[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/15096076/UVM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UVM-TP/15890468/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 
            16             64 
  BAP1 MUTATED BAP1 WILD-TYPE 
            16             64 
[1] "PRMT8 MUTATION ANALYSIS"
[1] 3
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              5              75 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              5              75 
[1] "CYSLTR2 MUTATION ANALYSIS"
[1] 3
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                3                77 
  CYSLTR2 MUTATED CYSLTR2 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] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATIONS_RADIATION_REGIMENINDICATION"
[12] "RACE"                                  
[13] "ETHNICITY"                             
[14] "BATCH_NUMBER"                          

Input Data has 14 rows and 80 columns.

[1] "Batch" "14"   
[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=13,	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=64,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              19-2-2015 2-4-2015
freq.values   "1"       "79"    
freq.contrast "79"      "1"     
both >= 3     "FALSE"   "FALSE" 
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'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 13:'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"               
Variable 14:'BATCH_NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER excluded in the analysis because there is no case of (both >= 3) in the table below"
              B417.12.0 B417.15.0
freq.values   "1"       "79"     
freq.contrast "79"      "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 5 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"        "NEOPLASM_DISEASESTAGE" "PATHOLOGY_T_STAGE"    
[4] "PATHOLOGY_M_STAGE"     "GENDER"               
YEARS_TO_BIRTH, nv=40, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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

Clustering(1) Variable = GNAQ MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  GNAQ MUTATED   35  5
  GNAQ WILD-TYPE 32  8
  GNAQ MUTATED GNAQ WILD-TYPE 
            40             40 
  GNAQ MUTATED GNAQ WILD-TYPE 
             5              8 
$`GNAQ MUTATED`
TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9EE 
       74.53        13.64        30.38        24.69        24.43        13.08 
TCGA-V4-A9EK TCGA-V4-A9EL TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9ES TCGA-V4-A9EW 
       18.64        23.44        22.03        19.53        37.81        30.05 
TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 
       24.00        25.02        19.69        24.10        21.73        12.20 
TCGA-V4-A9F4 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K9 TCGA-VD-A8KB TCGA-VD-A8KE 
       20.22        19.63         0.10         0.46        35.31        26.99 
TCGA-VD-A8KI TCGA-VD-A8KK TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M 
        1.25         2.10         0.13         2.24        26.14         0.20 
TCGA-VD-AA8Q TCGA-VD-AA8S TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A880 TCGA-WC-A883 
        0.23        14.04        70.65        51.98        31.99         7.92 
TCGA-WC-A885 TCGA-WC-AA9E TCGA-YZ-A983 TCGA-YZ-A985 
       10.36        14.20        17.98        25.81 

$`GNAQ WILD-TYPE`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E8 TCGA-V4-A9ED TCGA-V4-A9EF 
        4.90         4.50         4.04        26.56        28.41        27.09 
TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EQ TCGA-V4-A9ET TCGA-V4-A9EU 
       22.03        13.22        12.56        14.96        31.66        23.31 
TCGA-V4-A9EV TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-VD-A8K8 TCGA-VD-A8KA 
       27.48        22.03         6.67        32.28        16.87        37.28 
TCGA-VD-A8KD TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KJ TCGA-VD-A8KL 
        3.75         1.32         0.66         0.33        31.59        20.98 
TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8R TCGA-VD-AA8T TCGA-WC-A87W 
        1.45         7.50         2.83         0.20         0.49        45.57 
TCGA-WC-A87Y TCGA-WC-A881 TCGA-WC-A882 TCGA-WC-A884 TCGA-WC-A888 TCGA-WC-A88A 
       31.40        22.82        11.31         0.39        10.13         2.70 
TCGA-WC-AA9A TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A984 
       14.89        52.64        16.27        42.08 

