        3      1      0
  EIF1AX WILD-TYPE    115     73     95
D24V11, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              3              115
  CLUS_2              1               73
  CLUS_3              0               95
[1] 3 2
[1] 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
  EIF1AX MUTATED        2      2      0      0
  EIF1AX WILD-TYPE     50     64    122     47
D24V12, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              2               50
  CLUS_2              2               64
  CLUS_3              0              122
  CLUS_4              0               47
[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(25) Variable = FAM47C MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FAM47C MUTATED        0      0      0
  FAM47C WILD-TYPE      9     10      7
D25V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM47C MUTATED        0      0      0      0
  FAM47C WILD-TYPE      7      7      7      5
D25V2, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  FAM47C MUTATED        1      1      5
  FAM47C WILD-TYPE     95     68    116
D25V3, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              1               95
  CLUS_2              1               68
  CLUS_3              5              116
[1] 3 2
[1] 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
  FAM47C MUTATED        2      0      4      1
  FAM47C WILD-TYPE    127     42     84     29
D25V4, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              2              127
  CLUS_2              0               42
  CLUS_3              4               84
  CLUS_4              1               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 CLUS_4
  FAM47C MUTATED        1      0      1      4
  FAM47C WILD-TYPE     51     61     64     69
D25V5, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              1               51
  CLUS_2              0               61
  CLUS_3              1               64
  CLUS_4              4               69
[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
  FAM47C MUTATED        1      2      3
  FAM47C WILD-TYPE     65    126     54
D25V6, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              1               65
  CLUS_2              2              126
  CLUS_3              3               54
[1] 3 2
[1] 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
  FAM47C MUTATED        0      0      2      5      0
  FAM47C WILD-TYPE     75     65     49     78     14
D25V7, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              0               75
  CLUS_2              0               65
  CLUS_3              2               49
  CLUS_4              5               78
  CLUS_5              0               14
[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
  FAM47C MUTATED        0      0      2      5
  FAM47C WILD-TYPE     78     65     56     82
D25V8, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              0               78
  CLUS_2              0               65
  CLUS_3              2               56
  CLUS_4              5               82
[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
  FAM47C MUTATED        1      0      6      0
  FAM47C WILD-TYPE     82     57    107     36
D25V9, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              1               82
  CLUS_2              0               57
  CLUS_3              6              107
  CLUS_4              0               36
[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
  FAM47C MUTATED        1      6      0
  FAM47C WILD-TYPE    123    102     57
D25V10, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              1              123
  CLUS_2              6              102
  CLUS_3              0               57
[1] 3 2
[1] 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
  FAM47C MUTATED        0      1      6
  FAM47C WILD-TYPE    118     73     89
D25V11, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              0              118
  CLUS_2              1               73
  CLUS_3              6               89
[1] 3 2
[1] 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
  FAM47C MUTATED        0      1      6      0
  FAM47C WILD-TYPE     52     65    116     47
D25V12, multiclass
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  CLUS_1              0               52
  CLUS_2              1               65
  CLUS_3              6              116
  CLUS_4              0               47
[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(26) Variable = PLCG1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PLCG1 MUTATED        0      0      1
  PLCG1 WILD-TYPE      9     10      6
D26V1, multiclass
[1] "Remove cluster labels:" "PLCG1 MUTATED"         
clus
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              1              25 
     TCGA-CS-4942      TCGA-CS-4943      TCGA-CS-4944      TCGA-CS-5390 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-CS-5394      TCGA-CS-5396      TCGA-DB-5273      TCGA-DB-5274 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DB-5275      TCGA-DB-5276      TCGA-DB-5277      TCGA-DB-5278 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DB-5280      TCGA-DB-5281      TCGA-DH-5140      TCGA-DH-5141 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DH-5142      TCGA-DH-5143      TCGA-DH-5144      TCGA-E1-5302 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5311      TCGA-E1-5318 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-E1-5322 
"PLCG1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PLCG1 MUTATED        1      0      0      0
  PLCG1 WILD-TYPE      6      7      7      5
D26V2, multiclass
[1] "Remove cluster labels:" "PLCG1 MUTATED"         
clus
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              1              25 
     TCGA-CS-4942      TCGA-CS-4943      TCGA-CS-4944      TCGA-CS-5390 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-CS-5394      TCGA-CS-5396      TCGA-DB-5273      TCGA-DB-5274 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DB-5275      TCGA-DB-5276      TCGA-DB-5277      TCGA-DB-5278 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DB-5280      TCGA-DB-5281      TCGA-DH-5140      TCGA-DH-5141 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DH-5142      TCGA-DH-5143      TCGA-DH-5144      TCGA-E1-5302 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5311      TCGA-E1-5318 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-E1-5322 
"PLCG1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PLCG1 MUTATED        0      4      0
  PLCG1 WILD-TYPE     96     65    121
D26V3, multiclass
        clus
vv       PLCG1 MUTATED PLCG1 WILD-TYPE
  CLUS_1             0              96
  CLUS_2             4              65
  CLUS_3             0             121
[1] 3 2
[1] 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
  PLCG1 MUTATED        1      3      0      0
  PLCG1 WILD-TYPE    128     39     88     30
D26V4, multiclass
        clus
vv       PLCG1 MUTATED PLCG1 WILD-TYPE
  CLUS_1             1             128
  CLUS_2             3              39
  CLUS_3             0              88
  CLUS_4             0              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 CLUS_4
  PLCG1 MUTATED        0      2      0      0
  PLCG1 WILD-TYPE     52     59     65     73
D26V5, multiclass
[1] "Remove cluster labels:" "PLCG1 MUTATED"         
clus
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              2             249 
     TCGA-CS-4938      TCGA-CS-4942      TCGA-CS-4943      TCGA-CS-4944 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5394      TCGA-CS-5396 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188      TCGA-CS-6665 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-CS-6666      TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5273 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DB-5274      TCGA-DB-5275      TCGA-DB-5276      TCGA-DB-5277 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DB-5278      TCGA-DB-5279      TCGA-DB-5280      TCGA-DB-5281 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DB-A4X9      TCGA-DB-A4XA      TCGA-DB-A4XB      TCGA-DB-A4XC 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DB-A4XD      TCGA-DB-A4XE      TCGA-DB-A4XF      TCGA-DB-A4XG 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DB-A4XH      TCGA-DH-5140      TCGA-DH-5141      TCGA-DH-5142 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DU-5847      TCGA-DU-5849 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-5851      TCGA-DU-5853      TCGA-DU-5854      TCGA-DU-5870 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-5871      TCGA-DU-5872      TCGA-DU-5874      TCGA-DU-6393 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-6394      TCGA-DU-6395      TCGA-DU-6396      TCGA-DU-6397 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-6399      TCGA-DU-6400      TCGA-DU-6401      TCGA-DU-6402 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-6403      TCGA-DU-6404      