[1] "ofn"        "-oTLAML-TB"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/15098833/LAML-TB.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/15166008/transformed.cor.cli.txt"

nPatients in clinical file=200, in cluster file=195, common to both=195
[1] "Reduce the number of clustering variables from 28 to 25."
[1]  25 195
[1] "FLT3 MUTATION ANALYSIS"
[1] 3
  FLT3 MUTATED FLT3 WILD-TYPE 
            53            142 
  FLT3 MUTATED FLT3 WILD-TYPE 
            53            142 
[1] "NPM1 MUTATION ANALYSIS"
[1] 3
  NPM1 MUTATED NPM1 WILD-TYPE 
            52            143 
  NPM1 MUTATED NPM1 WILD-TYPE 
            52            143 
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              49              146 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              49              146 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
            20            175 
  IDH2 MUTATED IDH2 WILD-TYPE 
            20            175 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            18            177 
  IDH1 MUTATED IDH1 WILD-TYPE 
            18            177 
[1] "RUNX1 MUTATION ANALYSIS"
[1] 3
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             18             177 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             18             177 
[1] "TET2 MUTATION ANALYSIS"
[1] 3
  TET2 MUTATED TET2 WILD-TYPE 
            17            178 
  TET2 MUTATED TET2 WILD-TYPE 
            17            178 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            15            180 
  NRAS MUTATED NRAS WILD-TYPE 
            15            180 
[1] "WT1 MUTATION ANALYSIS"
[1] 3
  WT1 MUTATED WT1 WILD-TYPE 
           12           183 
  WT1 MUTATED WT1 WILD-TYPE 
           12           183 
[1] "U2AF1 MUTATION ANALYSIS"
[1] 3
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              8             187 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              8             187 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            15            180 
  TP53 MUTATED TP53 WILD-TYPE 
            15            180 
[1] "CEBPA MUTATION ANALYSIS"
[1] 3
  CEBPA MUTATED CEBPA WILD-TYPE 
             13             182 
  CEBPA MUTATED CEBPA WILD-TYPE 
             13             182 
[1] "PHF6 MUTATION ANALYSIS"
[1] 3
  PHF6 MUTATED PHF6 WILD-TYPE 
             6            189 
  PHF6 MUTATED PHF6 WILD-TYPE 
             6            189 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             8            187 
  KRAS MUTATED KRAS WILD-TYPE 
             8            187 
[1] "SMC3 MUTATION ANALYSIS"
[1] 3
  SMC3 MUTATED SMC3 WILD-TYPE 
             7            188 
  SMC3 MUTATED SMC3 WILD-TYPE 
             7            188 
[1] "KIT MUTATION ANALYSIS"
[1] 3
  KIT MUTATED KIT WILD-TYPE 
            8           187 
  KIT MUTATED KIT WILD-TYPE 
            8           187 
[1] "RAD21 MUTATION ANALYSIS"
[1] 3
  RAD21 MUTATED RAD21 WILD-TYPE 
              5             190 
  RAD21 MUTATED RAD21 WILD-TYPE 
              5             190 
[1] "EZH2 MUTATION ANALYSIS"
[1] 3
  EZH2 MUTATED EZH2 WILD-TYPE 
             3            192 
  EZH2 MUTATED EZH2 WILD-TYPE 
             3            192 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
              6             189 
  STAG2 MUTATED STAG2 WILD-TYPE 
              6             189 
[1] "PTPN11 MUTATION ANALYSIS"
[1] 3
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               9              186 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               9              186 
[1] "ASXL1 MUTATION ANALYSIS"
[1] 3
  ASXL1 MUTATED ASXL1 WILD-TYPE 
              5             190 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
              5             190 
[1] "SUZ12 MUTATION ANALYSIS"
[1] 3
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              3             192 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              3             192 
[1] "PHACTR1 MUTATION ANALYSIS"
[1] 3
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                3               192 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                3               192 
[1] "SMC1A MUTATION ANALYSIS"
[1] 3
  SMC1A MUTATED SMC1A WILD-TYPE 
              6             189 
  SMC1A MUTATED SMC1A WILD-TYPE 
              6             189 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
              3             192 
  KDM6A MUTATED KDM6A WILD-TYPE 
              3             192 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 6 rows and 195 columns.

Variable 1:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 195 columns, 0 survival variables, and 6 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = FLT3 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FLT3 MUTATED       48      3      0      0
  FLT3 WILD-TYPE     95     11     27      2
D1V1, multiclass
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1           48             95
  CLUS_2            3             11
  CLUS_3            0             27
  CLUS_4            0              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 CLUS_4
  FLT3 MUTATED        9      7     13     23
  FLT3 WILD-TYPE     24     56     35     22
D1V2, multiclass
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1            9             24
  CLUS_2            7             56
  CLUS_3           13             35
  CLUS_4           23             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FLT3 MUTATED        6     17     23
  FLT3 WILD-TYPE     67     33     22
D1V3, multiclass
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1            6             67
  CLUS_2           17             33
  CLUS_3           23             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  FLT3 MUTATED        5      2      2      6     14     17
  FLT3 WILD-TYPE     11     11     13     51     12     24
D1V4, multiclass
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1            5             11
  CLUS_2            2             11
  CLUS_3            2             13
  CLUS_4            6             51
  CLUS_5           14             12
  CLUS_6           17             24
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FLT3 MUTATED       23      4      6     18
  FLT3 WILD-TYPE     34     34     36     28
D1V5, multiclass
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1           23             34
  CLUS_2            4             34
  CLUS_3            6             36
  CLUS_4           18             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
  FLT3 MUTATED       30      5     16
  FLT3 WILD-TYPE     37     30     65
D1V6, multiclass
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1           30             37
  CLUS_2            5             30
  CLUS_3           16             65
[1] 3 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 = NPM1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NPM1 MUTATED       50      0      0      0
  NPM1 WILD-TYPE     93     14     27      2
D2V1, multiclass
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1           50             93
  CLUS_2            0             14
  CLUS_3            0             27
  CLUS_4            0              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 CLUS_4
  NPM1 MUTATED        8      4     13     26
  NPM1 WILD-TYPE     25     59     35     19
D2V2, multiclass
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1            8             25
  CLUS_2            4             59
  CLUS_3           13             35
  CLUS_4           26             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NPM1 MUTATED        1     20     25
  NPM1 WILD-TYPE     72     30     20
D2V3, multiclass
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1            1             72
  CLUS_2           20             30
  CLUS_3           25             20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NPM1 MUTATED        0      0      0      1     23     22
  NPM1 WILD-TYPE     16     13     15     56      3     19
D2V4, multiclass
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            0             13
  CLUS_3            0             15
  CLUS_4            1             56
  CLUS_5           23              3
  CLUS_6           22             19
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NPM1 MUTATED       35      2      1     12
  NPM1 WILD-TYPE     22     36     41     34
D2V5, multiclass
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1           35             22
  CLUS_2            2             36
  CLUS_3            1             41
  CLUS_4           12             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
  NPM1 MUTATED       48      1      1
  NPM1 WILD-TYPE     19     34     80
D2V6, multiclass
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1           48             19
  CLUS_2            1             34
  CLUS_3            1             80
[1] 3 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 = DNMT3A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DNMT3A MUTATED       36      4      5      0
  DNMT3A WILD-TYPE    107     10     22      2
D3V1, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1             36              107
  CLUS_2              4               10
  CLUS_3              5               22
  CLUS_4              0                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 CLUS_4
  DNMT3A MUTATED        5     16     19      7
  DNMT3A WILD-TYPE     28     47     29     38
D3V2, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1              5               28
  CLUS_2             16               47
  CLUS_3             19               29
  CLUS_4              7               38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  DNMT3A MUTATED       11     18     12
  DNMT3A WILD-TYPE     62     32     33
D3V3, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1             11               62
  CLUS_2             18               32
  CLUS_3             12               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 CLUS_6
  DNMT3A MUTATED        0      3      0     14     11     13
  DNMT3A WILD-TYPE     16     10     15     43     15     28
D3V4, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1              0               16
  CLUS_2              3               10
  CLUS_3              0               15
  CLUS_4             14               43
  CLUS_5             11               15
  CLUS_6             13               28
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DNMT3A MUTATED       22      4      5     13
  DNMT3A WILD-TYPE     35     34     37     33
D3V5, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1             22               35
  CLUS_2              4               34
  CLUS_3              5               37
  CLUS_4             13               33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  DNMT3A MUTATED       25      3     16
  DNMT3A WILD-TYPE     42     32     65
