[1] "ofn"       "-oTUVM-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UVM-TP/22507229/UVM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UVM-TP/22572045/transformed.cor.cli.txt"

nPatients in clinical file=80, in cluster file=80, common to both=80
[1] "Reduce the number of clustering variables from 9 to 7."
[1]  7 80
[1] "GNAQ MUTATION ANALYSIS"
[1] 3
  GNAQ MUTATED GNAQ WILD-TYPE 
            40             40 
  GNAQ MUTATED GNAQ WILD-TYPE 
            40             40 
[1] "GNA11 MUTATION ANALYSIS"
[1] 3
  GNA11 MUTATED GNA11 WILD-TYPE 
             36              44 
  GNA11 MUTATED GNA11 WILD-TYPE 
             36              44 
[1] "EIF1AX MUTATION ANALYSIS"
[1] 3
  EIF1AX MUTATED EIF1AX WILD-TYPE 
              10               70 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
              10               70 
[1] "SF3B1 MUTATION ANALYSIS"
[1] 3
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             18              62 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             18              62 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            22             58 
  BAP1 MUTATED BAP1 WILD-TYPE 
            22             58 
[1] "CYSLTR2 MUTATION ANALYSIS"
[1] 3
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                3                77 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                3                77 
[1] "SFRS2 MUTATION ANALYSIS"
[1] 3
  SFRS2 MUTATED SFRS2 WILD-TYPE 
              3              77 
  SFRS2 MUTATED SFRS2 WILD-TYPE 
              3              77 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "RACE"                                
[14] "ETHNICITY"                           

Input Data has 14 rows and 80 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RACE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "1"                "52"                  
freq.contrast "52"               "1"                   
both >= 3     "FALSE"            "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"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 80 columns, 1 survival variables, and 6 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "PATHOLOGIC_STAGE"  "PATHOLOGY_T_STAGE"
[4] "PATHOLOGY_M_STAGE" "GENDER"            "RADIATION_THERAPY"
YEARS_TO_BIRTH, nv=40, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T2 T3 T4 
14 32 34 
[1] "table(vv)"
vv
T2 T3 T4 
14 32 34 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T2 T3 T4 
14 32 34 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T2 T3 T4 
14 32 34 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = GNAQ MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  GNAQ MUTATED   32  8
  GNAQ WILD-TYPE 25 15
  GNAQ MUTATED GNAQ WILD-TYPE 
            40             40 
  GNAQ MUTATED GNAQ WILD-TYPE 
             8             15 
$`GNAQ MUTATED`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA 
       32.28        51.98        82.16        13.64        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9EE TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9ES 
       24.43        13.08        33.80        31.76        25.41        49.68 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 
       39.81        24.00        27.52        19.69        31.07        30.84 
TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K9 TCGA-VD-A8KB 
       24.13        20.84        19.63        47.97        46.82        44.52 
TCGA-VD-A8KE TCGA-VD-A8KI TCGA-VD-A8KK TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO 
       26.99        36.59         2.10         0.13         2.24        26.14 
TCGA-VD-AA8M TCGA-VD-AA8Q TCGA-VD-AA8S TCGA-WC-A87T TCGA-WC-A880 TCGA-WC-A883 
        0.20        20.91        14.04        85.48        41.36         7.92 
TCGA-WC-A885 TCGA-WC-AA9E TCGA-YZ-A983 TCGA-YZ-A985 
       22.55        27.55        26.24        38.93 

$`GNAQ WILD-TYPE`
TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E8 
       35.01        14.89         4.90        15.45        15.09        26.56 
TCGA-V4-A9ED TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EQ 
       35.44        38.30        22.03        12.79        24.53        14.96 
TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F7 
       44.78        23.31        41.72        28.70         6.67        41.29 
TCGA-VD-A8K8 TCGA-VD-A8KA TCGA-VD-A8KD TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH 
       45.27        38.73         3.75         1.32         0.62        38.07 
TCGA-VD-A8KJ TCGA-VD-A8KL TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8R 
       37.81        20.98         1.45        19.92         2.83         0.20 
TCGA-VD-AA8T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A882 TCGA-WC-A884 TCGA-WC-A888 
        1.61        55.99        43.20        36.56         0.39        18.90 
TCGA-WC-A88A TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A984 
        2.70        61.22        16.27        45.90 

