[1] "ofn"        "-oTTHCA-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/THCA-TP/22507188/THCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/22511440/transformed.cor.cli.txt"

nPatients in clinical file=503, in cluster file=499, common to both=499
[1] "Reduce the number of clustering variables from 82 to 59."
[1]  59 499
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4               495 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4               495 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               26               473 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               26               473 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               496 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               496 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5               494 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5               494 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               494 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               494 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               21               478 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               21               478 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               17               482 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               17               482 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18               481 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18               481 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               20               479 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               20               479 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6               493 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6               493 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7               492 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7               492 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               496 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               496 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               495 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               495 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                493 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                493 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                494 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                494 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                484 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                484 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                484 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                484 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                494 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                494 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                488 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                488 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                484 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                484 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                486 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                486 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                483 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                483 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                481 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                481 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                493 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                493 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                493 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                493 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 8                491 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 8                491 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                489 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                489 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                487 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                487 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                487 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                487 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                494 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                494 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                8               491 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                8               491 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7               492 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7               492 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               495 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               495 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               496 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               496 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               489 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               489 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               489 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               489 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               496 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               496 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               495 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               495 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4               495 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4               495 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7               492 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7               492 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4               495 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4               495 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               495 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               495 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               19               480 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               19               480 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               25               474 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               25               474 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                492 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                492 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                493 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                493 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                492 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                492 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                490 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                490 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                485 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                485 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                491 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                491 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                491 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                491 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                495 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                495 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                495 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                495 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                495 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                495 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                494 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                494 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                491 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                491 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                89                410 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                89                410 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                4               495 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                4               495 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               494 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               494 