D3V6, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1             25               42
  CLUS_2              3               32
  CLUS_3             16               65
[1] 3 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 = IDH2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH2 MUTATED       14      4      1      0
  IDH2 WILD-TYPE    129     10     26      2
D4V1, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1           14            129
  CLUS_2            4             10
  CLUS_3            1             26
  CLUS_4            0              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 CLUS_4
  IDH2 MUTATED        0     11      2      5
  IDH2 WILD-TYPE     33     52     46     40
D4V2, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0             33
  CLUS_2           11             52
  CLUS_3            2             46
  CLUS_4            5             40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        8      6      3
  IDH2 WILD-TYPE     65     44     42
D4V3, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            8             65
  CLUS_2            6             44
  CLUS_3            3             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  IDH2 MUTATED        0      2      0      9      2      4
  IDH2 WILD-TYPE     16     11     15     48     24     37
D4V4, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            2             11
  CLUS_3            0             15
  CLUS_4            9             48
  CLUS_5            2             24
  CLUS_6            4             37
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH2 MUTATED        5      2      5      5
  IDH2 WILD-TYPE     52     36     37     41
D4V5, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            5             52
  CLUS_2            2             36
  CLUS_3            5             37
  CLUS_4            5             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        5      1     11
  IDH2 WILD-TYPE     62     34     70
D4V6, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            5             62
  CLUS_2            1             34
  CLUS_3           11             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"

Clustering(5) Variable = IDH1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH1 MUTATED       14      1      2      0
  IDH1 WILD-TYPE    129     13     25      2
D5V1, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           14            129
  CLUS_2            1             13
  CLUS_3            2             25
  CLUS_4            0              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 CLUS_4
  IDH1 MUTATED        6     10      1      1
  IDH1 WILD-TYPE     27     53     47     44
D5V2, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            6             27
  CLUS_2           10             53
  CLUS_3            1             47
  CLUS_4            1             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
  IDH1 MUTATED        7      2      6
  IDH1 WILD-TYPE     66     48     39
D5V3, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            7             66
  CLUS_2            2             48
  CLUS_3            6             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  IDH1 MUTATED        0      0      0      8      4      3
  IDH1 WILD-TYPE     16     13     15     49     22     38
D5V4, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            0             13
  CLUS_3            0             15
  CLUS_4            8             49
  CLUS_5            4             22
  CLUS_6            3             38
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH1 MUTATED        4      4      2      8
  IDH1 WILD-TYPE     53     34     40     38
D5V5, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            4             53
  CLUS_2            4             34
  CLUS_3            2             40
  CLUS_4            8             38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        8      3      7
  IDH1 WILD-TYPE     59     32     74
D5V6, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            8             59
  CLUS_2            3             32
  CLUS_3            7             74
[1] 3 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 = RUNX1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RUNX1 MUTATED       12      3      3      0
  RUNX1 WILD-TYPE    131     11     24      2
D6V1, multiclass
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  CLUS_1            12             131
  CLUS_2             3              11
  CLUS_3             3              24
  CLUS_4             0               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 CLUS_4
  RUNX1 MUTATED        0     13      2      1
  RUNX1 WILD-TYPE     33     50     46     44
D6V2, multiclass
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  CLUS_1             0              33
  CLUS_2            13              50
  CLUS_3             2              46
  CLUS_4             1              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
  RUNX1 MUTATED       13      3      0
  RUNX1 WILD-TYPE     60     47     45
D6V3, multiclass
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  CLUS_1            13              60
  CLUS_2             3              47
  CLUS_3             0              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 CLUS_4 CLUS_5 CLUS_6
  RUNX1 MUTATED        0      1      0     15      0      0
  RUNX1 WILD-TYPE     16     12     15     42     26     41
D6V4, multiclass
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             1              12
  CLUS_3             0              15
  CLUS_4            15              42
  CLUS_5             0              26
  CLUS_6             0              41
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RUNX1 MUTATED        1      4     10      1
  RUNX1 WILD-TYPE     56     34     32     45
D6V5, multiclass
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  CLUS_1             1              56
  CLUS_2             4              34
  CLUS_3            10              32
  CLUS_4             1              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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RUNX1 MUTATED        0      4     12
  RUNX1 WILD-TYPE     67     31     69
D6V6, multiclass
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  CLUS_1             0              67
  CLUS_2             4              31
  CLUS_3            12              69
[1] 3 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 = TET2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TET2 MUTATED       11      3      2      0
  TET2 WILD-TYPE    132     11     25      2
D7V1, multiclass
        clus
vv       TET2 MUTATED TET2 WILD-TYPE
  CLUS_1           11            132
  CLUS_2            3             11
  CLUS_3            2             25
  CLUS_4            0              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 CLUS_4
  TET2 MUTATED        2      8      2      4
  TET2 WILD-TYPE     31     55     46     41
D7V2, multiclass
        clus
vv       TET2 MUTATED TET2 WILD-TYPE
  CLUS_1            2             31
  CLUS_2            8             55
  CLUS_3            2             46
  CLUS_4            4             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TET2 MUTATED        9      2      4
  TET2 WILD-TYPE     64     48     41
D7V3, multiclass
        clus
vv       TET2 MUTATED TET2 WILD-TYPE
  CLUS_1            9             64
  CLUS_2            2             48
  CLUS_3            4             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TET2 MUTATED        0      0      2      7      3      3
  TET2 WILD-TYPE     16     13     13     50     23     38
D7V4, multiclass
        clus
vv       TET2 MUTATED TET2 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            0             13
  CLUS_3            2             13
  CLUS_4            7             50
  CLUS_5            3             23
  CLUS_6            3             38
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TET2 MUTATED        6      2      3      6
  TET2 WILD-TYPE     51     36     39     40
D7V5, multiclass
        clus
vv       TET2 MUTATED TET2 WILD-TYPE
  CLUS_1            6             51
  CLUS_2            2             36
  CLUS_3            3             39
  CLUS_4            6             40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TET2 MUTATED        7      2      8
  TET2 WILD-TYPE     60     33     73
D7V6, multiclass
        clus
vv       TET2 MUTATED TET2 WILD-TYPE
  CLUS_1            7             60
  CLUS_2            2             33
  CLUS_3            8             73
[1] 3 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 = NRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NRAS MUTATED       10      1      4      0
  NRAS WILD-TYPE    133     13     23      2
D8V1, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           10            133
  CLUS_2            1             13
  CLUS_3            4             23
  CLUS_4            0              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 CLUS_4
  NRAS MUTATED        3      5      3      4
  NRAS WILD-TYPE     30     58     45     41
D8V2, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            3             30
  CLUS_2            5             58
  CLUS_3            3             45
  CLUS_4            4             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NRAS MUTATED        5      5      2
  NRAS WILD-TYPE     68     45     43
D8V3, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            5             68
  CLUS_2            5             45
  CLUS_3            2             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NRAS MUTATED        0      1      1      4      2      4
  NRAS WILD-TYPE     16     12     14     53     24     37
D8V4, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0             16
  CLUS_2            1             12
  CLUS_3            1             14
  CLUS_4            4             53
  CLUS_5            2             24
  CLUS_6            4             37
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NRAS MUTATED        5      3      4      2
  NRAS WILD-TYPE     52     35     38     44
D8V5, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            5             52
  CLUS_2            3             35
  CLUS_3            4             38
  CLUS_4            2             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
  NRAS MUTATED        7      2      5
  NRAS WILD-TYPE     60     33     76
D8V6, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            7             60
  CLUS_2            2             33
  CLUS_3            5             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"

Clustering(9) Variable = WT1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  WT1 MUTATED       11      1      0      0
  WT1 WILD-TYPE    132     13     27      2