  GNAQ MUTATED GNAQ WILD-TYPE 
          0.13           0.20 
  GNAQ MUTATED GNAQ WILD-TYPE 
         85.48          61.22 
  GNAQ MUTATED GNAQ WILD-TYPE 
        27.255         21.505 
[1] "0.1 - 85.5 (27.3)" "0.2 - 61.2 (21.5)"
[1] "hr=" "2.4"
D1V2, continuous
                vv
clus             STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GNAQ MUTATED           8        11         19          2          0        0
  GNAQ WILD-TYPE         4        16          6          8          1        4
D1V3, multiclass
            clus
vv           GNAQ MUTATED GNAQ WILD-TYPE
  STAGE IIA             8              4
  STAGE IIB            11             16
  STAGE IIIA           19              6
  STAGE IIIB            2              8
  STAGE IIIC            0              1
  STAGE IV              0              4
[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             T2 T3 T4
  GNAQ MUTATED    8 15 17
  GNAQ WILD-TYPE  6 17 17
D1V4, multiclass
    clus
vv   GNAQ MUTATED GNAQ WILD-TYPE
  T2            8              6
  T3           15             17
  T4           17             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                cls
clus              0  1
  GNAQ MUTATED   28  0
  GNAQ WILD-TYPE 23  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAQ MUTATED     28    0
  GNAQ WILD-TYPE   23    4
   clus
vv  GNAQ MUTATED GNAQ WILD-TYPE
  0           28             23
  1            0              4
[1] 2 2
[1] FALSE
D1V6, binary
                cls
clus              0  1
  GNAQ MUTATED   17 23
  GNAQ WILD-TYPE 18 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAQ MUTATED     17   23
  GNAQ WILD-TYPE   18   22
        clus
vv       GNAQ MUTATED GNAQ WILD-TYPE
  FEMALE           17             18
  MALE             23             22
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus              0  1
  GNAQ MUTATED   39  1
  GNAQ WILD-TYPE 37  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAQ MUTATED     39    1
  GNAQ WILD-TYPE   37    2
     clus
vv    GNAQ MUTATED GNAQ WILD-TYPE
  NO            39             37
  YES            1              2
[1] 2 2
[1] FALSE

Clustering(2) Variable = GNA11 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2              0  1
  GNA11 MUTATED   24 12
  GNA11 WILD-TYPE 33 11
  GNA11 MUTATED GNA11 WILD-TYPE 
             36              44 
  GNA11 MUTATED GNA11 WILD-TYPE 
             12              11 
$`GNA11 MUTATED`
TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E8 
       35.01        14.89         4.90        15.45        15.09        26.56 
TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EQ TCGA-V4-A9ET 
       38.30        22.03        12.79        24.53        14.96        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-VD-A8K8 
       23.31        41.72        28.70         6.67        41.29        45.27 
TCGA-VD-A8KA TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KL TCGA-VD-AA8N 
       38.73         1.32         0.62        38.07        20.98         1.45 
TCGA-VD-AA8P TCGA-VD-AA8R TCGA-VD-AA8T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A882 
        2.83         0.20         1.61        55.99        43.20        36.56 
TCGA-WC-A884 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A985 
        0.39        18.90         2.70        27.55        61.22        38.93 

$`GNA11 WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA 
       32.28        51.98        82.16        13.64        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO 
       24.43        35.44        13.08        33.80        31.76        25.41 
TCGA-V4-A9ES TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 
       49.68        39.81        24.00        27.52        19.69        31.07 
TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K9 
       30.84        24.13        20.84        19.63        47.97        46.82 
TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK 
       44.52         3.75        26.99        36.59        37.81         2.10 
TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8O TCGA-VD-AA8Q 
        0.13         2.24        26.14         0.20        19.92        20.91 
TCGA-VD-AA8S TCGA-WC-A87T TCGA-WC-A880 TCGA-WC-A883 TCGA-WC-A885 TCGA-YZ-A982 
       14.04        85.48        41.36         7.92        22.55        16.27 
TCGA-YZ-A983 TCGA-YZ-A984 
       26.24        45.90 