[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] "HISTOLOGICAL_TYPE"                   
[14] "RADIATION_EXPOSURE"                  
[15] "EXTRATHYROIDAL_EXTENSION"            
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "MULTIFOCALITY"                       
[19] "TUMOR_SIZE"                          
[20] "RACE"                                
[21] "ETHNICITY"                           

Input Data has 21 rows and 499 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=73,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=16,	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=433,	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=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	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=19,	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:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATION_EXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'EXTRATHYROIDAL_EXTENSION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'TUMOR_SIZE':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	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"
[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 499 columns, 1 survival variables, and 16 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"        
 [3] "PATHOLOGY_T_STAGE"        "PATHOLOGY_N_STAGE"       
 [5] "PATHOLOGY_M_STAGE"        "GENDER"                  
 [7] "RADIATION_THERAPY"        "HISTOLOGICAL_TYPE"       
 [9] "RADIATION_EXPOSURE"       "EXTRATHYROIDAL_EXTENSION"
[11] "RESIDUAL_TUMOR"           "NUMBER_OF_LYMPH_NODES"   
[13] "MULTIFOCALITY"            "TUMOR_SIZE"              
[15] "RACE"                     "ETHNICITY"               
YEARS_TO_BIRTH, nv=73, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
142 165 167  23 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
142 165 167  23 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
142 165 167  23 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
142 165 167  23 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_EXPOSURE, nv=2, binary=FALSE, numeric=FALSE
EXTRATHYROIDAL_EXTENSION, nv=4, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=28, binary=FALSE, numeric=TRUE
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SIZE, nv=61, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     4   0
  1P GAIN WILD-TYPE 478  16
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4               494 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                0                16 
$`1P GAIN MUTATED`
TCGA-4C-A93U TCGA-DO-A2HM TCGA-ET-A3BT TCGA-FY-A3NM 
        4.24         2.33        87.62        29.10 

$`1P GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       21.83        23.93        24.79        13.78        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 
       25.48        15.12        42.08        51.39        41.52        20.58 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ 
       15.81        35.38        54.90        21.53        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       27.02        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       33.24       106.09       107.41       108.46        84.89       123.32 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       79.10        76.64         5.79        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10       116.09         1.25        20.42        17.82         7.82 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             2.33              0.20 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            87.62            178.29 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            16.67             31.27 
[1] "2.3 - 87.6 (16.7)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "3300000"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  1P GAIN MUTATED         0        0         1        0         3         0
  1P GAIN WILD-TYPE     282       50       110        2        43         6
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 0               282
  STAGE II                0                50
  STAGE III               1               110
  STAGE IV                0                 2
  STAGE IVA               3                43
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  1P GAIN MUTATED     1   1   1   1
  1P GAIN WILD-TYPE 141 164 166  22
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               1               141
  T2               1               164
  T3               1               166
  T4               1                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"
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1   3
  1P GAIN WILD-TYPE 224 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    3
  1P GAIN WILD-TYPE  224  221
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               1               224
  1               3               221
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1   0
  1P GAIN WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    0
  1P GAIN WILD-TYPE  277    9
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               1               277
  1               0                 9
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     3   1
  1P GAIN WILD-TYPE 362 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    1
  1P GAIN WILD-TYPE  362  133
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               3               362
  MALE                 1               133
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1   1
  1P GAIN WILD-TYPE 179 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    1
  1P GAIN WILD-TYPE  179  302
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                1               179
  YES               1               302
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  1P GAIN MUTATED                0
  1P GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  1P GAIN MUTATED                                               3
  1P GAIN WILD-TYPE                                           353
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  1P GAIN MUTATED                                                                        0
  1P GAIN WILD-TYPE                                                                    100
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  1P GAIN MUTATED                                                                     1
  1P GAIN WILD-TYPE                                                                  35
D1V9, multiclass
                                                                        clus
vv                                                                       1P GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  1
                                                                        clus
vv                                                                       1P GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2   1
  1P GAIN WILD-TYPE 418  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    1
  1P GAIN WILD-TYPE  418   16
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                2               418
  YES               1                16
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  1P GAIN MUTATED              1                       1    2
  1P GAIN WILD-TYPE          131                      17  328
                   vv
clus                VERY ADVANCED (T4B)
  1P GAIN MUTATED                     0
  1P GAIN WILD-TYPE                   1
D1V11, multiclass
                         clus
vv                        1P GAIN MUTATED 1P GAIN WILD-TYPE
  MINIMAL (T3)                          1               131
  MODERATE/ADVANCED (T4A)               1                17
  NONE                                  2               328
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED     3   0   0   1
  1P GAIN WILD-TYPE 380  51   4  29
D1V12, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               3               380
  R1               0                51
  R2               0                 4
  RX               1                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, continuous
D1V14, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1   3
  1P GAIN WILD-TYPE 224 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    3
  1P GAIN WILD-TYPE  224  261
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  MULTIFOCAL               1               224
  UNIFOCAL                 3               261
[1] 2 2
[1] FALSE
D1V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     0
  1P GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           1     3