D9V1, multiclass
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  CLUS_1          11           132
  CLUS_2           1            13
  CLUS_3           0            27
  CLUS_4           0             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 CLUS_4
  WT1 MUTATED        1      0      3      7
  WT1 WILD-TYPE     32     63     45     38
D9V2, multiclass
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  CLUS_1           1            32
  CLUS_2           0            63
  CLUS_3           3            45
  CLUS_4           7            38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  WT1 MUTATED        2      2      6
  WT1 WILD-TYPE     71     48     39
D9V3, multiclass
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  CLUS_1           2            71
  CLUS_2           2            48
  CLUS_3           6            39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  WT1 MUTATED        0      1      0      3      4      2
  WT1 WILD-TYPE     16     12     15     54     22     39
D9V4, multiclass
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  CLUS_1           0            16
  CLUS_2           1            12
  CLUS_3           0            15
  CLUS_4           3            54
  CLUS_5           4            22
  CLUS_6           2            39
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  WT1 MUTATED        2      0      3      6
  WT1 WILD-TYPE     55     38     39     40
D9V5, multiclass
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  CLUS_1           2            55
  CLUS_2           0            38
  CLUS_3           3            39
  CLUS_4           6            40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  WT1 MUTATED        5      0      6
  WT1 WILD-TYPE     62     35     75
D9V6, multiclass
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  CLUS_1           5            62
  CLUS_2           0            35
  CLUS_3           6            75
[1] 3 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 = U2AF1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  U2AF1 MUTATED        5      0      1      0
  U2AF1 WILD-TYPE    138     14     26      2
D10V1, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             5             138
  CLUS_2             0              14
  CLUS_3             1              26
  CLUS_4             0               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 CLUS_4
  U2AF1 MUTATED        0      6      2      0
  U2AF1 WILD-TYPE     33     57     46     45
D10V2, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             0              33
  CLUS_2             6              57
  CLUS_3             2              46
  CLUS_4             0              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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  U2AF1 MUTATED        5      2      0
  U2AF1 WILD-TYPE     68     48     45
D10V3, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             5              68
  CLUS_2             2              48
  CLUS_3             0              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 CLUS_4 CLUS_5 CLUS_6
  U2AF1 MUTATED        0      0      0      6      0      1
  U2AF1 WILD-TYPE     16     13     15     51     26     40
D10V4, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             0              13
  CLUS_3             0              15
  CLUS_4             6              51
  CLUS_5             0              26
  CLUS_6             1              40
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  U2AF1 MUTATED        1      2      4      0
  U2AF1 WILD-TYPE     56     36     38     46
D10V5, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             1              56
  CLUS_2             2              36
  CLUS_3             4              38
  CLUS_4             0              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
  U2AF1 MUTATED        1      2      4
  U2AF1 WILD-TYPE     66     33     77
D10V6, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             1              66
  CLUS_2             2              33
  CLUS_3             4              77
[1] 3 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 = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        0      2     13      0
  TP53 WILD-TYPE    143     12     14      2
D11V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0            143
  CLUS_2            2             12
  CLUS_3           13             14
  CLUS_4            0              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 CLUS_4
  TP53 MUTATED        0     15      0      0
  TP53 WILD-TYPE     33     48     48     45
D11V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             33
  CLUS_2           15             48
  CLUS_3            0             48
  CLUS_4            0             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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       12      1      0
  TP53 WILD-TYPE     61     49     45
D11V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12             61
  CLUS_2            1             49
  CLUS_3            0             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 CLUS_4 CLUS_5 CLUS_6
  TP53 MUTATED        0      0      0     12      0      1
  TP53 WILD-TYPE     16     13     15     45     26     40
D11V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            0             13
  CLUS_3            0             15
  CLUS_4           12             45
  CLUS_5            0             26
  CLUS_6            1             40
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        0      9      3      2
  TP53 WILD-TYPE     57     29     39     44
D11V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             57
  CLUS_2            9             29
  CLUS_3            3             39
  CLUS_4            2             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        0      8      6
  TP53 WILD-TYPE     67     27     75
D11V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             67
  CLUS_2            8             27
  CLUS_3            6             75
[1] 3 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 = CEBPA MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CEBPA MUTATED        9      0      3      0
  CEBPA WILD-TYPE    134     14     24      2
D12V1, multiclass
        clus
vv       CEBPA MUTATED CEBPA WILD-TYPE
  CLUS_1             9             134
  CLUS_2             0              14
  CLUS_3             3              24
  CLUS_4             0               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 CLUS_4
  CEBPA MUTATED        2      2      5      4
  CEBPA WILD-TYPE     31     61     43     41
D12V2, multiclass
        clus
vv       CEBPA MUTATED CEBPA WILD-TYPE
  CLUS_1             2              31
  CLUS_2             2              61
  CLUS_3             5              43
  CLUS_4             4              41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CEBPA MUTATED        9      2      2
  CEBPA WILD-TYPE     64     48     43
D12V3, multiclass
        clus
vv       CEBPA MUTATED CEBPA WILD-TYPE
  CLUS_1             9              64
  CLUS_2             2              48
  CLUS_3             2              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CEBPA MUTATED        0      0      7      4      1      1
  CEBPA WILD-TYPE     16     13      8     53     25     40
D12V4, multiclass
        clus
vv       CEBPA MUTATED CEBPA WILD-TYPE
  CLUS_1             0              16
  CLUS_2             0              13
  CLUS_3             7               8
  CLUS_4             4              53
  CLUS_5             1              25
  CLUS_6             1              40
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CEBPA MUTATED        1      1      4      7
  CEBPA WILD-TYPE     56     37     38     39
D12V5, multiclass
        clus
vv       CEBPA MUTATED CEBPA WILD-TYPE
  CLUS_1             1              56
  CLUS_2             1              37
  CLUS_3             4              38
  CLUS_4             7              39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CEBPA MUTATED        2      0     11
  CEBPA WILD-TYPE     65     35     70
D12V6, multiclass
        clus
vv       CEBPA MUTATED CEBPA WILD-TYPE
  CLUS_1             2              65
  CLUS_2             0              35
  CLUS_3            11              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"

Clustering(13) Variable = PHF6 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PHF6 MUTATED        5      0      1      0
  PHF6 WILD-TYPE    138     14     26      2
D13V1, multiclass
        clus
vv       PHF6 MUTATED PHF6 WILD-TYPE
  CLUS_1            5            138
  CLUS_2            0             14
  CLUS_3            1             26
  CLUS_4            0              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 CLUS_4
  PHF6 MUTATED        1      1      3      1
  PHF6 WILD-TYPE     32     62     45     44
D13V2, multiclass
        clus
vv       PHF6 MUTATED PHF6 WILD-TYPE
  CLUS_1            1             32
  CLUS_2            1             62
  CLUS_3            3             45
  CLUS_4            1             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
  PHF6 MUTATED        2      1      2
  PHF6 WILD-TYPE     71     49     43
D13V3, multiclass
        clus
vv       PHF6 MUTATED PHF6 WILD-TYPE
  CLUS_1            2             71
  CLUS_2            1             49
  CLUS_3            2             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PHF6 MUTATED        0      0      0      4      1      0
  PHF6 WILD-TYPE     16     13     15     53     25     41
D13V4, multiclass
        clus
vv       PHF6 MUTATED PHF6 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            0             13
  CLUS_3            0             15
  CLUS_4            4             53
  CLUS_5            1             25
  CLUS_6            0             41
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PHF6 MUTATED        2      0      2      1
  PHF6 WILD-TYPE     55     38     40     45
D13V5, multiclass
        clus
vv       PHF6 MUTATED PHF6 WILD-TYPE
  CLUS_1            2             55
  CLUS_2            0             38
  CLUS_3            2             40
  CLUS_4            1             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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PHF6 MUTATED        1      0      4
  PHF6 WILD-TYPE     66     35     77
D13V6, multiclass
        clus
vv       PHF6 MUTATED PHF6 WILD-TYPE
  CLUS_1            1             66
  CLUS_2            0             35
  CLUS_3            4             77
[1] 3 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 = KRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        5      0      2      1
  KRAS WILD-TYPE    138     14     25      1
D14V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            5            138
  CLUS_2            0             14