  GNA11 MUTATED GNA11 WILD-TYPE 
           0.20            0.13 
  GNA11 MUTATED GNA11 WILD-TYPE 
          61.22           85.48 
  GNA11 MUTATED GNA11 WILD-TYPE 
         22.670          26.615 
[1] "0.2 - 61.2 (22.7)" "0.1 - 85.5 (26.6)"
[1] "hr=" "1.7"
D2V2, continuous
                 vv
clus              STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GNA11 MUTATED           5        13          6          7          1        3
  GNA11 WILD-TYPE         7        14         19          3          0        1
D2V3, multiclass
            clus
vv           GNA11 MUTATED GNA11 WILD-TYPE
  STAGE IIA              5               7
  STAGE IIB             13              14
  STAGE IIIA             6              19
  STAGE IIIB             7               3
  STAGE IIIC             1               0
  STAGE IV               3               1
[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              T2 T3 T4
  GNA11 MUTATED    7 13 16
  GNA11 WILD-TYPE  7 19 18
D2V4, multiclass
    clus
vv   GNA11 MUTATED GNA11 WILD-TYPE
  T2             7               7
  T3            13              19
  T4            16              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                 cls
clus               0  1
  GNA11 MUTATED   21  3
  GNA11 WILD-TYPE 30  1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA11 MUTATED     21    3
  GNA11 WILD-TYPE   30    1
   clus
vv  GNA11 MUTATED GNA11 WILD-TYPE
  0            21              30
  1             3               1
[1] 2 2
[1] FALSE
D2V6, binary
                 cls
clus               0  1
  GNA11 MUTATED   17 19
  GNA11 WILD-TYPE 18 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA11 MUTATED     17   19
  GNA11 WILD-TYPE   18   26
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  FEMALE            17              18
  MALE              19              26
[1] 2 2
[1] FALSE
D2V7, binary
                 cls
clus               0  1
  GNA11 MUTATED   32  3
  GNA11 WILD-TYPE 44  0
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA11 MUTATED     32    3
  GNA11 WILD-TYPE   44    0
     clus
vv    GNA11 MUTATED GNA11 WILD-TYPE
  NO             32              44
  YES             3               0
[1] 2 2
[1] FALSE

Clustering(3) Variable = EIF1AX MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2               0  1
  EIF1AX MUTATED    9  1
  EIF1AX WILD-TYPE 48 22
  EIF1AX MUTATED EIF1AX WILD-TYPE 
              10               70 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               1               22 
$`EIF1AX MUTATED`
TCGA-WC-A87U TCGA-V3-A9ZY TCGA-V4-A9EC TCGA-V4-A9EY TCGA-V4-A9F7 TCGA-VD-A8KE 
       51.98        15.09        24.43        27.52        41.29        26.99 
TCGA-VD-A8KO TCGA-VD-AA8R TCGA-WC-A880 TCGA-WC-A884 
       26.14         0.20        41.36         0.39 

$`EIF1AX WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E5 
       32.28        35.01        14.89         4.90        15.45        82.16 
TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9ED TCGA-V4-A9EE 
       13.64        26.56        40.96        44.32        35.44        13.08 
TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM 
       38.30        22.03        12.79        24.53        33.80        31.76 
TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV 
       25.41        14.96        49.68        44.78        23.31        41.72 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 
       39.81        24.00        19.69        31.07        30.84        24.13 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 
       28.70        20.84         6.67        19.63        47.97        45.27 
TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KF TCGA-VD-A8KG 
       46.82        38.73        44.52         3.75         1.32         0.62 
TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM 
       38.07        36.59        37.81         2.10        20.98         0.13 
TCGA-VD-A8KN TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q 
        2.24         0.20         1.45        19.92         2.83        20.91 
TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A882 
       14.04         1.61        85.48        55.99        43.20        36.56 
TCGA-WC-A883 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9E TCGA-YZ-A980 
        7.92        22.55        18.90         2.70        27.55        61.22 
TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       16.27        26.24        45.90        38.93 