  1P GAIN WILD-TYPE                        26   326
D1V16, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      1                26
  WHITE                                          3               326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V17, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0   4
  1P GAIN WILD-TYPE  38 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    4
  1P GAIN WILD-TYPE   38  356
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               4               356
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    24   2
  1Q GAIN WILD-TYPE 458  14
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               26               472 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                2                14 
$`1Q GAIN MUTATED`
TCGA-BJ-A290 TCGA-4C-A93U TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DJ-A13U 
       30.21         4.24        11.57        30.02        25.12        52.27 
TCGA-DO-A2HM TCGA-EL-A3GP TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3MZ TCGA-EL-A3T9 
        2.33        49.51       136.01        83.57        52.50         5.72 
TCGA-EL-A3ZO TCGA-EL-A4JX TCGA-EM-A3O3 TCGA-ET-A39P TCGA-ET-A3BT TCGA-FE-A231 
       72.69        45.96        14.50        95.34        87.62        31.59 
TCGA-FY-A3NM TCGA-FY-A40L TCGA-FY-A4B0 TCGA-H2-A26U TCGA-IM-A3EB TCGA-J8-A3O1 
       29.10        23.87        13.81        17.00        48.92        27.19 
TCGA-KS-A4IB TCGA-L6-A4EU 
       84.72         9.50 

$`1Q GAIN WILD-TYPE`
TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L TCGA-DJ-A2PR 
       22.88        23.18        12.66        35.84         9.96        27.45 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK TCGA-E3-A3E5 
       23.44        59.57        42.54         3.12        24.76        39.95 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 TCGA-EL-A3GQ 
        7.66        45.53         4.18       139.86        57.11        50.24 
TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO 
       33.50       150.48        17.52       178.29        29.72        50.40 
TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET 
       75.42         1.05         1.68        17.23         2.60        21.83 
TCGA-MK-A84Z TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
       23.93        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.97        11.08        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       12.82        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       21.63        50.17        37.64        27.32        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       30.12        14.70        14.27         2.76        48.79        38.17 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13V TCGA-DJ-A13W 
      169.32        18.58         8.71        56.19        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY 
        3.12        15.81        35.38        54.90        21.53        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
       64.87       115.10        65.39        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H7 
      101.13       139.99        49.32        43.36        49.71       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
      108.66        57.63        29.65       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB 
      132.07        98.24        41.29       107.47        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        91.17        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       34.72        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       15.02        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
        5.79        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 TCGA-FE-A233 
       33.17        31.40        73.74        71.44        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        4.11        22.03         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82         7.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08        23.31        21.63        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       17.36        15.16        22.49        19.04        14.04        21.60 
TCGA-GE-A2C6 TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       12.53        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       25.64        43.17        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-MK-A4N6 
       87.39        35.28        33.24        33.40        40.37        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       32.45        30.21        12.89         3.02 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             2.33              0.20 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           136.01            178.29 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           30.115            31.270 
[1] "2.3 - 136.0 (30.1)" "0.2 - 178.3 (31.3)"
[1] "hr=" "2.5"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  1Q GAIN MUTATED         6        0        11        1         8         0
  1Q GAIN WILD-TYPE     276       50       100        1        38         6
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 6               276
  STAGE II                0                50
  STAGE III              11               100
  STAGE IV                1                 1
  STAGE IVA               8                38
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  1Q GAIN MUTATED     2   3  16   5
  1Q GAIN WILD-TYPE 140 162 151  18
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               2               140
  T2               3               162
  T3              16               151
  T4               5                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     5  20
  1Q GAIN WILD-TYPE 220 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5   20
  1Q GAIN WILD-TYPE  220  204
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0               5               220
  1              20               204
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    13   0
  1Q GAIN WILD-TYPE 265   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     13    0
  1Q GAIN WILD-TYPE  265    9
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              13               265
  1               0                 9
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    18   8
  1Q GAIN WILD-TYPE 347 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     18    8
  1Q GAIN WILD-TYPE  347  126
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              18               347
  MALE                 8               126
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     5  18
  1Q GAIN WILD-TYPE 175 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5   18
  1Q GAIN WILD-TYPE  175  285
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                5               175
  YES              18               285
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  1Q GAIN MUTATED                0
  1Q GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  1Q GAIN MUTATED                                              23
  1Q GAIN WILD-TYPE                                           333
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  1Q GAIN MUTATED                                                                        0
  1Q GAIN WILD-TYPE                                                                    100
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  1Q GAIN MUTATED                                                                     3
  1Q GAIN WILD-TYPE                                                                  33
D2V9, multiclass
                                                                        clus
vv                                                                       1Q GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       23
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  3
                                                                        clus
vv                                                                       1Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        333
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   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"
D2V10, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    23   1
  1Q GAIN WILD-TYPE 397  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     23    1
  1Q GAIN WILD-TYPE  397   16
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               23               397
  YES               1                16
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  1Q GAIN MUTATED             12                       4    9
  1Q GAIN WILD-TYPE          120                      14  321
                   vv
clus                VERY ADVANCED (T4B)
  1Q GAIN MUTATED                     1
  1Q GAIN WILD-TYPE                   0