TCGA-DU-6405      TCGA-DU-6407 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-6408      TCGA-DU-6410      TCGA-DU-6542      TCGA-DU-7006 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-7007      TCGA-DU-7008      TCGA-DU-7009      TCGA-DU-7010 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-7012      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7290      TCGA-DU-7292      TCGA-DU-7294 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-7298      TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-7304      TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-8161      TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8164 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-8165      TCGA-DU-8166      TCGA-DU-8167      TCGA-DU-8168 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TT 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-A5TU      TCGA-DU-A5TW      TCGA-DU-A5TY      TCGA-E1-5302 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5305      TCGA-E1-5307 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-E1-5311      TCGA-E1-5318      TCGA-E1-5319      TCGA-E1-5322 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-EZ-7264      TCGA-FG-5962      TCGA-FG-5963      TCGA-FG-5964 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-FG-5965      TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-FG-6691      TCGA-FG-7634      TCGA-FG-7636      TCGA-FG-7637 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-FG-7638      TCGA-FG-7641      TCGA-FG-7643      TCGA-FG-8181 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-FG-8182      TCGA-FG-8185      TCGA-FG-8186      TCGA-FG-8187 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-FG-8188      TCGA-FG-8189      TCGA-FG-8191      TCGA-FG-A4MT 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-FG-A4MU      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A4MY 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-FG-A60J      TCGA-HT-7467      TCGA-HT-7468      TCGA-HT-7469 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7470      TCGA-HT-7471      TCGA-HT-7472      TCGA-HT-7473 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7474      TCGA-HT-7475      TCGA-HT-7476      TCGA-HT-7477 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7478      TCGA-HT-7479      TCGA-HT-7480      TCGA-HT-7481 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7482      TCGA-HT-7483      TCGA-HT-7485      TCGA-HT-7601 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7602      TCGA-HT-7603      TCGA-HT-7604      TCGA-HT-7605 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7606      TCGA-HT-7607      TCGA-HT-7608      TCGA-HT-7609 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7610      TCGA-HT-7611      TCGA-HT-7616      TCGA-HT-7620 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7676      TCGA-HT-7677      TCGA-HT-7680      TCGA-HT-7681 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7684      TCGA-HT-7686      TCGA-HT-7687      TCGA-HT-7688 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7689      TCGA-HT-7690      TCGA-HT-7691      TCGA-HT-7692 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7695      TCGA-HT-7854 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7855      TCGA-HT-7856      TCGA-HT-7857      TCGA-HT-7858 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7860      TCGA-HT-7873      TCGA-HT-7874      TCGA-HT-7875 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7877      TCGA-HT-7879      TCGA-HT-7880      TCGA-HT-7881 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7882      TCGA-HT-7884      TCGA-HT-7902      TCGA-HT-8010 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-8011      TCGA-HT-8012      TCGA-HT-8013      TCGA-HT-8015 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-8018      TCGA-HT-8019      TCGA-HT-8104      TCGA-HT-8105 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-8106      TCGA-HT-8107      TCGA-HT-8109      TCGA-HT-8110 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-8111      TCGA-HT-8113      TCGA-HT-8114      TCGA-HT-8558 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R5      TCGA-HT-A5R7 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-A5R9      TCGA-HT-A5RB      TCGA-HW-7486      TCGA-HW-7487 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HW-7489      TCGA-HW-7490      TCGA-HW-7491      TCGA-HW-7495 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HW-8319      TCGA-HW-8320      TCGA-HW-8321      TCGA-HW-8322 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HW-A5KJ      TCGA-HW-A5KK      TCGA-HW-A5KM      TCGA-IK-7675 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-IK-8125      TCGA-P5-A5ET      TCGA-P5-A5EU      TCGA-P5-A5EV 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-P5-A5EW      TCGA-P5-A5EX      TCGA-P5-A5EY      TCGA-P5-A5EZ 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-P5-A5F0      TCGA-P5-A5F1      TCGA-P5-A5F2      TCGA-P5-A5F4 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-P5-A5F6 
"PLCG1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PLCG1 MUTATED        0      2      0
  PLCG1 WILD-TYPE     66    126     57
D26V6, multiclass
[1] "Remove cluster labels:" "PLCG1 MUTATED"         
clus
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              2             249 
     TCGA-CS-4938      TCGA-CS-4942      TCGA-CS-4943      TCGA-CS-4944 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5394      TCGA-CS-5396 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188      TCGA-CS-6665 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-CS-6666      TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5273 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DB-5274      TCGA-DB-5275      TCGA-DB-5276      TCGA-DB-5277 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DB-5278      TCGA-DB-5279      TCGA-DB-5280      TCGA-DB-5281 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DB-A4X9      TCGA-DB-A4XA      TCGA-DB-A4XB      TCGA-DB-A4XC 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DB-A4XD      TCGA-DB-A4XE      TCGA-DB-A4XF      TCGA-DB-A4XG 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DB-A4XH      TCGA-DH-5140      TCGA-DH-5141      TCGA-DH-5142 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DU-5847      TCGA-DU-5849 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-5851      TCGA-DU-5853      TCGA-DU-5854      TCGA-DU-5870 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-5871      TCGA-DU-5872      TCGA-DU-5874      TCGA-DU-6393 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-6394      TCGA-DU-6395      TCGA-DU-6396      TCGA-DU-6397 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-6399      TCGA-DU-6400      TCGA-DU-6401      TCGA-DU-6402 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-6403      TCGA-DU-6404      TCGA-DU-6405      TCGA-DU-6407 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-6408      TCGA-DU-6410      TCGA-DU-6542      TCGA-DU-7006 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-7007      TCGA-DU-7008      TCGA-DU-7009      TCGA-DU-7010 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-7012      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7290      TCGA-DU-7292      TCGA-DU-7294 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-7298      TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-7304      TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-8161      TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8164 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-8165      TCGA-DU-8166      TCGA-DU-8167      TCGA-DU-8168 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TT 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-DU-A5TU      TCGA-DU-A5TW      TCGA-DU-A5TY      TCGA-E1-5302 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5305      TCGA-E1-5307 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-E1-5311      TCGA-E1-5318      TCGA-E1-5319      TCGA-E1-5322 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-EZ-7264      TCGA-FG-5962      TCGA-FG-5963      TCGA-FG-5964 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-FG-5965      TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-FG-6691      TCGA-FG-7634      TCGA-FG-7636      TCGA-FG-7637 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-FG-7638      TCGA-FG-7641      TCGA-FG-7643      TCGA-FG-8181 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-FG-8182      TCGA-FG-8185      TCGA-FG-8186      TCGA-FG-8187 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-FG-8188      TCGA-FG-8189      TCGA-FG-8191      TCGA-FG-A4MT 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-FG-A4MU      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A4MY 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-FG-A60J      TCGA-HT-7467      TCGA-HT-7468      TCGA-HT-7469 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7470      TCGA-HT-7471      TCGA-HT-7472      TCGA-HT-7473 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7474      