  CLUS_3            2             25
  CLUS_4            1              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        0      3      2      1
  KRAS WILD-TYPE     33     60     46     44
D14V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0             33
  CLUS_2            3             60
  CLUS_3            2             46
  CLUS_4            1             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
  KRAS MUTATED        4      3      0
  KRAS WILD-TYPE     69     47     45
D14V3, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            4             69
  CLUS_2            3             47
  CLUS_3            0             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 CLUS_4 CLUS_5 CLUS_6
  KRAS MUTATED        0      0      0      4      0      3
  KRAS WILD-TYPE     16     13     15     53     26     38
D14V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0             16
  CLUS_2            0             13
  CLUS_3            0             15
  CLUS_4            4             53
  CLUS_5            0             26
  CLUS_6            3             38
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        3      3      0      1
  KRAS WILD-TYPE     54     35     42     45
D14V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3             54
  CLUS_2            3             35
  CLUS_3            0             42
  CLUS_4            1             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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        3      2      2
  KRAS WILD-TYPE     64     33     79
D14V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3             64
  CLUS_2            2             33
  CLUS_3            2             79
[1] 3 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 = SMC3 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMC3 MUTATED        6      0      1      0
  SMC3 WILD-TYPE    137     14     26      2
D15V1, multiclass
        clus
vv       SMC3 MUTATED SMC3 WILD-TYPE
  CLUS_1            6            137
  CLUS_2            0             14
  CLUS_3            1             26
  CLUS_4            0              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 CLUS_4
  SMC3 MUTATED        0      1      4      2
  SMC3 WILD-TYPE     33     62     44     43
D15V2, multiclass
        clus
vv       SMC3 MUTATED SMC3 WILD-TYPE
  CLUS_1            0             33
  CLUS_2            1             62
  CLUS_3            4             44
  CLUS_4            2             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SMC3 MUTATED        2      2      3
  SMC3 WILD-TYPE     71     48     42
D15V3, multiclass
        clus
vv       SMC3 MUTATED SMC3 WILD-TYPE
  CLUS_1            2             71
  CLUS_2            2             48
  CLUS_3            3             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SMC3 MUTATED        0      0      1      2      3      1
  SMC3 WILD-TYPE     16     13     14     55     23     40
D15V4, multiclass
        clus
vv       SMC3 MUTATED SMC3 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            0             13
  CLUS_3            1             14
  CLUS_4            2             55
  CLUS_5            3             23
  CLUS_6            1             40
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMC3 MUTATED        1      0      3      3
  SMC3 WILD-TYPE     56     38     39     43
D15V5, multiclass
        clus
vv       SMC3 MUTATED SMC3 WILD-TYPE
  CLUS_1            1             56
  CLUS_2            0             38
  CLUS_3            3             39
  CLUS_4            3             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SMC3 MUTATED        4      0      3
  SMC3 WILD-TYPE     63     35     78
D15V6, multiclass
        clus
vv       SMC3 MUTATED SMC3 WILD-TYPE
  CLUS_1            4             63
  CLUS_2            0             35
  CLUS_3            3             78
[1] 3 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 = KIT MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIT MUTATED        6      0      0      1
  KIT WILD-TYPE    137     14     27      1
D16V1, multiclass
        clus
vv       KIT MUTATED KIT WILD-TYPE
  CLUS_1           6           137
  CLUS_2           0            14
  CLUS_3           0            27
  CLUS_4           1             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIT MUTATED        1      1      6      0
  KIT WILD-TYPE     32     62     42     45
D16V2, multiclass
        clus
vv       KIT MUTATED KIT WILD-TYPE
  CLUS_1           1            32
  CLUS_2           1            62
  CLUS_3           6            42
  CLUS_4           0            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"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  KIT MUTATED        4      3      0
  KIT WILD-TYPE     69     47     45
D16V3, multiclass
        clus
vv       KIT MUTATED KIT WILD-TYPE
  CLUS_1           4            69
  CLUS_2           3            47
  CLUS_3           0            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 CLUS_4 CLUS_5 CLUS_6
  KIT MUTATED        0      3      2      2      0      0
  KIT WILD-TYPE     16     10     13     55     26     41
D16V4, multiclass
        clus
vv       KIT MUTATED KIT WILD-TYPE
  CLUS_1           0            16
  CLUS_2           3            10
  CLUS_3           2            13
  CLUS_4           2            55
  CLUS_5           0            26
  CLUS_6           0            41
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIT MUTATED        1      3      3      1
  KIT WILD-TYPE     56     35     39     45
D16V5, multiclass
        clus
vv       KIT MUTATED KIT WILD-TYPE
  CLUS_1           1            56
  CLUS_2           3            35
  CLUS_3           3            39
  CLUS_4           1            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"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  KIT MUTATED        1      3      4
  KIT WILD-TYPE     66     32     77
D16V6, multiclass
        clus
vv       KIT MUTATED KIT WILD-TYPE
  CLUS_1           1            66
  CLUS_2           3            32
  CLUS_3           4            77
[1] 3 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 = RAD21 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RAD21 MUTATED        4      1      0      0
  RAD21 WILD-TYPE    139     13     27      2
D17V1, multiclass
        clus
vv       RAD21 MUTATED RAD21 WILD-TYPE
  CLUS_1             4             139
  CLUS_2             1              13
  CLUS_3             0              27
  CLUS_4             0               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 CLUS_4
  RAD21 MUTATED        0      1      1      3
  RAD21 WILD-TYPE     33     62     47     42
D17V2, multiclass
        clus
vv       RAD21 MUTATED RAD21 WILD-TYPE
  CLUS_1             0              33
  CLUS_2             1              62
  CLUS_3             1              47
  CLUS_4             3              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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RAD21 MUTATED        1      2      2
  RAD21 WILD-TYPE     72     48     43
D17V3, multiclass
        clus
vv       RAD21 MUTATED RAD21 WILD-TYPE
  CLUS_1             1              72
  CLUS_2             2              48
  CLUS_3             2              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  RAD21 MUTATED        0      0      1      0      2      2
  RAD21 WILD-TYPE     16     13     14     57     24     39
D17V4, multiclass
        clus
vv       RAD21 MUTATED RAD21 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             0              13
  CLUS_3             1              14
  CLUS_4             0              57
  CLUS_5             2              24
  CLUS_6             2              39
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RAD21 MUTATED        2      0      0      3
  RAD21 WILD-TYPE     55     38     42     43
D17V5, multiclass
        clus
vv       RAD21 MUTATED RAD21 WILD-TYPE
  CLUS_1             2              55
  CLUS_2             0              38
  CLUS_3             0              42
  CLUS_4             3              43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RAD21 MUTATED        3      0      2
  RAD21 WILD-TYPE     64     35     79
D17V6, multiclass
        clus
vv       RAD21 MUTATED RAD21 WILD-TYPE
  CLUS_1             3              64
  CLUS_2             0              35
  CLUS_3             2              79
[1] 3 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 = EZH2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EZH2 MUTATED        1      0      2      0
  EZH2 WILD-TYPE    142     14     25      2
D18V1, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            1            142
  CLUS_2            0             14
  CLUS_3            2             25
  CLUS_4            0              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 CLUS_4
  EZH2 MUTATED        0      2      0      0
  EZH2 WILD-TYPE     33     61     48     45
D18V2, multiclass
[1] "Remove cluster labels:" "EZH2 MUTATED"          
clus
  EZH2 MUTATED EZH2 WILD-TYPE 
             2            187 
    TCGA-AB-2802     TCGA-AB-2803     TCGA-AB-2804     TCGA-AB-2805 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2806     TCGA-AB-2807     TCGA-AB-2808     TCGA-AB-2809 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2810     TCGA-AB-2812     TCGA-AB-2813     TCGA-AB-2814 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2816     TCGA-AB-2818     TCGA-AB-2819     TCGA-AB-2820 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2821     TCGA-AB-2822     TCGA-AB-2823     TCGA-AB-2824 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2825     TCGA-AB-2826     TCGA-AB-2827     TCGA-AB-2828 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2829     TCGA-AB-2830     TCGA-AB-2831     TCGA-AB-2832 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2833     TCGA-AB-2834     TCGA-AB-2835     TCGA-AB-2836 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2837     TCGA-AB-2838     TCGA-AB-2839     TCGA-AB-2840 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2841     TCGA-AB-2842     TCGA-AB-2843     TCGA-AB-2844 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2845     TCGA-AB-2846     TCGA-AB-2847     TCGA-AB-2848 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2849     TCGA-AB-2851     TCGA-AB-2853     TCGA-AB-2854 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2855     TCGA-AB-2857     TCGA-AB-2858     TCGA-AB-2860 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2861     TCGA-AB-2862     TCGA-AB-2863     TCGA-AB-2866 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2867     TCGA-AB-2868     TCGA-AB-2869     TCGA-AB-2870 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2871     TCGA-AB-2872     TCGA-AB-2873     TCGA-AB-2874 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2875     TCGA-AB-2876     TCGA-AB-2877     TCGA-AB-2878 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2879     