D2V11, multiclass
                         clus
vv                        1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  MINIMAL (T3)                         12               120
  MODERATE/ADVANCED (T4A)               4                14
  NONE                                  9               321
  VERY ADVANCED (T4B)                   1                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED    15   6   0   3
  1Q GAIN WILD-TYPE 368  45   4  27
D2V12, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              15               368
  R1               6                45
  R2               0                 4
  RX               3                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, continuous
D2V14, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     7  19
  1Q GAIN WILD-TYPE 218 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      7   19
  1Q GAIN WILD-TYPE  218  245
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  MULTIFOCAL               7               218
  UNIFOCAL                19               245
[1] 2 2
[1] FALSE
D2V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  1     1
  1Q GAIN WILD-TYPE                                0    51
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                           5    18
  1Q GAIN WILD-TYPE                        22   311
D2V16, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                51
  BLACK OR AFRICAN AMERICAN                      5                22
  WHITE                                         18               311
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V17, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     4  20
  1Q GAIN WILD-TYPE  34 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      4   20
  1Q GAIN WILD-TYPE   34  340
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                34
  NOT HISPANIC OR LATINO              20               340
[1] 2 2
[1] FALSE

Clustering(3) Variable = 3P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED     2   1
  3P GAIN WILD-TYPE 480  15
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               495 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                15 
$`3P GAIN MUTATED`
TCGA-EL-A3MX TCGA-EM-A22N TCGA-EM-A2CO 
       57.63        10.65         6.05 

$`3P GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       31.30        30.84        25.45        30.61        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 
       37.94        57.01       106.62        79.50        98.53        69.57 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        49.51       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MZ 
       43.36        49.71        83.57       139.00       108.66        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        78.61        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP 
       95.34        94.13        55.10        98.20        28.24        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        87.62        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10       116.09         1.25        20.42        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       29.10        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08        23.31        21.63        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 
       23.87        22.49        19.04        13.81        14.04        21.60 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
       31.10         8.22        25.64        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.24        33.40        40.37         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             6.05              0.20 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            57.63            178.29 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            10.65             31.27 
[1] "6.0 - 57.6 (10.7)"  "0.2 - 178.3 (31.3)"
[1] "hr=" "13" 
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  3P GAIN MUTATED         1        1         0        0         0         1
  3P GAIN WILD-TYPE     281       49       111        2        46         5
D3V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 1               281
  STAGE II                1                49
  STAGE III               0               111
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               1                 5
[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                 T1  T2  T3  T4
  3P GAIN MUTATED     1   1   0   1
  3P GAIN WILD-TYPE 141 164 167  22
D3V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               1               141
  T2               1               164
  T3               0               167
  T4               1                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"
D3V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     1   1
  3P GAIN WILD-TYPE 224 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    1
  3P GAIN WILD-TYPE  224  223
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               1               224
  1               1               223
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0   1
  3P GAIN WILD-TYPE 278   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    1
  3P GAIN WILD-TYPE  278    8
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               0               278
  1               1                 8
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3   0
  3P GAIN WILD-TYPE 362 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    0
  3P GAIN WILD-TYPE  362  134
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               3               362
  MALE                 0               134
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0   3
  3P GAIN WILD-TYPE 180 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    3
  3P GAIN WILD-TYPE  180  300
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                0               180
  YES               3               300
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  3P GAIN MUTATED                0
  3P GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  3P GAIN MUTATED                                               1
  3P GAIN WILD-TYPE                                           355
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  3P GAIN MUTATED                                                                        2
  3P GAIN WILD-TYPE                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  3P GAIN MUTATED                                                                     0
  3P GAIN WILD-TYPE                                                                  36
D3V9, multiclass
                                                                        clus
vv                                                                       3P GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       3P GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        355
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3   0
  3P GAIN WILD-TYPE 417  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    0
  3P GAIN WILD-TYPE  417   17
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                3               417
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  3P GAIN MUTATED              0                       0    3
  3P GAIN WILD-TYPE          132                      18  327
                   vv
clus                VERY ADVANCED (T4B)
  3P GAIN MUTATED                     0
  3P GAIN WILD-TYPE                   1
D3V11, multiclass
                         clus
vv                        3P GAIN MUTATED 3P GAIN WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  3               327
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED     1   0   0   2
  3P GAIN WILD-TYPE 382  51   4  28
D3V12, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0               1               382
  R1               0                51
  R2               0                 4