TCGA-HT-7475      TCGA-HT-7476      TCGA-HT-7477 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7478      TCGA-HT-7479      TCGA-HT-7480      TCGA-HT-7481 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7482      TCGA-HT-7483      TCGA-HT-7485      TCGA-HT-7601 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7602      TCGA-HT-7603      TCGA-HT-7604      TCGA-HT-7605 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7606      TCGA-HT-7607      TCGA-HT-7608      TCGA-HT-7609 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7610      TCGA-HT-7611      TCGA-HT-7616      TCGA-HT-7620 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7676      TCGA-HT-7677      TCGA-HT-7680      TCGA-HT-7681 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7684      TCGA-HT-7686      TCGA-HT-7687      TCGA-HT-7688 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7689      TCGA-HT-7690      TCGA-HT-7691      TCGA-HT-7692 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7695      TCGA-HT-7854 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7855      TCGA-HT-7856      TCGA-HT-7857      TCGA-HT-7858 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7860      TCGA-HT-7873      TCGA-HT-7874      TCGA-HT-7875 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7877      TCGA-HT-7879      TCGA-HT-7880      TCGA-HT-7881 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-7882      TCGA-HT-7884      TCGA-HT-7902      TCGA-HT-8010 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-8011      TCGA-HT-8012      TCGA-HT-8013      TCGA-HT-8015 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-8018      TCGA-HT-8019      TCGA-HT-8104      TCGA-HT-8105 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-8106      TCGA-HT-8107      TCGA-HT-8109      TCGA-HT-8110 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-8111      TCGA-HT-8113      TCGA-HT-8114      TCGA-HT-8558 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R5      TCGA-HT-A5R7 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HT-A5R9      TCGA-HT-A5RB      TCGA-HW-7486      TCGA-HW-7487 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HW-7489      TCGA-HW-7490      TCGA-HW-7491      TCGA-HW-7495 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HW-8319      TCGA-HW-8320      TCGA-HW-8321      TCGA-HW-8322 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-HW-A5KJ      TCGA-HW-A5KK      TCGA-HW-A5KM      TCGA-IK-7675 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-IK-8125      TCGA-P5-A5ET      TCGA-P5-A5EU      TCGA-P5-A5EV 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-P5-A5EW      TCGA-P5-A5EX      TCGA-P5-A5EY      TCGA-P5-A5EZ 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-P5-A5F0      TCGA-P5-A5F1      TCGA-P5-A5F2      TCGA-P5-A5F4 
"PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" "PLCG1 WILD-TYPE" 
     TCGA-P5-A5F6 
"PLCG1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PLCG1 MUTATED        1      3      0      0      0
  PLCG1 WILD-TYPE     74     62     51     83     14
D26V7, multiclass
        clus
vv       PLCG1 MUTATED PLCG1 WILD-TYPE
  CLUS_1             1              74
  CLUS_2             3              62
  CLUS_3             0              51
  CLUS_4             0              83
  CLUS_5             0              14
[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
  PLCG1 MUTATED        1      2      0      1
  PLCG1 WILD-TYPE     77     63     58     86
D26V8, multiclass
        clus
vv       PLCG1 MUTATED PLCG1 WILD-TYPE
  CLUS_1             1              77
  CLUS_2             2              63
  CLUS_3             0              58
  CLUS_4             1              86
[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
  PLCG1 MUTATED        3      0      1      0
  PLCG1 WILD-TYPE     80     57    112     36
D26V9, multiclass
        clus
vv       PLCG1 MUTATED PLCG1 WILD-TYPE
  CLUS_1             3              80
  CLUS_2             0              57
  CLUS_3             1             112
  CLUS_4             0              36
[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
  PLCG1 MUTATED        2      0      2
  PLCG1 WILD-TYPE    122    108     55
D26V10, multiclass
        clus
vv       PLCG1 MUTATED PLCG1 WILD-TYPE
  CLUS_1             2             122
  CLUS_2             0             108
  CLUS_3             2              55
[1] 3 2
[1] 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
  PLCG1 MUTATED        4      0      0
  PLCG1 WILD-TYPE    114     74     95
D26V11, multiclass
        clus
vv       PLCG1 MUTATED PLCG1 WILD-TYPE
  CLUS_1             4             114
  CLUS_2             0              74
  CLUS_3             0              95
[1] 3 2
[1] 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
  PLCG1 MUTATED        0      1      1      2
  PLCG1 WILD-TYPE     52     65    121     45
D26V12, multiclass
        clus
vv       PLCG1 MUTATED PLCG1 WILD-TYPE
  CLUS_1             0              52
  CLUS_2             1              65
  CLUS_3             1             121
  CLUS_4             2              45
[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(27) Variable = DDX5 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DDX5 MUTATED        1      0      0
  DDX5 WILD-TYPE      8     10      7
D27V1, multiclass
[1] "Remove cluster labels:" "DDX5 MUTATED"          
clus
  DDX5 MUTATED DDX5 WILD-TYPE 
             1             25 
    TCGA-CS-4942     TCGA-CS-4944     TCGA-CS-5390     TCGA-CS-5394 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-CS-5395     TCGA-CS-5396     TCGA-DB-5273     TCGA-DB-5274 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277     TCGA-DB-5278 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140     TCGA-DH-5141 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144     TCGA-E1-5302 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311     TCGA-E1-5318 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-E1-5322 
"DDX5 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DDX5 MUTATED        0      1      0      0
  DDX5 WILD-TYPE      7      6      7      5
D27V2, multiclass
[1] "Remove cluster labels:" "DDX5 MUTATED"          
clus
  DDX5 MUTATED DDX5 WILD-TYPE 
             1             25 
    TCGA-CS-4942     TCGA-CS-4944     TCGA-CS-5390     TCGA-CS-5394 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-CS-5395     TCGA-CS-5396     TCGA-DB-5273     TCGA-DB-5274 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277     TCGA-DB-5278 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140     TCGA-DH-5141 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144     TCGA-E1-5302 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311     TCGA-E1-5318 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-E1-5322 
"DDX5 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DDX5 MUTATED        2      0      2
  DDX5 WILD-TYPE     94     69    119
D27V3, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            2             94
  CLUS_2            0             69
  CLUS_3            2            119
[1] 3 2
[1] 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
  DDX5 MUTATED        2      0      2      0
  DDX5 WILD-TYPE    127     42     86     30
D27V4, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            2            127
  CLUS_2            0             42
  CLUS_3            2             86
  CLUS_4            0             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 CLUS_4
  DDX5 MUTATED        1      1      1      1
  DDX5 WILD-TYPE     51     60     64     72
D27V5, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            1             51
  CLUS_2            1             60
  CLUS_3            1             64
  CLUS_4            1             72
[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
  DDX5 MUTATED        2      1      1
  DDX5 WILD-TYPE     64    127     56
D27V6, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            2             64
  CLUS_2            1            127
  CLUS_3            1             56
[1] 3 2
[1] 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
  DDX5 MUTATED        2      0      2      0      0
  DDX5 WILD-TYPE     73     65     49     83     14
D27V7, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            2             73
  CLUS_2            0             65
  CLUS_3            2             49
  CLUS_4            0             83
  CLUS_5            0             14
[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
  DDX5 MUTATED        2      0      2      0
  DDX5 WILD-TYPE     76     65     56     87
D27V8, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            2             76
  CLUS_2            0             65
  CLUS_3            2             56
  CLUS_4            0             87
[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
  DDX5 MUTATED        0      1      3      0
  DDX5 WILD-TYPE     83     56    110     36
D27V9, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            0             83