TCGA-AB-2880     TCGA-AB-2881     TCGA-AB-2882 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2883     TCGA-AB-2884     TCGA-AB-2885     TCGA-AB-2886 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2888     TCGA-AB-2889     TCGA-AB-2890     TCGA-AB-2891 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2892     TCGA-AB-2893     TCGA-AB-2894     TCGA-AB-2895 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2896     TCGA-AB-2897     TCGA-AB-2898     TCGA-AB-2899 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2900     TCGA-AB-2901     TCGA-AB-2903     TCGA-AB-2904 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2906     TCGA-AB-2907     TCGA-AB-2908     TCGA-AB-2909 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2910     TCGA-AB-2911     TCGA-AB-2912     TCGA-AB-2913 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2914     TCGA-AB-2915     TCGA-AB-2916     TCGA-AB-2917 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2918     TCGA-AB-2919     TCGA-AB-2920     TCGA-AB-2921 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2922     TCGA-AB-2923     TCGA-AB-2924     TCGA-AB-2925 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2926     TCGA-AB-2927     TCGA-AB-2928     TCGA-AB-2929 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2930     TCGA-AB-2931     TCGA-AB-2932     TCGA-AB-2933 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2934     TCGA-AB-2935     TCGA-AB-2936     TCGA-AB-2937 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2938     TCGA-AB-2939     TCGA-AB-2940     TCGA-AB-2941 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2942     TCGA-AB-2943     TCGA-AB-2945     TCGA-AB-2946 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2947     TCGA-AB-2948     TCGA-AB-2949     TCGA-AB-2950 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2952     TCGA-AB-2954     TCGA-AB-2955     TCGA-AB-2956 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2957     TCGA-AB-2959     TCGA-AB-2963     TCGA-AB-2964 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2965     TCGA-AB-2966     TCGA-AB-2967     TCGA-AB-2968 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2970     TCGA-AB-2971     TCGA-AB-2972     TCGA-AB-2973 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2974     TCGA-AB-2975     TCGA-AB-2976     TCGA-AB-2977 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2978     TCGA-AB-2979     TCGA-AB-2980     TCGA-AB-2981 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2982     TCGA-AB-2983     TCGA-AB-2984     TCGA-AB-2985 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2986     TCGA-AB-2987     TCGA-AB-2988     TCGA-AB-2989 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2990     TCGA-AB-2991     TCGA-AB-2992     TCGA-AB-2993 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2995     TCGA-AB-2996     TCGA-AB-2997     TCGA-AB-2998 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2999     TCGA-AB-3000     TCGA-AB-3001     TCGA-AB-3002 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-3005     TCGA-AB-3006     TCGA-AB-3007     TCGA-AB-3008 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-3009     TCGA-AB-3011     TCGA-AB-3012 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EZH2 MUTATED        3      0      0
  EZH2 WILD-TYPE     70     50     45
D18V3, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            3             70
  CLUS_2            0             50
  CLUS_3            0             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 CLUS_4 CLUS_5 CLUS_6
  EZH2 MUTATED        0      0      0      3      0      0
  EZH2 WILD-TYPE     16     13     15     54     26     41
D18V4, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            0             13
  CLUS_3            0             15
  CLUS_4            3             54
  CLUS_5            0             26
  CLUS_6            0             41
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EZH2 MUTATED        0      1      2      0
  EZH2 WILD-TYPE     57     37     40     46
D18V5, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            0             57
  CLUS_2            1             37
  CLUS_3            2             40
  CLUS_4            0             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
  EZH2 MUTATED        0      1      2
  EZH2 WILD-TYPE     67     34     79
D18V6, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            0             67
  CLUS_2            1             34
  CLUS_3            2             79
[1] 3 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 = STAG2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STAG2 MUTATED        5      1      0      0
  STAG2 WILD-TYPE    138     13     27      2
D19V1, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             5             138
  CLUS_2             1              13
  CLUS_3             0              27
  CLUS_4             0               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 CLUS_4
  STAG2 MUTATED        0      2      0      3
  STAG2 WILD-TYPE     33     61     48     42
D19V2, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             0              33
  CLUS_2             2              61
  CLUS_3             0              48
  CLUS_4             3              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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STAG2 MUTATED        2      0      3
  STAG2 WILD-TYPE     71     50     42
D19V3, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             2              71
  CLUS_2             0              50
  CLUS_3             3              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  STAG2 MUTATED        0      0      0      1      4      0
  STAG2 WILD-TYPE     16     13     15     56     22     41
D19V4, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             0              13
  CLUS_3             0              15
  CLUS_4             1              56
  CLUS_5             4              22
  CLUS_6             0              41
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STAG2 MUTATED        2      1      0      2
  STAG2 WILD-TYPE     55     37     42     44
D19V5, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             2              55
  CLUS_2             1              37
  CLUS_3             0              42
  CLUS_4             2              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
  STAG2 MUTATED        4      1      0
  STAG2 WILD-TYPE     63     34     81
D19V6, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             4              63
  CLUS_2             1              34
  CLUS_3             0              81
[1] 3 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 = PTPN11 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTPN11 MUTATED        6      0      2      0
  PTPN11 WILD-TYPE    137     14     25      2
D20V1, multiclass
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  CLUS_1              6              137
  CLUS_2              0               14
  CLUS_3              2               25
  CLUS_4              0                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 CLUS_4
  PTPN11 MUTATED        2      1      3      3
  PTPN11 WILD-TYPE     31     62     45     42
D20V2, multiclass
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  CLUS_1              2               31
  CLUS_2              1               62
  CLUS_3              3               45
  CLUS_4              3               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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PTPN11 MUTATED        1      2      5
  PTPN11 WILD-TYPE     72     48     40
D20V3, multiclass
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  CLUS_1              1               72
  CLUS_2              2               48
  CLUS_3              5               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 CLUS_4 CLUS_5 CLUS_6
  PTPN11 MUTATED        0      1      0      2      3      2
  PTPN11 WILD-TYPE     16     12     15     55     23     39
D20V4, multiclass
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  CLUS_1              0               16
  CLUS_2              1               12
  CLUS_3              0               15
  CLUS_4              2               55
  CLUS_5              3               23
  CLUS_6              2               39
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTPN11 MUTATED        6      1      0      2
  PTPN11 WILD-TYPE     51     37     42     44
D20V5, multiclass
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  CLUS_1              6               51
  CLUS_2              1               37
  CLUS_3              0               42
  CLUS_4              2               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
  PTPN11 MUTATED        6      1      2
  PTPN11 WILD-TYPE     61     34     79
D20V6, multiclass
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  CLUS_1              6               61
  CLUS_2              1               34
  CLUS_3              2               79
[1] 3 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 = ASXL1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASXL1 MUTATED        4      0      1      0
  ASXL1 WILD-TYPE    139     14     26      2
D21V1, multiclass
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  CLUS_1             4             139
  CLUS_2             0              14
  CLUS_3             1              26
  CLUS_4             0               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 CLUS_4
  ASXL1 MUTATED        0      4      0      0
  ASXL1 WILD-TYPE     33     59     48     45
D21V2, multiclass
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  CLUS_1             0              33
  CLUS_2             4              59
  CLUS_3             0              48
  CLUS_4             0              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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ASXL1 MUTATED        3      0      0
  ASXL1 WILD-TYPE     70     50     45
D21V3, multiclass
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  CLUS_1             3              70
  CLUS_2             0              50
  CLUS_3             0              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 CLUS_4 CLUS_5 CLUS_6
  ASXL1 MUTATED        0      0      0      3      0      0
  ASXL1 WILD-TYPE     16     13     15     54     26     41
D21V4, multiclass
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             0              13
  CLUS_3             0              15
  CLUS_4             3              54
  CLUS_5             0              26
  CLUS_6             0              41
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASXL1 MUTATED        0      1      2      0
  ASXL1 WILD-TYPE     57     37     40     46
D21V5, multiclass
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  CLUS_1             0              57
  CLUS_2             1              37
  CLUS_3             2              40