  RX               2                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2               384 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A45K        TCGA-CE-A13K 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DJ-A2PR        TCGA-DJ-A3UU        TCGA-DJ-A3UW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3V4        TCGA-DJ-A3VI        TCGA-DJ-A3VK        TCGA-E3-A3E5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CY        TCGA-EL-A3D0 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3GQ        TCGA-EL-A3H8        TCGA-EM-A3AQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BV        TCGA-J8-A3NZ        TCGA-J8-A4HW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-4C-A93U        TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZJ        TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A191        TCGA-BJ-A28R        TCGA-BJ-A28T        TCGA-BJ-A28W 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A28X        TCGA-BJ-A28Z        TCGA-BJ-A2N8        TCGA-BJ-A2N9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR        TCGA-BJ-A3PU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45G 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A4O8        TCGA-BJ-A4O9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN        TCGA-DE-A4M8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13V        TCGA-DJ-A13W 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PO        TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PT        TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PX        TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UM        TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UQ        TCGA-DJ-A3UR        TCGA-DJ-A3UX        TCGA-DJ-A3UZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3V0        TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9        TCGA-DJ-A3VA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3VB        TCGA-DJ-A3VD        TCGA-DJ-A3VF        TCGA-DJ-A3VG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A4UL        TCGA-DJ-A4UP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW        TCGA-DJ-A4V2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A4V5        TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E3-A3E3        TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A414 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A415        TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A436        TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CT        TCGA-EL-A3CU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D6        TCGA-EL-A3GO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3MW        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3T0        TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3TB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3ZH        TCGA-EL-A3ZK        TCGA-EL-A3ZL        TCGA-EL-A3ZM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP        TCGA-EL-A3ZS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4KD        TCGA-EL-A4KG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4KI        TCGA-EM-A1CS        TCGA-EM-A1CT        TCGA-EM-A1CU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YC        TCGA-EM-A1YD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A22Q        TCGA-EM-A2CK        TCGA-EM-A2CN        TCGA-EM-A2CP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2CQ        TCGA-EM-A2CT        TCGA-EM-A2CU        TCGA-EM-A2OV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2OX        TCGA-EM-A2OY        TCGA-EM-A2OZ        TCGA-EM-A2P0 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A2P2        TCGA-EM-A3AJ        TCGA-EM-A3AK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FK        TCGA-EM-A3FM        TCGA-EM-A3FN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FQ        TCGA-EM-A3FR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3O3        TCGA-EM-A3O8        TCGA-EM-A3O9        TCGA-EM-A3OA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3OB        TCGA-EM-A3ST        TCGA-EM-A3SU        TCGA-EM-A3SX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3SZ        TCGA-EM-A4FF        TCGA-EM-A4FM        TCGA-EM-A4FN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A4FO        TCGA-EM-A4FQ        TCGA-EM-A4FR        TCGA-EM-A4FV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A4G1        TCGA-ET-A25G        TCGA-ET-A25I        TCGA-ET-A25J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A2MX        TCGA-ET-A2MZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A39K 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39L        TCGA-ET-A39O        TCGA-ET-A39P        TCGA-ET-A39R 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BP        TCGA-ET-A3BQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3I4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3I5        TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3R6        TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-H2-A3RI        TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IM-A3ED        TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IM-A41Z        TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3O0 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I        TCGA-KS-A41J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3        TCGA-KS-A4I5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB        TCGA-KS-A4IC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ        TCGA-L6-A4EU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9        TCGA-QD-A8IV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D3V14, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     1   2
  3P GAIN WILD-TYPE 224 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    2
  3P GAIN WILD-TYPE  224  262
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  MULTIFOCAL               1               224
  UNIFOCAL                 2               262
[1] 2 2
[1] FALSE
D3V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     0
  3P GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           0     1
  3P GAIN WILD-TYPE                        27   328
D3V16, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1               408 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A45K        TCGA-CE-A13K 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DJ-A13L        TCGA-DJ-A2PR        TCGA-DJ-A3UU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UW        TCGA-DJ-A3V4        TCGA-DJ-A3VI        TCGA-DJ-A3VK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D5        TCGA-EL-A3GQ        TCGA-EL-A3H2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MY        TCGA-EL-A3N3        TCGA-ET-A3BO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-FK-A3SD        TCGA-FY-A76V        TCGA-J8-A3NZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-L6-A4ET        TCGA-MK-A84Z        TCGA-4C-A93U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A2N7        TCGA-BJ-A2N8        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-BJ-A3PR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A3PT        TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A45E        TCGA-BJ-A45F        TCGA-BJ-A45G        TCGA-BJ-A45H 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A4O8        TCGA-BJ-A4O9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CE-A482        TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL        TCGA-DE-A3KN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA        TCGA-DE-A4MB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J        TCGA-DE-A69K 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13T        TCGA-DJ-A13U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13W        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QI        TCGA-DJ-A1QM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A1QO        TCGA-DJ-A1QQ        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PS        TCGA-DJ-A2PT        TCGA-DJ-A2PU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX        TCGA-DJ-A2PY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q7        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN        TCGA-DJ-A3UO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UQ        TCGA-DJ-A3UR        TCGA-DJ-A3US        TCGA-DJ-A3UT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UX        TCGA-DJ-A3UY        TCGA-DJ-A3UZ        TCGA-DJ-A3V2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3V3        TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3V9        TCGA-DJ-A3VD        TCGA-DJ-A3VE        TCGA-DJ-A3VF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A3VM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A4UL        TCGA-DJ-A4UP        TCGA-DJ-A4UQ        TCGA-DJ-A4UR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A4UT        TCGA-DJ-A4UW        TCGA-DJ-A4V0        TCGA-DJ-A4V4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A4V5        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-DO-A2HM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E8-A242        TCGA-E8-A2EA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A3X7        TCGA-E8-A413        TCGA-E8-A414        TCGA-E8-A415 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A416        TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A432 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A433        TCGA-E8-A434        TCGA-E8-A436        TCGA-E8-A437 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-E8-A44M        TCGA-EL-A3CL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CZ        TCGA-EL-A3D1        TCGA-EL-A3D4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3T3        TCGA-EL-A3T6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3T7        TCGA-EL-A3T8        