  EIF1AX MUTATED EIF1AX WILD-TYPE 
            0.20             0.13 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
           51.98            85.48 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
          26.565           24.970 
[1] "0.2 - 52.0 (26.6)" "0.1 - 85.5 (25.0)"
[1] "hr=" "3"  
D3V2, continuous
                  vv
clus               STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  EIF1AX MUTATED           2         4          3          1          0
  EIF1AX WILD-TYPE        10        23         22          9          1
                  vv
clus               STAGE IV
  EIF1AX MUTATED          0
  EIF1AX WILD-TYPE        4
D3V3, multiclass
            clus
vv           EIF1AX MUTATED EIF1AX WILD-TYPE
  STAGE IIA               2               10
  STAGE IIB               4               23
  STAGE IIIA              3               22
  STAGE IIIB              1                9
  STAGE IIIC              0                1
  STAGE IV                0                4
[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               T2 T3 T4
  EIF1AX MUTATED    2  5  3
  EIF1AX WILD-TYPE 12 27 31
D3V4, multiclass
    clus
vv   EIF1AX MUTATED EIF1AX WILD-TYPE
  T2              2               12
  T3              5               27
  T4              3               31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                  cls
clus                0  1
  EIF1AX MUTATED    7  0
  EIF1AX WILD-TYPE 44  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      7    0
  EIF1AX WILD-TYPE   44    4
   clus
vv  EIF1AX MUTATED EIF1AX WILD-TYPE
  0              7               44
  1              0                4
[1] 2 2
[1] FALSE
D3V6, binary
                  cls
clus                0  1
  EIF1AX MUTATED    6  4
  EIF1AX WILD-TYPE 29 41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      6    4
  EIF1AX WILD-TYPE   29   41
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  FEMALE              6               29
  MALE                4               41
[1] 2 2
[1] FALSE
D3V7, binary
                  cls
clus                0  1
  EIF1AX MUTATED   10  0
  EIF1AX WILD-TYPE 66  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED     10    0
  EIF1AX WILD-TYPE   66    3
     clus
vv    EIF1AX MUTATED EIF1AX WILD-TYPE
  NO              10               66
  YES              0                3
[1] 2 2
[1] FALSE

Clustering(4) Variable = SF3B1 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2              0  1
  SF3B1 MUTATED   17  1
  SF3B1 WILD-TYPE 40 22
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             18              62 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
              1              22 
$`SF3B1 MUTATED`
TCGA-WC-A881 TCGA-WC-AA9A TCGA-V4-A9E5 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
       35.01        14.89        82.16        40.96        44.32        24.43 
TCGA-V4-A9EJ TCGA-V4-A9ES TCGA-V4-A9EW TCGA-V4-A9EZ TCGA-V4-A9F4 TCGA-VD-A8K9 
       24.53        49.68        39.81        19.69        20.84        46.82 
TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KH TCGA-WC-A885 TCGA-WC-AA9E TCGA-YZ-A985 
       38.73        44.52        38.07        22.55        27.55        38.93 

$`SF3B1 WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E7 
       32.28        51.98         4.90        15.45        15.09        13.64 
TCGA-V4-A9E8 TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       26.56        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ET TCGA-V4-A9EU 
       33.80        31.76        25.41        14.96        44.78        23.31 
TCGA-V4-A9EV TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 
       41.72        24.00        27.52        31.07        30.84        24.13 
TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 
       28.70         6.67        41.29        19.63        47.97        45.27 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KI TCGA-VD-A8KJ 
        3.75        26.99         1.32         0.62        36.59        37.81 
TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M 
        2.10        20.98         0.13         2.24        26.14         0.20 
TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S 
        1.45        19.92         2.83        20.91         0.20        14.04 
TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 
        1.61        85.48        55.99        43.20        41.36        36.56 
TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A888 TCGA-WC-A88A TCGA-YZ-A980 TCGA-YZ-A982 
        7.92         0.39        18.90         2.70        61.22        16.27 
TCGA-YZ-A983 TCGA-YZ-A984 
       26.24        45.90 