  CLUS_4             0              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
  ASXL1 MUTATED        0      1      2
  ASXL1 WILD-TYPE     67     34     79
D21V6, multiclass
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  CLUS_1             0              67
  CLUS_2             1              34
  CLUS_3             2              79
[1] 3 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 = SUZ12 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SUZ12 MUTATED        2      1      0      0
  SUZ12 WILD-TYPE    141     13     27      2
D22V1, multiclass
        clus
vv       SUZ12 MUTATED SUZ12 WILD-TYPE
  CLUS_1             2             141
  CLUS_2             1              13
  CLUS_3             0              27
  CLUS_4             0               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 CLUS_4
  SUZ12 MUTATED        0      2      1      0
  SUZ12 WILD-TYPE     33     61     47     45
D22V2, multiclass
        clus
vv       SUZ12 MUTATED SUZ12 WILD-TYPE
  CLUS_1             0              33
  CLUS_2             2              61
  CLUS_3             1              47
  CLUS_4             0              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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SUZ12 MUTATED        3      0      0
  SUZ12 WILD-TYPE     70     50     45
D22V3, multiclass
        clus
vv       SUZ12 MUTATED SUZ12 WILD-TYPE
  CLUS_1             3              70
  CLUS_2             0              50
  CLUS_3             0              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 CLUS_4 CLUS_5 CLUS_6
  SUZ12 MUTATED        0      0      0      3      0      0
  SUZ12 WILD-TYPE     16     13     15     54     26     41
D22V4, multiclass
        clus
vv       SUZ12 MUTATED SUZ12 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             0              13
  CLUS_3             0              15
  CLUS_4             3              54
  CLUS_5             0              26
  CLUS_6             0              41
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SUZ12 MUTATED        0      1      0      2
  SUZ12 WILD-TYPE     57     37     42     44
D22V5, multiclass
        clus
vv       SUZ12 MUTATED SUZ12 WILD-TYPE
  CLUS_1             0              57
  CLUS_2             1              37
  CLUS_3             0              42
  CLUS_4             2              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
  SUZ12 MUTATED        0      2      1
  SUZ12 WILD-TYPE     67     33     80
D22V6, multiclass
        clus
vv       SUZ12 MUTATED SUZ12 WILD-TYPE
  CLUS_1             0              67
  CLUS_2             2              33
  CLUS_3             1              80
[1] 3 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 = PHACTR1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PHACTR1 MUTATED        0      1      1      0
  PHACTR1 WILD-TYPE    143     13     26      2
D23V1, multiclass
[1] "Remove cluster labels:" "PHACTR1 MUTATED"       
clus
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                2               184 
       TCGA-AB-2803        TCGA-AB-2804        TCGA-AB-2805        TCGA-AB-2806 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2807        TCGA-AB-2808        TCGA-AB-2809        TCGA-AB-2810 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2812        TCGA-AB-2813        TCGA-AB-2814        TCGA-AB-2816 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2817        TCGA-AB-2818        TCGA-AB-2819        TCGA-AB-2820 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2821        TCGA-AB-2822        TCGA-AB-2823        TCGA-AB-2824 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2825        TCGA-AB-2826        TCGA-AB-2827        TCGA-AB-2828 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2829        TCGA-AB-2830        TCGA-AB-2831        TCGA-AB-2832 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836        TCGA-AB-2837 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840        TCGA-AB-2841 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2842        TCGA-AB-2844        TCGA-AB-2845        TCGA-AB-2846 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2848        TCGA-AB-2849        TCGA-AB-2850        TCGA-AB-2851 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2853        TCGA-AB-2854        TCGA-AB-2855        TCGA-AB-2857 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2858        TCGA-AB-2859        TCGA-AB-2860        TCGA-AB-2861 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2862        TCGA-AB-2863        TCGA-AB-2864        TCGA-AB-2865 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2866        TCGA-AB-2867        TCGA-AB-2869        TCGA-AB-2870 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2871        TCGA-AB-2872        TCGA-AB-2873        TCGA-AB-2874 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2875        TCGA-AB-2877        TCGA-AB-2878        TCGA-AB-2879 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2880        TCGA-AB-2881        TCGA-AB-2882        TCGA-AB-2883 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2884        TCGA-AB-2885        TCGA-AB-2886        TCGA-AB-2887 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2888        TCGA-AB-2889        TCGA-AB-2890        TCGA-AB-2892 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2893        TCGA-AB-2894        TCGA-AB-2895        TCGA-AB-2896 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2897        TCGA-AB-2898        TCGA-AB-2899        TCGA-AB-2900 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2901        TCGA-AB-2903        TCGA-AB-2904        TCGA-AB-2905 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2906        TCGA-AB-2907        TCGA-AB-2908        TCGA-AB-2909 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2910        TCGA-AB-2911        TCGA-AB-2912        TCGA-AB-2913 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2914        TCGA-AB-2915        TCGA-AB-2917        TCGA-AB-2919 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2920        TCGA-AB-2921        TCGA-AB-2922        TCGA-AB-2923 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2924        TCGA-AB-2925        TCGA-AB-2926        TCGA-AB-2927 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2928        TCGA-AB-2929        TCGA-AB-2930        TCGA-AB-2931 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2932        TCGA-AB-2933        TCGA-AB-2934        TCGA-AB-2935 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2936        TCGA-AB-2937        TCGA-AB-2938        TCGA-AB-2939 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2940        TCGA-AB-2941        TCGA-AB-2942        TCGA-AB-2943 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2945        TCGA-AB-2946        TCGA-AB-2947        TCGA-AB-2948 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952        TCGA-AB-2954 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2957        TCGA-AB-2959 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2963        TCGA-AB-2964        TCGA-AB-2965        TCGA-AB-2966 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2967        TCGA-AB-2968        TCGA-AB-2970        TCGA-AB-2971 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2972        TCGA-AB-2973        TCGA-AB-2974        TCGA-AB-2975 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2976        TCGA-AB-2977        TCGA-AB-2978        TCGA-AB-2980 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2982        TCGA-AB-2983        TCGA-AB-2984        TCGA-AB-2985 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2986        TCGA-AB-2987        TCGA-AB-2988        TCGA-AB-2989 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2990        TCGA-AB-2991        TCGA-AB-2992        TCGA-AB-2993 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2994        TCGA-AB-2995        TCGA-AB-2996        TCGA-AB-2997 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2998        TCGA-AB-2999        TCGA-AB-3000        TCGA-AB-3001 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-3002        TCGA-AB-3005        TCGA-AB-3006        TCGA-AB-3007 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-3008        TCGA-AB-3009        TCGA-AB-3011        TCGA-AB-3012 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PHACTR1 MUTATED        0      1      1      1
  PHACTR1 WILD-TYPE     33     62     47     44
D23V2, multiclass
        clus
vv       PHACTR1 MUTATED PHACTR1 WILD-TYPE
  CLUS_1               0                33
  CLUS_2               1                62
  CLUS_3               1                47
  CLUS_4               1                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
  PHACTR1 MUTATED        1      1      0
  PHACTR1 WILD-TYPE     72     49     45
D23V3, multiclass
[1] "Remove cluster labels:" "PHACTR1 MUTATED"       
clus
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                2               166 
       TCGA-AB-2803        TCGA-AB-2805        TCGA-AB-2806        TCGA-AB-2807 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2808        TCGA-AB-2810        TCGA-AB-2812        TCGA-AB-2813 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2814        TCGA-AB-2816        TCGA-AB-2817        TCGA-AB-2818 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2819        TCGA-AB-2820        TCGA-AB-2821        TCGA-AB-2822 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2823        TCGA-AB-2824        TCGA-AB-2825        TCGA-AB-2826 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2828        TCGA-AB-2830        TCGA-AB-2832        TCGA-AB-2833 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836        TCGA-AB-2837 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840        TCGA-AB-2841 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2842        TCGA-AB-2843        TCGA-AB-2844        TCGA-AB-2845 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2846        TCGA-AB-2847        TCGA-AB-2848        TCGA-AB-2849 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2851        TCGA-AB-2853        TCGA-AB-2854        TCGA-AB-2855 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2857        TCGA-AB-2858        TCGA-AB-2859        TCGA-AB-2860 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2861        TCGA-AB-2862        TCGA-AB-2863        TCGA-AB-2865 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2866        TCGA-AB-2867        TCGA-AB-2869        TCGA-AB-2870 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2871        TCGA-AB-2872        TCGA-AB-2873        TCGA-AB-2874 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2875        TCGA-AB-2877        TCGA-AB-2879        TCGA-AB-2880 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2881        TCGA-AB-2882        TCGA-AB-2884        TCGA-AB-2885 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2886        TCGA-AB-2887        TCGA-AB-2888        TCGA-AB-2889 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2890        