TCGA-EL-A3T9        TCGA-EL-A3TA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3TB        TCGA-EL-A3ZG        TCGA-EL-A3ZH        TCGA-EL-A3ZK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3ZQ        TCGA-EL-A3ZR        TCGA-EL-A3ZS        TCGA-EL-A3ZT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4K9        TCGA-EL-A4KD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4KG        TCGA-EL-A4KH        TCGA-EL-A4KI        TCGA-EM-A22M 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A22O        TCGA-EM-A2OV        TCGA-EM-A3AI        TCGA-ET-A25G 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25R        TCGA-ET-A2MX        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N3        TCGA-ET-A2N4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39K 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39O        TCGA-ET-A39P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A40P        TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A40T        TCGA-ET-A4KN        TCGA-ET-A4KQ        TCGA-FE-A22Z 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG        TCGA-FK-A3SH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3I4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3I5        TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3TY        TCGA-FY-A3W9        TCGA-FY-A3WA        TCGA-FY-A3YR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A4B0        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3O0        TCGA-J8-A3O1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE        TCGA-J8-A3YF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S        TCGA-J8-A4HY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A41F        TCGA-KS-A41I        TCGA-KS-A41J        TCGA-KS-A41L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A4I1        TCGA-KS-A4I3        TCGA-KS-A4I5        TCGA-KS-A4I7 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A4I9        TCGA-KS-A4IB        TCGA-KS-A4IC        TCGA-KS-A4ID 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-L6-A4EP        TCGA-L6-A4EQ        TCGA-L6-A4EU        TCGA-MK-A4N6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-MK-A4N7        TCGA-MK-A4N9        TCGA-QD-A8IV        TCGA-E8-A418 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D3V17, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0   1
  3P GAIN WILD-TYPE  38 359
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    1
  3P GAIN WILD-TYPE   38  359
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               1               359
[1] 2 2
[1] FALSE

Clustering(4) Variable = 4P GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     4   1
  4P GAIN WILD-TYPE 478  15
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5               493 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                15 
$`4P GAIN MUTATED`
TCGA-EM-A1YD TCGA-EM-A22N TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       57.01        10.65        33.63         7.82        29.10 

$`4P GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       31.30        30.84        25.45        30.61        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 
       37.94        57.01       106.62        79.50        98.53        69.57 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        49.51       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX 
       43.36        49.71        83.57       139.00       108.66        57.63 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       52.50        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        91.17        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       72.69        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        61.02        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        53.36        44.15        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       24.30        27.06        23.90        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE 
       48.49        18.05        19.79        19.46        78.61        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       27.02        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       33.24       106.09       107.41       108.46        84.89       123.32 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW 
       79.10        76.64         5.79        87.62        77.82        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       66.77       112.80        39.95        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       48.10       116.09         1.25        20.42        17.82        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
       21.63        17.06        17.36        15.16        23.87        22.49 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04        13.81        14.04        21.60        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46        11.01        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       24.69        22.29         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV 
       40.37         9.50        36.10        32.45        30.21        12.89 
TCGA-E8-A418 
        3.02 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             7.82              0.20 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            57.01            178.29 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            29.10             31.27 
[1] "7.8 - 57.0 (29.1)"  "0.2 - 178.3 (31.3)"
[1] "hr=" "9.3"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  4P GAIN MUTATED         1        1         3        0         0         0
  4P GAIN WILD-TYPE     281       49       108        2        46         6
D4V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 1               281
  STAGE II                1                49
  STAGE III               3               108
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  4P GAIN MUTATED     1   1   3   0
  4P GAIN WILD-TYPE 141 164 164  23
D4V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               1               141
  T2               1               164
  T3               3               164
  T4               0                23
[1] 4 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
  4P GAIN MUTATED     5   0
  4P GAIN WILD-TYPE 220 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      5    0
  4P GAIN WILD-TYPE  220  224
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               5               220
  1               0               224
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   0
  4P GAIN WILD-TYPE 278   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    0
  4P GAIN WILD-TYPE  278    9
D4V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4   1
  4P GAIN WILD-TYPE 361 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    1
  4P GAIN WILD-TYPE  361  133
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               4               361
  MALE                 1               133
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1   2
  4P GAIN WILD-TYPE 179 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    2
  4P GAIN WILD-TYPE  179  301
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                1               179
  YES               2               301
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  4P GAIN MUTATED                0
  4P GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  4P GAIN MUTATED                                               2
  4P GAIN WILD-TYPE                                           354
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  4P GAIN MUTATED                                                                        3
  4P GAIN WILD-TYPE                                                                     97
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  4P GAIN MUTATED                                                                     0
  4P GAIN WILD-TYPE                                                                  36
D4V9, multiclass
                                                                        clus
vv                                                                       4P GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       4P GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4   0
  4P GAIN WILD-TYPE 416  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    0
  4P GAIN WILD-TYPE  416   17
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                4               416
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  4P GAIN MUTATED              1                       0    4
  4P GAIN WILD-TYPE          131                      18  326
                   vv
clus                VERY ADVANCED (T4B)
  4P GAIN MUTATED                     0
  4P GAIN WILD-TYPE                   1
D4V11, multiclass
                         clus
vv                        4P GAIN MUTATED 4P GAIN WILD-TYPE