  GNAQ MUTATED GNAQ WILD-TYPE 
           0.1            0.2 
  GNAQ MUTATED GNAQ WILD-TYPE 
         74.53          52.64 
  GNAQ MUTATED GNAQ WILD-TYPE 
        19.955         14.925 
[1] "0.1 - 74.5 (20.0)" "0.2 - 52.6 (14.9)"
[1] "hr=" "2"  
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

Clustering(2) Variable = GNA11 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2              0  1
  GNA11 MUTATED   29  7
  GNA11 WILD-TYPE 38  6
  GNA11 MUTATED GNA11 WILD-TYPE 
             36              44 
  GNA11 MUTATED GNA11 WILD-TYPE 
              7               6 
$`GNA11 MUTATED`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E8 TCGA-V4-A9EF TCGA-V4-A9EH 
        4.90         4.50         4.04        26.56        27.09        22.03 
TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EQ TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV 
       13.22        12.56        14.96        31.66        23.31        27.48 
TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-VD-A8K8 TCGA-VD-A8KA TCGA-VD-A8KF 
       22.03         6.67        32.28        16.87        37.28         1.32 
TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KL TCGA-VD-AA8N TCGA-VD-AA8P TCGA-VD-AA8R 
        0.66         0.33        20.98         1.45         2.83         0.20 
TCGA-VD-AA8T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A881 TCGA-WC-A882 TCGA-WC-A884 
        0.49        45.57        31.40        22.82        11.31         0.39 
TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A985 
       10.13         2.70        14.89        14.20        52.64        25.81 

$`GNA11 WILD-TYPE`
TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED 
       74.53        13.64        30.38        24.69        24.43        28.41 
TCGA-V4-A9EE TCGA-V4-A9EK TCGA-V4-A9EL TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9ES 
       13.08        18.64        23.44        22.03        19.53        37.81 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 
       30.05        24.00        25.02        19.69        24.10        21.73 
TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K9 TCGA-VD-A8KB 
       12.20        20.22        19.63         0.10         0.46        35.31 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KM 
        3.75        26.99         1.25        31.59         2.10         0.13 
TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8O TCGA-VD-AA8Q TCGA-VD-AA8S 
        2.24        26.14         0.20         7.50         0.23        14.04 
TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A880 TCGA-WC-A883 TCGA-WC-A885 TCGA-YZ-A982 
       70.65        51.98        31.99         7.92        10.36        16.27 
TCGA-YZ-A983 TCGA-YZ-A984 
       17.98        42.08 

  GNA11 MUTATED GNA11 WILD-TYPE 
            0.2             0.1 
  GNA11 MUTATED GNA11 WILD-TYPE 
          52.64           74.53 
  GNA11 MUTATED GNA11 WILD-TYPE 
         14.545          19.955 
[1] "0.2 - 52.6 (14.5)" "0.1 - 74.5 (20.0)"
[1] "hr=" "1.8"
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

Clustering(3) Variable = EIF1AX MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2               0  1
  EIF1AX MUTATED    9  1
  EIF1AX WILD-TYPE 58 12
  EIF1AX MUTATED EIF1AX WILD-TYPE 
              10               70 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               1               12 
$`EIF1AX MUTATED`
TCGA-V3-A9ZY TCGA-V4-A9EC TCGA-V4-A9EY TCGA-V4-A9F7 TCGA-VD-A8KE TCGA-VD-A8KO 
        4.04        24.43        25.02        32.28        26.99        26.14 
TCGA-VD-AA8R TCGA-WC-A87U TCGA-WC-A880 TCGA-WC-A884 
        0.20        51.98        31.99         0.39 