  CLUS_2            1             56
  CLUS_3            3            110
  CLUS_4            0             36
[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
  DDX5 MUTATED        1      3      0
  DDX5 WILD-TYPE    123    105     57
D27V10, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            1            123
  CLUS_2            3            105
  CLUS_3            0             57
[1] 3 2
[1] 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
  DDX5 MUTATED        0      1      3
  DDX5 WILD-TYPE    118     73     92
D27V11, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            0            118
  CLUS_2            1             73
  CLUS_3            3             92
[1] 3 2
[1] 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
  DDX5 MUTATED        0      1      3      0
  DDX5 WILD-TYPE     52     65    119     47
D27V12, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            0             52
  CLUS_2            1             65
  CLUS_3            3            119
  CLUS_4            0             47
[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(28) Variable = ZNF709 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF709 MUTATED        0      0      0
  ZNF709 WILD-TYPE      9     10      7
D28V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF709 MUTATED        0      0      0      0
  ZNF709 WILD-TYPE      7      7      7      5
D28V2, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF709 MUTATED        1      0      2
  ZNF709 WILD-TYPE     95     69    119
D28V3, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              1               95
  CLUS_2              0               69
  CLUS_3              2              119
[1] 3 2
[1] 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
  ZNF709 MUTATED        1      0      2      0
  ZNF709 WILD-TYPE    128     42     86     30
D28V4, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              1              128
  CLUS_2              0               42
  CLUS_3              2               86
  CLUS_4              0               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 CLUS_4
  ZNF709 MUTATED        1      0      1      1
  ZNF709 WILD-TYPE     51     61     64     72
D28V5, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              1               51
  CLUS_2              0               61
  CLUS_3              1               64
  CLUS_4              1               72
[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
  ZNF709 MUTATED        1      1      1
  ZNF709 WILD-TYPE     65    127     56
D28V6, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              1               65
  CLUS_2              1              127
  CLUS_3              1               56
[1] 3 2
[1] 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
  ZNF709 MUTATED        0      0      0      2      1
  ZNF709 WILD-TYPE     75     65     51     81     13
D28V7, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              0               75
  CLUS_2              0               65
  CLUS_3              0               51
  CLUS_4              2               81
  CLUS_5              1               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
  ZNF709 MUTATED        0      0      2      1
  ZNF709 WILD-TYPE     78     65     56     86
D28V8, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              0               78
  CLUS_2              0               65
  CLUS_3              2               56
  CLUS_4              1               86
[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
  ZNF709 MUTATED        1      0      2      0
  ZNF709 WILD-TYPE     82     57    111     36
D28V9, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              1               82
  CLUS_2              0               57
  CLUS_3              2              111
  CLUS_4              0               36
[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
  ZNF709 MUTATED        1      2      0
  ZNF709 WILD-TYPE    123    106     57
D28V10, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              1              123
  CLUS_2              2              106
  CLUS_3              0               57
[1] 3 2
[1] 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
  ZNF709 MUTATED        2      0      1
  ZNF709 WILD-TYPE    116     74     94
D28V11, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              2              116
  CLUS_2              0               74
  CLUS_3              1               94
[1] 3 2
[1] 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
  ZNF709 MUTATED        0      1      2      0
  ZNF709 WILD-TYPE     52     65    120     47
D28V12, multiclass
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  CLUS_1              0               52
  CLUS_2              1               65
  CLUS_3              2              120
  CLUS_4              0               47
[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(29) Variable = TRERF1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TRERF1 MUTATED        0      0      0
  TRERF1 WILD-TYPE      9     10      7
D29V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TRERF1 MUTATED        0      0      0      0
  TRERF1 WILD-TYPE      7      7      7      5
D29V2, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TRERF1 MUTATED        3      0      0
  TRERF1 WILD-TYPE     93     69    121
D29V3, multiclass
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  CLUS_1              3               93
  CLUS_2              0               69
  CLUS_3              0              121
[1] 3 2
[1] 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
  TRERF1 MUTATED        2      0      0      1
  TRERF1 WILD-TYPE    127     42     88     29
D29V4, multiclass
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  CLUS_1              2              127
  CLUS_2              0               42
  CLUS_3              0               88
  CLUS_4              1               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 CLUS_4
  TRERF1 MUTATED        1      0      0      2
  TRERF1 WILD-TYPE     51     61     65     71
D29V5, multiclass
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  CLUS_1              1               51
  CLUS_2              0               61
  CLUS_3              0               65
  CLUS_4              2               71
[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
  TRERF1 MUTATED        1      0      2
  TRERF1 WILD-TYPE     65    128     55
D29V6, multiclass
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  CLUS_1              1               65
  CLUS_2              0              128
  CLUS_3              2               55
[1] 3 2
[1] 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
  TRERF1 MUTATED        1      0      0      1      1
  TRERF1 WILD-TYPE     74     65     51     82     13
D29V7, multiclass
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  CLUS_1              1               74
  CLUS_2              0               65
  CLUS_3              0               51
  CLUS_4              1               82
  CLUS_5              1               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
  TRERF1 MUTATED        2      0      0      1
  TRERF1 WILD-TYPE     76     65     58     86
D29V8, multiclass
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  CLUS_1              2               76
  CLUS_2              0               65
  CLUS_3              0               58
  CLUS_4              1               86
[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
  TRERF1 MUTATED        1      0      2      0
  TRERF1 WILD-TYPE     82     57    111     36
D29V9, multiclass
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  CLUS_1              1               82
  CLUS_2              0               57
  CLUS_3              2              111
  CLUS_4              0               36
[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
  TRERF1 MUTATED        1      2      0
  TRERF1 WILD-TYPE    123    106     57
D29V10, multiclass
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  CLUS_1              1              123
  CLUS_2              2              106
  CLUS_3              0               57
[1] 3 2
[1] 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
  TRERF1 MUTATED        1      0      2
  TRERF1 WILD-TYPE    117     74     93
D29V11, multiclass
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  CLUS_1              1              117
  CLUS_2              0               74
  CLUS_3              2               93
[1] 3 2
[1] 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
  TRERF1 MUTATED        1      0      2      0
  TRERF1 WILD-TYPE     51     66    120     47
D29V12, multiclass
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  CLUS_1              1               51
  CLUS_2              0               66
  CLUS_3              2              120
  CLUS_4              0               47
[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(30) Variable = BCOR MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BCOR MUTATED        1      1      1