  MINIMAL (T3)                          1               131
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  4               326
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED     4   0   0   1
  4P GAIN WILD-TYPE 379  51   4  29
D4V12, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               4               379
  R1               0                51
  R2               0                 4
  RX               1                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, continuous
D4V14, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4   1
  4P GAIN WILD-TYPE 221 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    1
  4P GAIN WILD-TYPE  221  263
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  MULTIFOCAL               4               221
  UNIFOCAL                 1               263
[1] 2 2
[1] FALSE
D4V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     0
  4P GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           0     3
  4P GAIN WILD-TYPE                        27   326
D4V16, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                          3               326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V17, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   3
  4P GAIN WILD-TYPE  38 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    3
  4P GAIN WILD-TYPE   38  357
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               357
[1] 2 2
[1] FALSE

Clustering(5) Variable = 4Q GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     4   1
  4Q GAIN WILD-TYPE 478  15
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               493 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                15 
$`4Q GAIN MUTATED`
TCGA-EM-A1YD TCGA-EM-A22N TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       57.01        10.65        33.63         7.82        29.10 

$`4Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       31.30        30.84        25.45        30.61        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 
       37.94        57.01       106.62        79.50        98.53        69.57 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        49.51       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX 
       43.36        49.71        83.57       139.00       108.66        57.63 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       52.50        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        91.17        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       72.69        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        61.02        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        53.36        44.15        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       24.30        27.06        23.90        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE 
       48.49        18.05        19.79        19.46        78.61        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       27.02        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       33.24       106.09       107.41       108.46        84.89       123.32 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW 
       79.10        76.64         5.79        87.62        77.82        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       66.77       112.80        39.95        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       48.10       116.09         1.25        20.42        17.82        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
       21.63        17.06        17.36        15.16        23.87        22.49 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04        13.81        14.04        21.60        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46        11.01        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       24.69        22.29         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV 
       40.37         9.50        36.10        32.45        30.21        12.89 
TCGA-E8-A418 
        3.02 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             7.82              0.20 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            57.01            178.29 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            29.10             31.27 
[1] "7.8 - 57.0 (29.1)"  "0.2 - 178.3 (31.3)"
[1] "hr=" "9.3"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  4Q GAIN MUTATED         1        1         3        0         0         0
  4Q GAIN WILD-TYPE     281       49       108        2        46         6
D5V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 1               281
  STAGE II                1                49
  STAGE III               3               108
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  4Q GAIN MUTATED     1   1   3   0
  4Q GAIN WILD-TYPE 141 164 164  23
D5V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               1               141
  T2               1               164
  T3               3               164
  T4               0                23
[1] 4 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
  4Q GAIN MUTATED     5   0
  4Q GAIN WILD-TYPE 220 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5    0
  4Q GAIN WILD-TYPE  220  224
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               5               220
  1               0               224
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   0
  4Q GAIN WILD-TYPE 278   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    0
  4Q GAIN WILD-TYPE  278    9
D5V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4   1
  4Q GAIN WILD-TYPE 361 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    1
  4Q GAIN WILD-TYPE  361  133
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               4               361
  MALE                 1               133
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1   2
  4Q GAIN WILD-TYPE 179 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    2
  4Q GAIN WILD-TYPE  179  301
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                1               179
  YES               2               301
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  4Q GAIN MUTATED                0
  4Q GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  4Q GAIN MUTATED                                               2
  4Q GAIN WILD-TYPE                                           354
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  4Q GAIN MUTATED                                                                        3
  4Q GAIN WILD-TYPE                                                                     97
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  4Q GAIN MUTATED                                                                     0
  4Q GAIN WILD-TYPE                                                                  36
D5V9, multiclass
                                                                        clus
vv                                                                       4Q GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       4Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4   0
  4Q GAIN WILD-TYPE 416  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    0
  4Q GAIN WILD-TYPE  416   17
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                4               416
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  4Q GAIN MUTATED              1                       0    4
  4Q GAIN WILD-TYPE          131                      18  326
                   vv
clus                VERY ADVANCED (T4B)
  4Q GAIN MUTATED                     0
  4Q GAIN WILD-TYPE                   1
D5V11, multiclass
                         clus
vv                        4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  MINIMAL (T3)                          1               131
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  4               326
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     4   0   0   1
  4Q GAIN WILD-TYPE 379  51   4  29
D5V12, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               4               379
  R1               0                51
  R2               0                 4
  RX               1                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, continuous
D5V14, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4   1
  4Q GAIN WILD-TYPE 221 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    1
  4Q GAIN WILD-TYPE  221  263
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  MULTIFOCAL               4               221
  UNIFOCAL                 1               263
[1] 2 2
[1] FALSE
D5V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           0     3
  4Q GAIN WILD-TYPE                        27   326