$`EIF1AX WILD-TYPE`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 
        4.90         4.50        74.53        13.64        26.56        30.38 
TCGA-V4-A9EA TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI 
       24.69        28.41        13.08        27.09        22.03        13.22 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EL TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ 
       12.56        18.64        23.44        22.03        19.53        14.96 
TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX 
       37.81        31.66        23.31        27.48        30.05        24.00 
TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 
       19.69        24.10        21.73        12.20        22.03        20.22 
TCGA-V4-A9F5 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA 
        6.67        19.63         0.10        16.87         0.46        37.28 
TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI 
       35.31         3.75         1.32         0.66         0.33         1.25 
TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-AA8M 
       31.59         2.10        20.98         0.13         2.24         0.20 
TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8S TCGA-VD-AA8T 
        1.45         7.50         2.83         0.23        14.04         0.49 
TCGA-WC-A87T TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A881 TCGA-WC-A882 TCGA-WC-A883 
       70.65        45.57        31.40        22.82        11.31         7.92 
TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9A TCGA-WC-AA9E TCGA-YZ-A980 
       10.36        10.13         2.70        14.89        14.20        52.64 
TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       16.27        17.98        42.08        25.81 

  EIF1AX MUTATED EIF1AX WILD-TYPE 
             0.2              0.1 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
           51.98            74.53 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
          25.580           17.425 
[1] "0.2 - 52.0 (25.6)" "0.1 - 74.5 (17.4)"
[1] "hr=" "2.2"
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

Clustering(4) Variable = SF3B1 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2              0  1
  SF3B1 MUTATED   17  1
  SF3B1 WILD-TYPE 50 12
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             18              62 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
              1              12 
$`SF3B1 MUTATED`
TCGA-V4-A9E5 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9EJ TCGA-V4-A9ES 
       74.53        30.38        24.69        24.43        12.56        37.81 
TCGA-V4-A9EW TCGA-V4-A9EZ TCGA-V4-A9F4 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB 
       30.05        19.69        20.22         0.46        37.28        35.31 
TCGA-VD-A8KH TCGA-WC-A881 TCGA-WC-A885 TCGA-WC-AA9A TCGA-WC-AA9E TCGA-YZ-A985 
        0.33        22.82        10.36        14.89        14.20        25.81 

$`SF3B1 WILD-TYPE`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9ED 
        4.90         4.50         4.04        13.64        26.56        28.41 
TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EK TCGA-V4-A9EL 
       13.08        27.09        22.03        13.22        18.64        23.44 
TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV 
       22.03        19.53        14.96        31.66        23.31        27.48 
TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 
       24.00        25.02        24.10        21.73        12.20        22.03 
TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8KD 
        6.67        32.28        19.63         0.10        16.87         3.75 
TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK 
       26.99         1.32         0.66         1.25        31.59         2.10 
TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N 
       20.98         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-VD-AA8T 
        7.50         2.83         0.23         0.20        14.04         0.49 
TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 
       70.65        51.98        45.57        31.40        31.99        11.31 
TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A888 TCGA-WC-A88A TCGA-YZ-A980 TCGA-YZ-A982 
        7.92         0.39        10.13         2.70        52.64        16.27 
TCGA-YZ-A983 TCGA-YZ-A984 
       17.98        42.08 

  SF3B1 MUTATED SF3B1 WILD-TYPE 
           0.33            0.10 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
          74.53           70.65 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
         23.625          16.570 
[1] "0.3 - 74.5 (23.6)" "0.1 - 70.7 (16.6)"
[1] "hr=" "4.5"
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

Clustering(5) Variable = BAP1 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2             0  1
  BAP1 MUTATED   13  3
  BAP1 WILD-TYPE 54 10
  BAP1 MUTATED BAP1 WILD-TYPE 
            16             64 
  BAP1 MUTATED BAP1 WILD-TYPE 
             3             10 
$`BAP1 MUTATED`
TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EO TCGA-V4-A9EU TCGA-V4-A9EX TCGA-V4-A9F0 
       27.09        13.22        19.53        23.31        24.00        24.10 
TCGA-V4-A9F1 TCGA-V4-A9F8 TCGA-VD-A8KI TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-AA8N 
       21.73        19.63         1.25         2.10        20.98         1.45 
TCGA-VD-AA8T TCGA-WC-AA9A TCGA-YZ-A980 TCGA-YZ-A984 
        0.49        14.89        52.64        42.08 