  BCOR WILD-TYPE      8      9      6
D30V1, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            1              8
  CLUS_2            1              9
  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 CLUS_4
  BCOR MUTATED        1      0      1      1
  BCOR WILD-TYPE      6      7      6      4
D30V2, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            1              6
  CLUS_2            0              7
  CLUS_3            1              6
  CLUS_4            1              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
  BCOR MUTATED        1      2      6
  BCOR WILD-TYPE     95     67    115
D30V3, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            1             95
  CLUS_2            2             67
  CLUS_3            6            115
[1] 3 2
[1] 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
  BCOR MUTATED        3      1      4      1
  BCOR WILD-TYPE    126     41     84     29
D30V4, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            3            126
  CLUS_2            1             41
  CLUS_3            4             84
  CLUS_4            1             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 CLUS_4
  BCOR MUTATED        2      2      1      2
  BCOR WILD-TYPE     50     59     64     71
D30V5, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            2             50
  CLUS_2            2             59
  CLUS_3            1             64
  CLUS_4            2             71
[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
  BCOR MUTATED        2      3      2
  BCOR WILD-TYPE     64    125     55
D30V6, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            2             64
  CLUS_2            3            125
  CLUS_3            2             55
[1] 3 2
[1] 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
  BCOR MUTATED        2      1      2      4      0
  BCOR WILD-TYPE     73     64     49     79     14
D30V7, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            2             73
  CLUS_2            1             64
  CLUS_3            2             49
  CLUS_4            4             79
  CLUS_5            0             14
[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
  BCOR MUTATED        1      1      2      5
  BCOR WILD-TYPE     77     64     56     82
D30V8, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            1             77
  CLUS_2            1             64
  CLUS_3            2             56
  CLUS_4            5             82
[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
  BCOR MUTATED        3      1      4      1
  BCOR WILD-TYPE     80     56    109     35
D30V9, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            3             80
  CLUS_2            1             56
  CLUS_3            4            109
  CLUS_4            1             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
  BCOR MUTATED        3      4      2
  BCOR WILD-TYPE    121    104     55
D30V10, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            3            121
  CLUS_2            4            104
  CLUS_3            2             55
[1] 3 2
[1] 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
  BCOR MUTATED        2      4      3
  BCOR WILD-TYPE    116     70     92
D30V11, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            2            116
  CLUS_2            4             70
  CLUS_3            3             92
[1] 3 2
[1] 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
  BCOR MUTATED        0      5      3      1
  BCOR WILD-TYPE     52     61    119     46
D30V12, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            0             52
  CLUS_2            5             61
  CLUS_3            3            119
  CLUS_4            1             46
[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(31) Variable = SRPX MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SRPX MUTATED        0      1      0
  SRPX WILD-TYPE      9      9      7
D31V1, multiclass
[1] "Remove cluster labels:" "SRPX MUTATED"          
clus
  SRPX MUTATED SRPX WILD-TYPE 
             1             25 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-CS-5394     TCGA-CS-5395     TCGA-CS-5396     TCGA-DB-5273 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DH-5141     TCGA-DH-5142     TCGA-DH-5143     TCGA-E1-5302 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311     TCGA-E1-5318 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-E1-5322 
"SRPX WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SRPX MUTATED        0      0      1      0
  SRPX WILD-TYPE      7      7      6      5
D31V2, multiclass
[1] "Remove cluster labels:" "SRPX MUTATED"          
clus
  SRPX MUTATED SRPX WILD-TYPE 
             1             25 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-CS-5394     TCGA-CS-5395     TCGA-CS-5396     TCGA-DB-5273 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DH-5141     TCGA-DH-5142     TCGA-DH-5143     TCGA-E1-5302 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311     TCGA-E1-5318 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-E1-5322 
"SRPX WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SRPX MUTATED        0      1      2
  SRPX WILD-TYPE     96     68    119
D31V3, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            0             96
  CLUS_2            1             68
  CLUS_3            2            119
[1] 3 2
[1] 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
  SRPX MUTATED        0      1      2      0
  SRPX WILD-TYPE    129     41     86     30
D31V4, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            0            129
  CLUS_2            1             41
  CLUS_3            2             86
  CLUS_4            0             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 CLUS_4
  SRPX MUTATED        0      1      2      0
  SRPX WILD-TYPE     52     60     63     73
D31V5, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            0             52
  CLUS_2            1             60
  CLUS_3            2             63
  CLUS_4            0             73
[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
  SRPX MUTATED        1      2      0
  SRPX WILD-TYPE     65    126     57
D31V6, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            1             65
  CLUS_2            2            126
  CLUS_3            0             57
[1] 3 2
[1] 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
  SRPX MUTATED        0      1      2      0      0
  SRPX WILD-TYPE     75     64     49     83     14
D31V7, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            0             75
  CLUS_2            1             64
  CLUS_3            2             49
  CLUS_4            0             83
  CLUS_5            0             14
[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
  SRPX MUTATED        0      1      2      0
  SRPX WILD-TYPE     78     64     56     87
D31V8, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            0             78
  CLUS_2            1             64
  CLUS_3            2             56
  CLUS_4            0             87
[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
  SRPX MUTATED        1      1      0      1
  SRPX WILD-TYPE     82     56    113     35
D31V9, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            1             82
  CLUS_2            1             56
  CLUS_3            0            113
  CLUS_4            1             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
  SRPX MUTATED        2      0      1
  SRPX WILD-TYPE    122    108     56
D31V10, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            2            122
  CLUS_2            0            108
  CLUS_3            1             56
[1] 3 2
[1] 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
  SRPX MUTATED        2      1      0
  SRPX WILD-TYPE    116     73     95
D31V11, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            2            116
  CLUS_2            1             73
  CLUS_3            0             95
[1] 3 2
[1] 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
  SRPX MUTATED        0      2      0      1
  SRPX WILD-TYPE     52     64    122     46
D31V12, multiclass
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  CLUS_1            0             52
  CLUS_2            2             64
  CLUS_3            0            122
  CLUS_4            1             46
[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(32) Variable = DOCK5 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DOCK5 MUTATED        0      0      0
  DOCK5 WILD-TYPE      9     10      7
D32V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DOCK5 MUTATED        0      0      0      0
  DOCK5 WILD-TYPE      7      7      7      5
D32V2, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DOCK5 MUTATED        1      4      1
  DOCK5 WILD-TYPE     95     65    120