  SF3B1 MUTATED SF3B1 WILD-TYPE 
          14.89            0.13 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
          82.16           85.48 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
         38.400          23.655 
[1] "14.9 - 82.2 (38.4)" "0.1 - 85.5 (23.7)" 
[1] "hr=" "9.5"
D4V2, continuous
                 vv
clus              STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SF3B1 MUTATED           4         6          6          2          0        0
  SF3B1 WILD-TYPE         8        21         19          8          1        4
D4V3, multiclass
            clus
vv           SF3B1 MUTATED SF3B1 WILD-TYPE
  STAGE IIA              4               8
  STAGE IIB              6              21
  STAGE IIIA             6              19
  STAGE IIIB             2               8
  STAGE IIIC             0               1
  STAGE IV               0               4
[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              T2 T3 T4
  SF3B1 MUTATED    4  7  7
  SF3B1 WILD-TYPE 10 25 27
D4V4, multiclass
    clus
vv   SF3B1 MUTATED SF3B1 WILD-TYPE
  T2             4              10
  T3             7              25
  T4             7              27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                 cls
clus               0  1
  SF3B1 MUTATED   11  0
  SF3B1 WILD-TYPE 40  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED     11    0
  SF3B1 WILD-TYPE   40    4
   clus
vv  SF3B1 MUTATED SF3B1 WILD-TYPE
  0            11              40
  1             0               4
[1] 2 2
[1] FALSE
D4V6, binary
                 cls
clus               0  1
  SF3B1 MUTATED    9  9
  SF3B1 WILD-TYPE 26 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED      9    9
  SF3B1 WILD-TYPE   26   36
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  FEMALE             9              26
  MALE               9              36
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus               0  1
  SF3B1 MUTATED   17  1
  SF3B1 WILD-TYPE 59  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED     17    1
  SF3B1 WILD-TYPE   59    2
     clus
vv    SF3B1 MUTATED SF3B1 WILD-TYPE
  NO             17              59
  YES             1               2
[1] 2 2
[1] FALSE

Clustering(5) Variable = BAP1 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2             0  1
  BAP1 MUTATED   11 11
  BAP1 WILD-TYPE 46 12
  BAP1 MUTATED BAP1 WILD-TYPE 
            22             58 
  BAP1 MUTATED BAP1 WILD-TYPE 
            11             12 
$`BAP1 MUTATED`
TCGA-V4-A9EL TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E7 TCGA-V4-A9ED 
       32.28        14.89         4.90        15.45        13.64        35.44 
TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EO TCGA-V4-A9EU TCGA-V4-A9EV 
       13.08        38.30        12.79        25.41        23.31        41.72 
TCGA-V4-A9F0 TCGA-VD-A8KI TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-AA8T TCGA-WC-A888 
       31.07        36.59         2.10        20.98         1.61        18.90 
TCGA-WC-A88A TCGA-YZ-A980 TCGA-YZ-A984 TCGA-YZ-A985 
        2.70        61.22        45.90        38.93 

$`BAP1 WILD-TYPE`
TCGA-WC-A87U TCGA-WC-A881 TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E8 TCGA-V4-A9E9 
       51.98        35.01        15.09        82.16        26.56        40.96 
TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM 
       44.32        24.43        22.03        24.53        33.80        31.76 
TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY 
       14.96        49.68        44.78        39.81        24.00        27.52 
TCGA-V4-A9EZ TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 
       19.69        30.84        24.13        28.70        20.84         6.67 
TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA 
       41.29        19.63        47.97        45.27        46.82        38.73 
TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH 
       44.52         3.75        26.99         1.32         0.62        38.07 
TCGA-VD-A8KJ TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N 
       37.81         0.13         2.24        26.14         0.20         1.45 
TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-WC-A87T 
       19.92         2.83        20.91         0.20        14.04        85.48 
TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 
       55.99        43.20        41.36        36.56         7.92         0.39 
TCGA-WC-A885 TCGA-WC-AA9E TCGA-YZ-A982 TCGA-YZ-A983 
       22.55        27.55        16.27        26.24 