$`BAP1 WILD-TYPE`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 
        4.90         4.50         4.04        74.53        13.64        26.56 
TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EH 
       30.38        24.69        24.43        28.41        13.08        22.03 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EL TCGA-V4-A9EM TCGA-V4-A9EQ TCGA-V4-A9ES 
       12.56        18.64        23.44        22.03        14.96        37.81 
TCGA-V4-A9ET TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F2 
       31.66        27.48        30.05        25.02        19.69        12.20 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-VD-A8K7 TCGA-VD-A8K8 
       22.03        20.22         6.67        32.28         0.10        16.87 
TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF 
        0.46        37.28        35.31         3.75        26.99         1.32 
TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KJ TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO 
        0.66         0.33        31.59         0.13         2.24        26.14 
TCGA-VD-AA8M TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S 
        0.20         7.50         2.83         0.23         0.20        14.04 
TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A881 
       70.65        51.98        45.57        31.40        31.99        22.82 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A 
       11.31         7.92         0.39        10.36        10.13         2.70 
TCGA-WC-AA9E TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A985 
       14.20        16.27        17.98        25.81 

  BAP1 MUTATED BAP1 WILD-TYPE 
          0.49           0.10 
  BAP1 MUTATED BAP1 WILD-TYPE 
         52.64          74.53 
  BAP1 MUTATED BAP1 WILD-TYPE 
        20.305         17.425 
[1] "0.5 - 52.6 (20.3)" "0.1 - 74.5 (17.4)"
[1] "hr=" "1.1"
D5V2, continuous
                vv
clus             STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BAP1 MUTATED           2         5          5          3          1        0
  BAP1 WILD-TYPE        10        22         20          7          0        4
D5V3, multiclass
            clus
vv           BAP1 MUTATED BAP1 WILD-TYPE
  STAGE IIA             2             10
  STAGE IIB             5             22
  STAGE IIIA            5             20
  STAGE IIIB            3              7
  STAGE IIIC            1              0
  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
  BAP1 MUTATED    2  6  8
  BAP1 WILD-TYPE 12 26 26
D5V4, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  T2            2             12
  T3            6             26
  T4            8             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                cls
clus              0  1
  BAP1 MUTATED   10  0
  BAP1 WILD-TYPE 41  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     10    0
  BAP1 WILD-TYPE   41    4
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0           10             41
  1            0              4
[1] 2 2
[1] FALSE
D5V6, binary
                cls
clus              0  1
  BAP1 MUTATED    7  9
  BAP1 WILD-TYPE 28 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      7    9
  BAP1 WILD-TYPE   28   36
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE            7             28
  MALE              9             36
[1] 2 2
[1] FALSE

Clustering(6) Variable = PRMT8 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2              0  1
  PRMT8 MUTATED    4  1
  PRMT8 WILD-TYPE 63 12
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              5              75 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              1              12 
$`PRMT8 MUTATED`
TCGA-V4-A9EI TCGA-VD-A8KE TCGA-VD-AA8O TCGA-VD-AA8T TCGA-WC-A884 
       13.22        26.99         7.50         0.49         0.39 

$`PRMT8 WILD-TYPE`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 
        4.90         4.50         4.04        74.53        13.64        26.56 
TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF 
       30.38        24.69        24.43        28.41        13.08        27.09 
TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EL TCGA-V4-A9EM TCGA-V4-A9EO 
       22.03        12.56        18.64        23.44        22.03        19.53 
TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW 
       14.96        37.81        31.66        23.31        27.48        30.05 
TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 
       24.00        25.02        19.69        24.10        21.73        12.20 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 
       22.03        20.22         6.67        32.28        19.63         0.10 
TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KF 
       16.87         0.46        37.28        35.31         3.75         1.32 
TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL 
        0.66         0.33         1.25        31.59         2.10        20.98 
TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8P 
        0.13         2.24        26.14         0.20         1.45         2.83 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W 
        0.23         0.20        14.04        70.65        51.98        45.57 
TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A881 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A885 
       31.40        31.99        22.82        11.31         7.92        10.36 
TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 
       10.13         2.70        14.89        14.20        52.64        16.27 
TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       17.98        42.08        25.81 