D32V3, multiclass
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  CLUS_1             1              95
  CLUS_2             4              65
  CLUS_3             1             120
[1] 3 2
[1] 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
  DOCK5 MUTATED        1      3      2      0
  DOCK5 WILD-TYPE    128     39     86     30
D32V4, multiclass
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  CLUS_1             1             128
  CLUS_2             3              39
  CLUS_3             2              86
  CLUS_4             0              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 CLUS_4
  DOCK5 MUTATED        2      2      0      1
  DOCK5 WILD-TYPE     50     59     65     72
D32V5, multiclass
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  CLUS_1             2              50
  CLUS_2             2              59
  CLUS_3             0              65
  CLUS_4             1              72
[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
  DOCK5 MUTATED        3      2      0
  DOCK5 WILD-TYPE     63    126     57
D32V6, multiclass
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  CLUS_1             3              63
  CLUS_2             2             126
  CLUS_3             0              57
[1] 3 2
[1] 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
  DOCK5 MUTATED        0      4      1      1      0
  DOCK5 WILD-TYPE     75     61     50     82     14
D32V7, multiclass
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  CLUS_1             0              75
  CLUS_2             4              61
  CLUS_3             1              50
  CLUS_4             1              82
  CLUS_5             0              14
[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
  DOCK5 MUTATED        0      4      1      1
  DOCK5 WILD-TYPE     78     61     57     86
D32V8, multiclass
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  CLUS_1             0              78
  CLUS_2             4              61
  CLUS_3             1              57
  CLUS_4             1              86
[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
  DOCK5 MUTATED        2      3      1      0
  DOCK5 WILD-TYPE     81     54    112     36
D32V9, multiclass
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  CLUS_1             2              81
  CLUS_2             3              54
  CLUS_3             1             112
  CLUS_4             0              36
[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
  DOCK5 MUTATED        2      1      3
  DOCK5 WILD-TYPE    122    107     54
D32V10, multiclass
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  CLUS_1             2             122
  CLUS_2             1             107
  CLUS_3             3              54
[1] 3 2
[1] 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
  DOCK5 MUTATED        3      1      2
  DOCK5 WILD-TYPE    115     73     93
D32V11, multiclass
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  CLUS_1             3             115
  CLUS_2             1              73
  CLUS_3             2              93
[1] 3 2
[1] 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
  DOCK5 MUTATED        1      1      2      2
  DOCK5 WILD-TYPE     51     65    120     45
D32V12, multiclass
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  CLUS_1             1              51
  CLUS_2             1              65
  CLUS_3             2             120
  CLUS_4             2              45
[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(33) Variable = GIGYF2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GIGYF2 MUTATED        0      0      0
  GIGYF2 WILD-TYPE      9     10      7
D33V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GIGYF2 MUTATED        0      0      0      0
  GIGYF2 WILD-TYPE      7      7      7      5
D33V2, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  GIGYF2 MUTATED        1      3      0
  GIGYF2 WILD-TYPE     95     66    121
D33V3, multiclass
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  CLUS_1              1               95
  CLUS_2              3               66
  CLUS_3              0              121
[1] 3 2
[1] 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
  GIGYF2 MUTATED        1      2      1      0
  GIGYF2 WILD-TYPE    128     40     87     30
D33V4, multiclass
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  CLUS_1              1              128
  CLUS_2              2               40
  CLUS_3              1               87
  CLUS_4              0               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 CLUS_4
  GIGYF2 MUTATED        0      3      1      0
  GIGYF2 WILD-TYPE     52     58     64     73
D33V5, multiclass
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  CLUS_1              0               52
  CLUS_2              3               58
  CLUS_3              1               64
  CLUS_4              0               73
[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
  GIGYF2 MUTATED        1      3      0
  GIGYF2 WILD-TYPE     65    125     57
D33V6, multiclass
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  CLUS_1              1               65
  CLUS_2              3              125
  CLUS_3              0               57
[1] 3 2
[1] 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
  GIGYF2 MUTATED        1      2      1      0      0
  GIGYF2 WILD-TYPE     74     63     50     83     14
D33V7, multiclass
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  CLUS_1              1               74
  CLUS_2              2               63
  CLUS_3              1               50
  CLUS_4              0               83
  CLUS_5              0               14
[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
  GIGYF2 MUTATED        1      2      1      0
  GIGYF2 WILD-TYPE     77     63     57     87
D33V8, multiclass
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  CLUS_1              1               77
  CLUS_2              2               63
  CLUS_3              1               57
  CLUS_4              0               87
[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
  GIGYF2 MUTATED        0      2      1      1
  GIGYF2 WILD-TYPE     83     55    112     35
D33V9, multiclass
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  CLUS_1              0               83
  CLUS_2              2               55
  CLUS_3              1              112
  CLUS_4              1               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
  GIGYF2 MUTATED        0      2      2
  GIGYF2 WILD-TYPE    124    106     55
D33V10, multiclass
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  CLUS_1              0              124
  CLUS_2              2              106
  CLUS_3              2               55
[1] 3 2
[1] 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
  GIGYF2 MUTATED        2      1      1
  GIGYF2 WILD-TYPE    116     73     94
D33V11, multiclass
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  CLUS_1              2              116
  CLUS_2              1               73
  CLUS_3              1               94
[1] 3 2
[1] 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
  GIGYF2 MUTATED        0      1      1      2
  GIGYF2 WILD-TYPE     52     65    121     45
D33V12, multiclass
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  CLUS_1              0               52
  CLUS_2              1               65
  CLUS_3              1              121
  CLUS_4              2               45
[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(34) Variable = NIPBL MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NIPBL MUTATED        0      1      0
  NIPBL WILD-TYPE      9      9      7
D34V1, multiclass
[1] "Remove cluster labels:" "NIPBL MUTATED"         
clus
  NIPBL MUTATED NIPBL WILD-TYPE 
              1              25 
     TCGA-CS-4942      TCGA-CS-4943      TCGA-CS-4944      TCGA-CS-5390 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-CS-5394      TCGA-CS-5395      TCGA-CS-5396      TCGA-DB-5273 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DB-5274      TCGA-DB-5275      TCGA-DB-5276      TCGA-DB-5277 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DB-5278      TCGA-DB-5280      TCGA-DB-5281      TCGA-DH-5140 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DH-5142      TCGA-DH-5143      TCGA-DH-5144      TCGA-E1-5302 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5311      TCGA-E1-5318 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-E1-5322 
"NIPBL WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NIPBL MUTATED        0      0      1      0
  NIPBL WILD-TYPE      7      7      6      5
D34V2, multiclass
[1] "Remove cluster labels:" "NIPBL MUTATED"         
clus
  NIPBL MUTATED NIPBL WILD-TYPE 
              1              25 