  BAP1 MUTATED BAP1 WILD-TYPE 
          1.61           0.13 
  BAP1 MUTATED BAP1 WILD-TYPE 
         61.22          85.48 
  BAP1 MUTATED BAP1 WILD-TYPE 
        22.145         26.400 
[1] "1.6 - 61.2 (22.1)" "0.1 - 85.5 (26.4)"
[1] "hr=" "2.9"
D5V2, continuous
                vv
clus             STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BAP1 MUTATED           2         6          8          3          1        2
  BAP1 WILD-TYPE        10        21         17          7          0        2
D5V3, multiclass
            clus
vv           BAP1 MUTATED BAP1 WILD-TYPE
  STAGE IIA             2             10
  STAGE IIB             6             21
  STAGE IIIA            8             17
  STAGE IIIB            3              7
  STAGE IIIC            1              0
  STAGE IV              2              2
[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             T2 T3 T4
  BAP1 MUTATED    3  7 12
  BAP1 WILD-TYPE 11 25 22
D5V4, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  T2            3             11
  T3            7             25
  T4           12             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"
D5V5, binary
                cls
clus              0  1
  BAP1 MUTATED   12  2
  BAP1 WILD-TYPE 39  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     12    2
  BAP1 WILD-TYPE   39    2
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0           12             39
  1            2              2
[1] 2 2
[1] FALSE
D5V6, binary
                cls
clus              0  1
  BAP1 MUTATED    8 14
  BAP1 WILD-TYPE 27 31
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      8   14
  BAP1 WILD-TYPE   27   31
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE            8             27
  MALE             14             31
[1] 2 2
[1] FALSE
D5V7, binary
                cls
clus              0  1
  BAP1 MUTATED   20  1
  BAP1 WILD-TYPE 56  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     20    1
  BAP1 WILD-TYPE   56    2
     clus
vv    BAP1 MUTATED BAP1 WILD-TYPE
  NO            20             56
  YES            1              2
[1] 2 2
[1] FALSE

Clustering(6) Variable = CYSLTR2 MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  CYSLTR2 MUTATED    2  1
  CYSLTR2 WILD-TYPE 55 22
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                3                77 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                1                22 
$`CYSLTR2 MUTATED`
TCGA-V4-A9ED TCGA-VD-AA8O TCGA-YZ-A982 
       35.44        19.92        16.27 

$`CYSLTR2 WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ 
       24.43        13.08        38.30        22.03        12.79        24.53 
TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET 
       33.80        31.76        25.41        14.96        49.68        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ 
       23.31        41.72        39.81        24.00        27.52        19.69 
TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 
       31.07        30.84        24.13        28.70        20.84         6.67 
TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA 
       41.29        19.63        47.97        45.27        46.82        38.73 
TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH 
       44.52         3.75        26.99         1.32         0.62        38.07 
TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN 
       36.59        37.81         2.10        20.98         0.13         2.24 
TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R 
       26.14         0.20         1.45         2.83        20.91         0.20 
TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 
       14.04         1.61        85.48        55.99        43.20        41.36 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A 
       36.56         7.92         0.39        22.55        18.90         2.70 
TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       27.55        61.22        26.24        45.90        38.93 

  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
            16.27              0.13 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
            35.44             85.48 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
            19.92             26.14 
[1] "16.3 - 35.4 (19.9)" "0.1 - 85.5 (26.1)" 
[1] "hr=" "1.5"
D6V2, continuous
                   vv
clus                STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  CYSLTR2 MUTATED           0         1          1          1          0
  CYSLTR2 WILD-TYPE        12        26         24          9          1
                   vv
clus                STAGE IV
  CYSLTR2 MUTATED          0
  CYSLTR2 WILD-TYPE        4
D6V3, multiclass
            clus
vv           CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  STAGE IIA                0                12
  STAGE IIB                1                26
  STAGE IIIA               1                24
  STAGE IIIB               1                 9
  STAGE IIIC               0                 1
  STAGE IV                 0                 4
[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                T2 T3 T4
  CYSLTR2 MUTATED    0  2  1
  CYSLTR2 WILD-TYPE 14 30 33
D6V4, multiclass
    clus
vv   CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  T2               0                14
  T3               2                30
  T4               1                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                   cls
clus                 0  1
  CYSLTR2 MUTATED    2  0
  CYSLTR2 WILD-TYPE 49  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED      2    0
  CYSLTR2 WILD-TYPE   49    4
   clus
vv  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  0               2                49
  1               0                 4
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                 0  1
  CYSLTR2 MUTATED    1  2
  CYSLTR2 WILD-TYPE 34 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED      1    2
  CYSLTR2 WILD-TYPE   34   43
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  FEMALE               1                34
  MALE                 2                43
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  CYSLTR2 MUTATED    3  0
  CYSLTR2 WILD-TYPE 73  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED      3    0
  CYSLTR2 WILD-TYPE   73    3
     clus
vv    CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  NO                3                73
  YES               0                 3
[1] 2 2
[1] FALSE