TCGA-AB-2891        TCGA-AB-2895        TCGA-AB-2896 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2897        TCGA-AB-2898        TCGA-AB-2899        TCGA-AB-2900 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2901        TCGA-AB-2903        TCGA-AB-2904        TCGA-AB-2908 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2909        TCGA-AB-2910        TCGA-AB-2911        TCGA-AB-2912 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2913        TCGA-AB-2914        TCGA-AB-2915        TCGA-AB-2917 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2918        TCGA-AB-2919        TCGA-AB-2920        TCGA-AB-2921 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2924        TCGA-AB-2925        TCGA-AB-2927        TCGA-AB-2928 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2929        TCGA-AB-2930        TCGA-AB-2931        TCGA-AB-2932 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2933        TCGA-AB-2934        TCGA-AB-2935        TCGA-AB-2936 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2937        TCGA-AB-2938        TCGA-AB-2939        TCGA-AB-2940 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2941        TCGA-AB-2942        TCGA-AB-2943        TCGA-AB-2946 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2948        TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2954        TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2959 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2963        TCGA-AB-2964        TCGA-AB-2965        TCGA-AB-2966 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2967        TCGA-AB-2970        TCGA-AB-2971        TCGA-AB-2972 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2973        TCGA-AB-2975        TCGA-AB-2976        TCGA-AB-2977 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2978        TCGA-AB-2979        TCGA-AB-2980        TCGA-AB-2981 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2982        TCGA-AB-2983        TCGA-AB-2984        TCGA-AB-2985 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2986        TCGA-AB-2987        TCGA-AB-2988        TCGA-AB-2990 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2991        TCGA-AB-2992        TCGA-AB-2993        TCGA-AB-2994 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2995        TCGA-AB-2996        TCGA-AB-2998        TCGA-AB-2999 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-3000        TCGA-AB-3001        TCGA-AB-3002        TCGA-AB-3005 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-3006        TCGA-AB-3007        TCGA-AB-3008        TCGA-AB-3009 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-3011        TCGA-AB-3012 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PHACTR1 MUTATED        0      1      0      1      0      0
  PHACTR1 WILD-TYPE     16     12     15     56     26     41
D23V4, multiclass
[1] "Remove cluster labels:" "PHACTR1 MUTATED"       
clus
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                2               166 
       TCGA-AB-2803        TCGA-AB-2805        TCGA-AB-2806        TCGA-AB-2807 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2808        TCGA-AB-2810        TCGA-AB-2812        TCGA-AB-2813 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2814        TCGA-AB-2816        TCGA-AB-2817        TCGA-AB-2818 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2819        TCGA-AB-2820        TCGA-AB-2821        TCGA-AB-2822 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2823        TCGA-AB-2824        TCGA-AB-2825        TCGA-AB-2826 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2828        TCGA-AB-2830        TCGA-AB-2832        TCGA-AB-2833 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836        TCGA-AB-2837 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840        TCGA-AB-2841 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2842        TCGA-AB-2843        TCGA-AB-2844        TCGA-AB-2845 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2846        TCGA-AB-2847        TCGA-AB-2848        TCGA-AB-2849 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2851        TCGA-AB-2853        TCGA-AB-2854        TCGA-AB-2855 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2857        TCGA-AB-2858        TCGA-AB-2859        TCGA-AB-2860 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2861        TCGA-AB-2862        TCGA-AB-2863        TCGA-AB-2865 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2866        TCGA-AB-2867        TCGA-AB-2869        TCGA-AB-2870 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2871        TCGA-AB-2872        TCGA-AB-2873        TCGA-AB-2874 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2875        TCGA-AB-2877        TCGA-AB-2879        TCGA-AB-2880 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2881        TCGA-AB-2882        TCGA-AB-2884        TCGA-AB-2885 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2886        TCGA-AB-2887        TCGA-AB-2888        TCGA-AB-2889 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2890        TCGA-AB-2891        TCGA-AB-2895        TCGA-AB-2896 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2897        TCGA-AB-2898        TCGA-AB-2899        TCGA-AB-2900 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2901        TCGA-AB-2903        TCGA-AB-2904        TCGA-AB-2908 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2909        TCGA-AB-2910        TCGA-AB-2911        TCGA-AB-2912 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2913        TCGA-AB-2914        TCGA-AB-2915        TCGA-AB-2917 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2918        TCGA-AB-2919        TCGA-AB-2920        TCGA-AB-2921 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2924        TCGA-AB-2925        TCGA-AB-2927        TCGA-AB-2928 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2929        TCGA-AB-2930        TCGA-AB-2931        TCGA-AB-2932 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2933        TCGA-AB-2934        TCGA-AB-2935        TCGA-AB-2936 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2937        TCGA-AB-2938        TCGA-AB-2939        TCGA-AB-2940 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2941        TCGA-AB-2942        TCGA-AB-2943        TCGA-AB-2946 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2948        TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2954        TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2959 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2963        TCGA-AB-2964        TCGA-AB-2965        TCGA-AB-2966 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2967        TCGA-AB-2970        TCGA-AB-2971        TCGA-AB-2972 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2973        TCGA-AB-2975        TCGA-AB-2976        TCGA-AB-2977 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2978        TCGA-AB-2979        TCGA-AB-2980        TCGA-AB-2981 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2982        TCGA-AB-2983        TCGA-AB-2984        TCGA-AB-2985 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2986        TCGA-AB-2987        TCGA-AB-2988        TCGA-AB-2990 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2991        TCGA-AB-2992        TCGA-AB-2993        TCGA-AB-2994 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2995        TCGA-AB-2996        TCGA-AB-2998        TCGA-AB-2999 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-3000        TCGA-AB-3001        TCGA-AB-3002        TCGA-AB-3005 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-3006        TCGA-AB-3007        TCGA-AB-3008        TCGA-AB-3009 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-3011        TCGA-AB-3012 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PHACTR1 MUTATED        1      1      0      1
  PHACTR1 WILD-TYPE     56     37     42     45
D23V5, multiclass
        clus
vv       PHACTR1 MUTATED PHACTR1 WILD-TYPE
  CLUS_1               1                56
  CLUS_2               1                37
  CLUS_3               0                42
  CLUS_4               1                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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PHACTR1 MUTATED        0      1      2
  PHACTR1 WILD-TYPE     67     34     79
D23V6, multiclass
        clus
vv       PHACTR1 MUTATED PHACTR1 WILD-TYPE
  CLUS_1               0                67
  CLUS_2               1                34
  CLUS_3               2                79
[1] 3 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 = SMC1A MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMC1A MUTATED        6      0      0      0
  SMC1A WILD-TYPE    137     14     27      2
D24V1, multiclass
        clus
vv       SMC1A MUTATED SMC1A WILD-TYPE
  CLUS_1             6             137
  CLUS_2             0              14
  CLUS_3             0              27
  CLUS_4             0               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 CLUS_4
  SMC1A MUTATED        0      1      1      4
  SMC1A WILD-TYPE     33     62     47     41
D24V2, multiclass
        clus
vv       SMC1A MUTATED SMC1A WILD-TYPE
  CLUS_1             0              33
  CLUS_2             1              62
  CLUS_3             1              47
  CLUS_4             4              41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SMC1A MUTATED        2      3      1
  SMC1A WILD-TYPE     71     47     44
D24V3, multiclass
        clus
vv       SMC1A MUTATED SMC1A WILD-TYPE
  CLUS_1             2              71
  CLUS_2             3              47
  CLUS_3             1              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 CLUS_4 CLUS_5 CLUS_6
  SMC1A MUTATED        0      0      1      1      0      4
  SMC1A WILD-TYPE     16     13     14     56     26     37
D24V4, multiclass
        clus
vv       SMC1A MUTATED SMC1A WILD-TYPE
  CLUS_1             0              16
  CLUS_2             0              13
  CLUS_3             1              14
  CLUS_4             1              56
  CLUS_5             0              26
  CLUS_6             4              37
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMC1A MUTATED        3      0      0      3
  SMC1A WILD-TYPE     54     38     42     43
D24V5, multiclass
        clus
vv       SMC1A MUTATED SMC1A WILD-TYPE
  CLUS_1             3              54
  CLUS_2             0              38
  CLUS_3             0              42
  CLUS_4             3              43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SMC1A MUTATED        3      0      3
  SMC1A WILD-TYPE     64     35     78
D24V6, multiclass
        clus
vv       SMC1A MUTATED SMC1A WILD-TYPE
  CLUS_1             3              64
  CLUS_2             0              35
  CLUS_3             3              78
[1] 3 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 = KDM6A MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KDM6A MUTATED        2      0      1      0
  KDM6A WILD-TYPE    141     14     26      2