  PRMT8 MUTATED PRMT8 WILD-TYPE 
           0.39            0.10 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
          26.99           74.53 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
           7.50           19.63 
[1] "0.4 - 27.0 (7.5)"  "0.1 - 74.5 (19.6)"
[1] "hr=" "2.3"
D6V2, continuous
                 vv
clus              STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRMT8 MUTATED           2         1          0          2          0        0
  PRMT8 WILD-TYPE        10        26         25          8          1        4
D6V3, multiclass
            clus
vv           PRMT8 MUTATED PRMT8 WILD-TYPE
  STAGE IIA              2              10
  STAGE IIB              1              26
  STAGE IIIA             0              25
  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
  PRMT8 MUTATED    2  1  2
  PRMT8 WILD-TYPE 12 31 32
D6V4, multiclass
    clus
vv   PRMT8 MUTATED PRMT8 WILD-TYPE
  T2             2              12
  T3             1              31
  T4             2              32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                 cls
clus               0  1
  PRMT8 MUTATED    4  0
  PRMT8 WILD-TYPE 47  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT8 MUTATED      4    0
  PRMT8 WILD-TYPE   47    4
   clus
vv  PRMT8 MUTATED PRMT8 WILD-TYPE
  0             4              47
  1             0               4
[1] 2 2
[1] FALSE
D6V6, binary
                 cls
clus               0  1
  PRMT8 MUTATED    3  2
  PRMT8 WILD-TYPE 32 43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT8 MUTATED      3    2
  PRMT8 WILD-TYPE   32   43
        clus
vv       PRMT8 MUTATED PRMT8 WILD-TYPE
  FEMALE             3              32
  MALE               2              43
[1] 2 2
[1] FALSE

Clustering(7) Variable = CYSLTR2 MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  CYSLTR2 MUTATED    3  0
  CYSLTR2 WILD-TYPE 64 13
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                3                77 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                0                13 
$`CYSLTR2 MUTATED`
TCGA-V4-A9ED TCGA-VD-AA8O TCGA-YZ-A982 
       28.41         7.50        16.27 

$`CYSLTR2 WILD-TYPE`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 
        4.90         4.50         4.04        74.53        13.64        26.56 
TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH 
       30.38        24.69        24.43        13.08        27.09        22.03 
TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EL TCGA-V4-A9EM TCGA-V4-A9EO 
       13.22        12.56        18.64        23.44        22.03        19.53 
TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW 
       14.96        37.81        31.66        23.31        27.48        30.05 
TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 
       24.00        25.02        19.69        24.10        21.73        12.20 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 
       22.03        20.22         6.67        32.28        19.63         0.10 
TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE 
       16.87         0.46        37.28        35.31         3.75        26.99 
TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK 
        1.32         0.66         0.33         1.25        31.59         2.10 
TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N 
       20.98         0.13         2.24        26.14         0.20         1.45 
TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T 
        2.83         0.23         0.20        14.04         0.49        70.65 
TCGA-WC-A87U TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A881 TCGA-WC-A882 
       51.98        45.57        31.40        31.99        22.82        11.31 
TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9A 
        7.92         0.39        10.36        10.13         2.70        14.89 
TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       14.20        52.64        17.98        42.08        25.81 

  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
              7.5               0.1 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
            28.41             74.53 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
            16.27             19.53 
[1] "7.5 - 28.4 (16.3)" "0.1 - 74.5 (19.5)"
[1] "hr="     "2.6e+07"
D7V2, 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
D7V3, 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
D7V4, 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"
D7V5, 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
D7V6, 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