Clustering(7) Variable = SFRS2 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2              0  1
  SFRS2 MUTATED    2  1
  SFRS2 WILD-TYPE 55 22
  SFRS2 MUTATED SFRS2 WILD-TYPE 
              3              77 
  SFRS2 MUTATED SFRS2 WILD-TYPE 
              1              22 
$`SFRS2 MUTATED`
TCGA-V4-A9EM TCGA-WC-A882 TCGA-WC-A888 
       31.76        36.56        18.90 

$`SFRS2 WILD-TYPE`
TCGA-V4-A9EL TCGA-WC-A87U TCGA-WC-A881 TCGA-WC-AA9A TCGA-RZ-AB0B TCGA-V3-A9ZX 
       32.28        51.98        35.01        14.89         4.90        15.45 
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
       15.09        82.16        13.64        26.56        40.96        44.32 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.43        35.44        13.08        38.30        22.03        12.79 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET 
       24.53        33.80        25.41        14.96        49.68        44.78 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ 
       23.31        41.72        39.81        24.00        27.52        19.69 
TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 
       31.07        30.84        24.13        28.70        20.84         6.67 
TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA 
       41.29        19.63        47.97        45.27        46.82        38.73 
TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH 
       44.52         3.75        26.99         1.32         0.62        38.07 
TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN 
       36.59        37.81         2.10        20.98         0.13         2.24 
TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q 
       26.14         0.20         1.45        19.92         2.83        20.91 
TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y 
        0.20        14.04         1.61        85.48        55.99        43.20 
TCGA-WC-A880 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A88A TCGA-WC-AA9E 
       41.36         7.92         0.39        22.55         2.70        27.55 
TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       61.22        16.27        26.24        45.90        38.93 

  SFRS2 MUTATED SFRS2 WILD-TYPE 
          18.90            0.13 
  SFRS2 MUTATED SFRS2 WILD-TYPE 
          36.56           85.48 
  SFRS2 MUTATED SFRS2 WILD-TYPE 
          31.76           25.41 
[1] "18.9 - 36.6 (31.8)" "0.1 - 85.5 (25.4)" 
[1] "hr=" "1.2"
D7V2, continuous
                 vv
clus              STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFRS2 MUTATED           0         2          1          0          0        0
  SFRS2 WILD-TYPE        12        25         24         10          1        4
D7V3, multiclass
            clus
vv           SFRS2 MUTATED SFRS2 WILD-TYPE
  STAGE IIA              0              12
  STAGE IIB              2              25
  STAGE IIIA             1              24
  STAGE IIIB             0              10
  STAGE IIIC             0               1
  STAGE IV               0               4
[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              T2 T3 T4
  SFRS2 MUTATED    1  1  1
  SFRS2 WILD-TYPE 13 31 33
D7V4, multiclass
    clus
vv   SFRS2 MUTATED SFRS2 WILD-TYPE
  T2             1              13
  T3             1              31
  T4             1              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                 cls
clus               0  1
  SFRS2 MUTATED    3  0
  SFRS2 WILD-TYPE 48  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRS2 MUTATED      3    0
  SFRS2 WILD-TYPE   48    4
   clus
vv  SFRS2 MUTATED SFRS2 WILD-TYPE
  0             3              48
  1             0               4
[1] 2 2
[1] FALSE
D7V6, binary
                 cls
clus               0  1
  SFRS2 MUTATED    1  2
  SFRS2 WILD-TYPE 34 43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRS2 MUTATED      1    2
  SFRS2 WILD-TYPE   34   43
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  FEMALE             1              34
  MALE               2              43
[1] 2 2
[1] FALSE
D7V7, binary
                 cls
clus               0  1
  SFRS2 MUTATED    3  0
  SFRS2 WILD-TYPE 73  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRS2 MUTATED      3    0
  SFRS2 WILD-TYPE   73    3
     clus
vv    SFRS2 MUTATED SFRS2 WILD-TYPE
  NO              3              73
  YES             0               3
[1] 2 2
[1] FALSE