D25V1, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             2             141
  CLUS_2             0              14
  CLUS_3             1              26
  CLUS_4             0               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 CLUS_4
  KDM6A MUTATED        0      1      2      0
  KDM6A WILD-TYPE     33     62     46     45
D25V2, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             0              33
  CLUS_2             1              62
  CLUS_3             2              46
  CLUS_4             0              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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED        1      1      0
  KDM6A WILD-TYPE     72     49     45
D25V3, multiclass
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              2             166 
     TCGA-AB-2803      TCGA-AB-2805      TCGA-AB-2807      TCGA-AB-2808 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2810      TCGA-AB-2812      TCGA-AB-2813      TCGA-AB-2814 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2816      TCGA-AB-2817      TCGA-AB-2818      TCGA-AB-2819 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2820      TCGA-AB-2821      TCGA-AB-2822      TCGA-AB-2823 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2824      TCGA-AB-2825      TCGA-AB-2826      TCGA-AB-2828 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2830      TCGA-AB-2832      TCGA-AB-2833      TCGA-AB-2834 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2835      TCGA-AB-2836      TCGA-AB-2837      TCGA-AB-2838 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2839      TCGA-AB-2840      TCGA-AB-2841      TCGA-AB-2842 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2843      TCGA-AB-2844      TCGA-AB-2845      TCGA-AB-2846 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2847      TCGA-AB-2848      TCGA-AB-2849      TCGA-AB-2851 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2853      TCGA-AB-2854      TCGA-AB-2855      TCGA-AB-2857 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2858      TCGA-AB-2859      TCGA-AB-2860      TCGA-AB-2861 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2862      TCGA-AB-2863      TCGA-AB-2865      TCGA-AB-2866 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2868      TCGA-AB-2869      TCGA-AB-2870      TCGA-AB-2871 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2872      TCGA-AB-2873      TCGA-AB-2874      TCGA-AB-2875 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2877      TCGA-AB-2879      TCGA-AB-2880      TCGA-AB-2881 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2882      TCGA-AB-2884      TCGA-AB-2885      TCGA-AB-2886 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2887      TCGA-AB-2888      TCGA-AB-2889      TCGA-AB-2890 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2891      TCGA-AB-2895      TCGA-AB-2896      TCGA-AB-2897 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2898      TCGA-AB-2899      TCGA-AB-2900      TCGA-AB-2901 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2903      TCGA-AB-2904      TCGA-AB-2908      TCGA-AB-2909 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2910      TCGA-AB-2911      TCGA-AB-2912      TCGA-AB-2913 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2914      TCGA-AB-2915      TCGA-AB-2916      TCGA-AB-2917 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2918      TCGA-AB-2919      TCGA-AB-2920      TCGA-AB-2921 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2924      TCGA-AB-2925      TCGA-AB-2927      TCGA-AB-2928 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2929      TCGA-AB-2930      TCGA-AB-2931      TCGA-AB-2932 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2933      TCGA-AB-2934      TCGA-AB-2935      TCGA-AB-2936 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2937      TCGA-AB-2938      TCGA-AB-2939      TCGA-AB-2940 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2941      TCGA-AB-2942      TCGA-AB-2943      TCGA-AB-2946 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2948      TCGA-AB-2949      TCGA-AB-2950      TCGA-AB-2952 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2954      TCGA-AB-2955      TCGA-AB-2956      TCGA-AB-2959 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2963      TCGA-AB-2964      TCGA-AB-2965      TCGA-AB-2966 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2967      TCGA-AB-2970      TCGA-AB-2971      TCGA-AB-2972 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2973      TCGA-AB-2975      TCGA-AB-2976      TCGA-AB-2977 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2978      TCGA-AB-2979      TCGA-AB-2980      TCGA-AB-2981 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2982      TCGA-AB-2983      TCGA-AB-2984      TCGA-AB-2985 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2986      TCGA-AB-2987      TCGA-AB-2988      TCGA-AB-2990 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2991      TCGA-AB-2992      TCGA-AB-2993      TCGA-AB-2994 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2995      TCGA-AB-2996      TCGA-AB-2998      TCGA-AB-2999 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-3000      TCGA-AB-3001      TCGA-AB-3002      TCGA-AB-3005 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-3006      TCGA-AB-3007      TCGA-AB-3008      TCGA-AB-3009 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-3011      TCGA-AB-3012 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KDM6A MUTATED        0      0      1      1      0      0
  KDM6A WILD-TYPE     16     13     14     56     26     41
D25V4, multiclass
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              2             166 
     TCGA-AB-2803      TCGA-AB-2805      TCGA-AB-2807      TCGA-AB-2808 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2810      TCGA-AB-2812      TCGA-AB-2813      TCGA-AB-2814 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2816      TCGA-AB-2817      TCGA-AB-2818      TCGA-AB-2819 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2820      TCGA-AB-2821      TCGA-AB-2822      TCGA-AB-2823 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2824      TCGA-AB-2825      TCGA-AB-2826      TCGA-AB-2828 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2830      TCGA-AB-2832      TCGA-AB-2833      TCGA-AB-2834 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2835      TCGA-AB-2836      TCGA-AB-2837      TCGA-AB-2838 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2839      TCGA-AB-2840      TCGA-AB-2841      TCGA-AB-2842 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2843      TCGA-AB-2844      TCGA-AB-2845      TCGA-AB-2846 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2847      TCGA-AB-2848      TCGA-AB-2849      TCGA-AB-2851 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2853      TCGA-AB-2854      TCGA-AB-2855      TCGA-AB-2857 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2858      TCGA-AB-2859      TCGA-AB-2860      TCGA-AB-2861 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2862      TCGA-AB-2863      TCGA-AB-2865      TCGA-AB-2866 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2868      TCGA-AB-2869      TCGA-AB-2870      TCGA-AB-2871 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2872      TCGA-AB-2873      TCGA-AB-2874      TCGA-AB-2875 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2877      TCGA-AB-2879      TCGA-AB-2880      TCGA-AB-2881 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2882      TCGA-AB-2884      TCGA-AB-2885      TCGA-AB-2886 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2887      TCGA-AB-2888      TCGA-AB-2889      TCGA-AB-2890 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2891      TCGA-AB-2895      TCGA-AB-2896      TCGA-AB-2897 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2898      TCGA-AB-2899      TCGA-AB-2900      TCGA-AB-2901 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2903      TCGA-AB-2904      TCGA-AB-2908      TCGA-AB-2909 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2910      TCGA-AB-2911      TCGA-AB-2912      TCGA-AB-2913 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2914      TCGA-AB-2915      TCGA-AB-2916      TCGA-AB-2917 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2918      TCGA-AB-2919      TCGA-AB-2920      TCGA-AB-2921 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2924      TCGA-AB-2925      TCGA-AB-2927      TCGA-AB-2928 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2929      TCGA-AB-2930      TCGA-AB-2931      TCGA-AB-2932 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2933      TCGA-AB-2934      TCGA-AB-2935      TCGA-AB-2936 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2937      TCGA-AB-2938      TCGA-AB-2939      TCGA-AB-2940 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2941      TCGA-AB-2942      TCGA-AB-2943      TCGA-AB-2946 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2948      TCGA-AB-2949      TCGA-AB-2950      TCGA-AB-2952 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2954      TCGA-AB-2955      TCGA-AB-2956      TCGA-AB-2959 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2963      TCGA-AB-2964      TCGA-AB-2965      TCGA-AB-2966 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2967      TCGA-AB-2970      TCGA-AB-2971      TCGA-AB-2972 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2973      TCGA-AB-2975      TCGA-AB-2976      TCGA-AB-2977 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2978      TCGA-AB-2979      TCGA-AB-2980      TCGA-AB-2981 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2982      TCGA-AB-2983      TCGA-AB-2984      TCGA-AB-2985 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2986      TCGA-AB-2987      TCGA-AB-2988      TCGA-AB-2990 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2991      TCGA-AB-2992      TCGA-AB-2993      TCGA-AB-2994 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-2995      TCGA-AB-2996      TCGA-AB-2998      TCGA-AB-2999 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-3000      TCGA-AB-3001      TCGA-AB-3002      TCGA-AB-3005 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-3006      TCGA-AB-3007      TCGA-AB-3008      TCGA-AB-3009 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AB-3011      TCGA-AB-3012 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KDM6A MUTATED        1      1      0      1
  KDM6A WILD-TYPE     56     37     42     45
D25V5, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             1              56
  CLUS_2             1              37
  CLUS_3             0              42
  CLUS_4             1              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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED        1      1      1
  KDM6A WILD-TYPE     66     34     80
D25V6, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             1              66
  CLUS_2             1              34
  CLUS_3             1              80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