     TCGA-CS-4942      TCGA-CS-4943      TCGA-CS-4944      TCGA-CS-5390 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-CS-5394      TCGA-CS-5395      TCGA-CS-5396      TCGA-DB-5273 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DB-5274      TCGA-DB-5275      TCGA-DB-5276      TCGA-DB-5277 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DB-5278      TCGA-DB-5280      TCGA-DB-5281      TCGA-DH-5140 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DH-5142      TCGA-DH-5143      TCGA-DH-5144      TCGA-E1-5302 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5311      TCGA-E1-5318 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-E1-5322 
"NIPBL WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NIPBL MUTATED        1      1      4
  NIPBL WILD-TYPE     95     68    117
D34V3, multiclass
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  CLUS_1             1              95
  CLUS_2             1              68
  CLUS_3             4             117
[1] 3 2
[1] 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
  NIPBL MUTATED        1      0      5      0
  NIPBL WILD-TYPE    128     42     83     30
D34V4, multiclass
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  CLUS_1             1             128
  CLUS_2             0              42
  CLUS_3             5              83
  CLUS_4             0              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 CLUS_4
  NIPBL MUTATED        0      1      2      1
  NIPBL WILD-TYPE     52     60     63     72
D34V5, multiclass
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  CLUS_1             0              52
  CLUS_2             1              60
  CLUS_3             2              63
  CLUS_4             1              72
[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
  NIPBL MUTATED        1      3      0
  NIPBL WILD-TYPE     65    125     57
D34V6, multiclass
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  CLUS_1             1              65
  CLUS_2             3             125
  CLUS_3             0              57
[1] 3 2
[1] 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
  NIPBL MUTATED        1      0      4      1      0
  NIPBL WILD-TYPE     74     65     47     82     14
D34V7, multiclass
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  CLUS_1             1              74
  CLUS_2             0              65
  CLUS_3             4              47
  CLUS_4             1              82
  CLUS_5             0              14
[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
  NIPBL MUTATED        1      0      4      1
  NIPBL WILD-TYPE     77     65     54     86
D34V8, multiclass
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  CLUS_1             1              77
  CLUS_2             0              65
  CLUS_3             4              54
  CLUS_4             1              86
[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
  NIPBL MUTATED        2      2      2      0
  NIPBL WILD-TYPE     81     55    111     36
D34V9, multiclass
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  CLUS_1             2              81
  CLUS_2             2              55
  CLUS_3             2             111
  CLUS_4             0              36
[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
  NIPBL MUTATED        4      2      0
  NIPBL WILD-TYPE    120    106     57
D34V10, multiclass
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  CLUS_1             4             120
  CLUS_2             2             106
  CLUS_3             0              57
[1] 3 2
[1] 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
  NIPBL MUTATED        1      4      1
  NIPBL WILD-TYPE    117     70     94
D34V11, multiclass
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  CLUS_1             1             117
  CLUS_2             4              70
  CLUS_3             1              94
[1] 3 2
[1] 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
  NIPBL MUTATED        1      3      2      0
  NIPBL WILD-TYPE     51     63    120     47
D34V12, multiclass
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  CLUS_1             1              51
  CLUS_2             3              63
  CLUS_3             2             120
  CLUS_4             0              47
[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(35) Variable = ZBTB20 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZBTB20 MUTATED        0      0      0
  ZBTB20 WILD-TYPE      9     10      7
D35V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZBTB20 MUTATED        0      0      0      0
  ZBTB20 WILD-TYPE      7      7      7      5
D35V2, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZBTB20 MUTATED        2      1     10
  ZBTB20 WILD-TYPE     94     68    111
D35V3, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              2               94
  CLUS_2              1               68
  CLUS_3             10              111
[1] 3 2
[1] 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
  ZBTB20 MUTATED        2      1     10      0
  ZBTB20 WILD-TYPE    127     41     78     30
D35V4, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              2              127
  CLUS_2              1               41
  CLUS_3             10               78
  CLUS_4              0               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 CLUS_4
  ZBTB20 MUTATED        3      1      2      4
  ZBTB20 WILD-TYPE     49     60     63     69
D35V5, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              3               49
  CLUS_2              1               60
  CLUS_3              2               63
  CLUS_4              4               69
[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
  ZBTB20 MUTATED        4      3      3
  ZBTB20 WILD-TYPE     62    125     54
D35V6, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              4               62
  CLUS_2              3              125
  CLUS_3              3               54
[1] 3 2
[1] 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
  ZBTB20 MUTATED        1      1      3      6      2
  ZBTB20 WILD-TYPE     74     64     48     77     12
D35V7, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              1               74
  CLUS_2              1               64
  CLUS_3              3               48
  CLUS_4              6               77
  CLUS_5              2               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
  ZBTB20 MUTATED        1      1      5      6
  ZBTB20 WILD-TYPE     77     64     53     81
D35V8, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              1               77
  CLUS_2              1               64
  CLUS_3              5               53
  CLUS_4              6               81
[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
  ZBTB20 MUTATED        3      1      8      1
  ZBTB20 WILD-TYPE     80     56    105     35
D35V9, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              3               80
  CLUS_2              1               56
  CLUS_3              8              105
  CLUS_4              1               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
  ZBTB20 MUTATED        4      8      1
  ZBTB20 WILD-TYPE    120    100     56
D35V10, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              4              120
  CLUS_2              8              100
  CLUS_3              1               56
[1] 3 2
[1] 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
  ZBTB20 MUTATED        3      2      8
  ZBTB20 WILD-TYPE    115     72     87
D35V11, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              3              115
  CLUS_2              2               72
  CLUS_3              8               87
[1] 3 2
[1] 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
  ZBTB20 MUTATED        1      3      8      1
  ZBTB20 WILD-TYPE     51     63    114     46
D35V12, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              1               51
  CLUS_2              3               63
  CLUS_3              8              114
  CLUS_4              1               46
[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(36) Variable = TRIP12 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TRIP12 MUTATED        0      1      0
  TRIP12 WILD-TYPE      9      9      7
D36V1, multiclass
[1] "Remove cluster labels:" "TRIP12 MUTATED"        
clus
  TRIP12 MUTATED TRIP12 WILD-TYPE 
               1               25 
      TCGA-CS-4942       TCGA-CS-4943       TCGA-CS-4944       TCGA-CS-5390 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-CS-5394       TCGA-CS-5395       TCGA-CS-5396       TCGA-DB-5273 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DB-5275       TCGA-DB-5276       TCGA-DB-5277       TCGA-DB-5278 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DB-5280       TCGA-DB-5281       TCGA-DH-5140       TCGA-DH-5141 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144       TCGA-E1-5302 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5311       TCGA-E1-5318 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-E1-5322 
"TRIP12 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TRIP12 MUTATED        0      0      1      0
  TRIP12 WILD-TYPE      7      7      6      5
D36V2, multiclass
[1] "Remove cluster labels:" "TRIP12 MUTATED"        
clus
  TRIP12 MUTATED TRIP12 WILD-TYPE 
               1               25 
      TCGA-CS-4942       TCGA-CS-4943       TCGA-CS-4944       TCGA-CS-5390 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-CS-5394       TCGA-CS-5395       TCGA-CS-5396       TCGA-DB-5273 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DB-5275       TCGA-DB-5276       TCGA-DB-5277       TCGA-DB-5278 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DB-5280       TCGA-DB-5281       TCGA-DH-5140       TCGA-DH-5141 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144       TCGA-E1-5302 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5311       TCGA-E1-5318 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-E1-5322 
"TRIP12 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TRIP12 MUTATED        1      0      4
  TRIP12 WILD-TYPE     95     69    117
D36V3, multiclass
        clus
vv       TRIP12 MUTATED TRIP12 WILD-TYPE
  CLUS_1              1               95
  CLUS_2              0               69
  CLUS_3              4              117
[1] 3 2
[1] 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
  TRIP12 MUTATED        2      0      3      0
  TRIP12 WILD-TYPE    127     42     85     30
D36V4, multiclass
        clus
vv       TRIP12 MUTATED TRIP12 WILD-TYPE
  CLUS_1              2              127
  CLUS_2              0               42
  CLUS_3              3               85
  CLUS_4              0               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 CLUS_4
  TRIP12 MUTATED        1      0      1      3
  TRIP12 WILD-TYPE     51     61     64     70
D36V5, multiclass
        clus
vv       TRIP12 MUTATED TRIP12 WILD-TYPE
  CLUS_1              1               51
  CLUS_2              0               61
  CLUS_3              1               64
  CLUS_4              3               70
[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
  TRIP12 MUTATED        2      1      2
  TRIP12 WILD-TYPE     64    127     55
D36V6, multiclass
        clus
vv       TRIP12 MUTATED TRIP12 WILD-TYPE
  CLUS_1              2               64
  CLUS_2              1              127
  CLUS_3              2               55
[1] 3 2
[1] 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
  TRIP12 MUTATED        1      0      2      2      0
  TRIP12 WILD-TYPE     74     65     49     81     14
D36V7, multiclass
        clus
vv       TRIP12 MUTATED TRIP12 WILD-TYPE
  CLUS_1              1               74
  CLUS_2              0               65
  CLUS_3              2               49
  CLUS_4              2               81
  CLUS_5              0               14
[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
  TRIP12 MUTATED        1      0      2      2
  TRIP12 WILD-TYPE     77     65     56     85
D36V8, multiclass
        clus
vv       TRIP12 MUTATED TRIP12 WILD-TYPE
  CLUS_1              1               77
  CLUS_2              0               65
  CLUS_3              2               56
  CLUS_4              2               85
[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
  TRIP12 MUTATED        1      1      2      1
  TRIP12 WILD-TYPE     82     56    111     35
D36V9, multiclass
        clus
vv       TRIP12 MUTATED TRIP12 WILD-TYPE
  CLUS_1              1               82
  CLUS_2              1               56
  CLUS_3              2              111
  CLUS_4              1               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
  TRIP12 MUTATED        3      2      0
  TRIP12 WILD-TYPE    121    106     57
D36V10, multiclass
        clus
vv       TRIP12 MUTATED TRIP12 WILD-TYPE
  CLUS_1              3              121
  CLUS_2              2              106
  CLUS_3              0               57
[1] 3 2
[1] 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
  TRIP12 MUTATED        2      1      2
  TRIP12 WILD-TYPE    116     73     93
D36V11, multiclass
        clus
vv       TRIP12 MUTATED TRIP12 WILD-TYPE
  CLUS_1              2              116
  CLUS_2              1               73
  CLUS_3              2               93
[1] 3 2
[1] 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
  TRIP12 MUTATED        1      2      2      0
  TRIP12 WILD-TYPE     51     64    120     47
D36V12, multiclass
        clus
vv       TRIP12 MUTATED TRIP12 WILD-TYPE
  CLUS_1              1               51
  CLUS_2              2               64
  CLUS_3              2              120
  CLUS_4              0               47
[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(37) Variable = KIAA0664 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA0664 MUTATED        0      0      0
  KIAA0664 WILD-TYPE      9     10      7
D37V1, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIAA0664 MUTATED        0      0      0      0
  KIAA0664 WILD-TYPE      7      7      7      5
D37V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA0664 MUTATED        1      2      2
  KIAA0664 WILD-TYPE     95     67    119
D37V3, multiclass
        clus
vv       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  CLUS_1                1                 95
  CLUS_2                2                 67
  CLUS_3                2                119
[1] 3 2
[1] 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
  KIAA0664 MUTATED        1      2      2      0
  KIAA0664 WILD-TYPE    128     40     86     30
D37V4, multiclass
        clus
vv       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  CLUS_1                1                128
  CLUS_2                2                 40
  CLUS_3                2                 86
  CLUS_4                0                 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 CLUS_4
  KIAA0664 MUTATED        1      1      0      2
  KIAA0664 WILD-TYPE     51     60     65     71
D37V5, multiclass
        clus
vv       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  CLUS_1                1                 51
  CLUS_2                1                 60
  CLUS_3                0                 65
  CLUS_4                2                 71
[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
  KIAA0664 MUTATED        0      2      2
  KIAA0664 WILD-TYPE     66    126     55
D37V6, multiclass
        clus
vv       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  CLUS_1                0                 66
  CLUS_2                2                126
  CLUS_3                2                 55
[1] 3 2
[1] 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
  KIAA0664 MUTATED        0      2      1      2      0
  KIAA0664 WILD-TYPE     75     63     50     81     14
D37V7, multiclass
        clus
vv       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  CLUS_1                0                 75
  CLUS_2                2                 63
  CLUS_3                1                 50
  CLUS_4                2                 81
  CLUS_5                0                 14
[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
  KIAA0664 MUTATED        0      2      1      2
  KIAA0664 WILD-TYPE     78     63     57     85
D37V8, multiclass
        clus
vv       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  CLUS_1                0                 78
  CLUS_2                2                 63
  CLUS_3                1                 57
  CLUS_4                2                 85
[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
  KIAA0664 MUTATED        0      2      2      1
  KIAA0664 WILD-TYPE     83     55    111     35
D37V9, multiclass
        clus
vv       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  CLUS_1                0                 83
  CLUS_2                2                 55
  CLUS_3                2                111
  CLUS_4                1                 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
  KIAA0664 MUTATED        0      3      2
  KIAA0664 WILD-TYPE    124    105     55
D37V10, multiclass
        clus
vv       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  CLUS_1                0                124
  CLUS_2                3                105
  CLUS_3                2                 55
[1] 3 2
[1] 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
  KIAA0664 MUTATED        2      0      3
  KIAA0664 WILD-TYPE    116     74     92
D37V11, multiclass
        clus
vv       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  CLUS_1                2                116
  CLUS_2                0                 74
  CLUS_3                3                 92
[1] 3 2
[1] 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
  KIAA0664 MUTATED        0      0      3      2
  KIAA0664 WILD-TYPE     52     66    119     45
D37V12, multiclass
        clus
vv       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  CLUS_1                0                 52
  CLUS_2                0                 66
  CLUS_3                3                119
  CLUS_4                2                 45
[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"