D5V16, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                          3               326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V17, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   3
  4Q GAIN WILD-TYPE  38 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    3
  4Q GAIN WILD-TYPE   38  357
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               357
[1] 2 2
[1] FALSE

Clustering(6) Variable = 5P GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    19   2
  5P GAIN WILD-TYPE 463  14
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               21               477 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                14 
$`5P GAIN MUTATED`
TCGA-BJ-A0ZB TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-EL-A3GU TCGA-EL-A3T9 TCGA-EL-A3ZM 
        4.01        20.58        20.48       136.01         5.72        36.03 
TCGA-EL-A3ZO TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO 
       72.69        23.90        78.61        57.01        10.65         6.05 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O3 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       32.32        22.52        14.50        13.51        37.25       123.32 
TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       33.63         7.82        29.10 

$`5P GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       16.34        14.73        41.33        18.87        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 
       25.48        15.12        42.08        51.39        41.52         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.97        11.08        18.38        16.57        18.97        12.82 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 
       11.38        10.68        15.02        12.43        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        27.32        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       52.27        43.17        52.37         8.32        48.07       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.99        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       35.41        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74        43.96 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        39.95        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       36.33        11.34        35.87        40.96        36.99        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       30.61        19.20        23.21        21.27        20.48        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        40.70        18.97         9.60        35.67        36.43 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       23.44        27.62        30.87        30.12        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       80.52        63.19        52.44        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 
       29.98        31.50        31.04        31.30        30.84        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       30.61        31.27        31.33        14.96        39.88        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       31.00        30.15        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
      158.83        60.95       157.15        37.94        57.01       106.62 
TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       79.50        98.53        69.57       108.36        64.87        49.51 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
      115.10        65.39        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      108.66        57.63        52.50        29.65       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       132.07        98.24        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        89.56        91.17        51.78        62.30        53.06 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       27.06        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       17.88        13.18        23.51         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        40.34        19.73        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.46        17.29        14.60        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       15.02        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        63.45        88.41        58.75        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A 
       68.22       117.40        66.77       112.80        39.95        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       17.82        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08        23.31        21.63        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 
       23.87        22.49        19.04        13.81        14.04        21.60 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
       31.10         8.22        25.64        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.24        33.40        40.37         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             4.01              0.20 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           136.01            178.29 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            23.90             31.27 
[1] "4.0 - 136.0 (23.9)" "0.2 - 178.3 (31.3)"
[1] "hr=" "3.5"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  5P GAIN MUTATED         5        5         8        1         2         0
  5P GAIN WILD-TYPE     277       45       103        1        44         6
D6V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 5               277
  STAGE II                5                45
  STAGE III               8               103
  STAGE IV                1                 1
  STAGE IVA               2                44
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  5P GAIN MUTATED     3   7   9   2
  5P GAIN WILD-TYPE 139 158 158  21
D6V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               3               139
  T2               7               158
  T3               9               158
  T4               2                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    11   6
  5P GAIN WILD-TYPE 214 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11    6
  5P GAIN WILD-TYPE  214  218
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              11               214
  1               6               218
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     5   0
  5P GAIN WILD-TYPE 273   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      5    0
  5P GAIN WILD-TYPE  273    9
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0               5               273
  1               0                 9
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    14   7
  5P GAIN WILD-TYPE 351 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     14    7
  5P GAIN WILD-TYPE  351  127
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              14               351
  MALE                 7               127
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     5  13
  5P GAIN WILD-TYPE 175 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      5   13
  5P GAIN WILD-TYPE  175  290
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                5               175
  YES              13               290
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  5P GAIN MUTATED                0
  5P GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  5P GAIN MUTATED                                              13
  5P GAIN WILD-TYPE                                           343
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  5P GAIN MUTATED                                                                        8
  5P GAIN WILD-TYPE                                                                     92
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  5P GAIN MUTATED                                                                     0
  5P GAIN WILD-TYPE                                                                  36
D6V9, multiclass
                                                                        clus
vv                                                                       5P GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       13
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       5P GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        343
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                92
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    20   0
  5P GAIN WILD-TYPE 400  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     20    0
  5P GAIN WILD-TYPE  400   17
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               20               400
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  5P GAIN MUTATED              4                       2   14
  5P GAIN WILD-TYPE          128                      16  316
                   vv
clus                VERY ADVANCED (T4B)
  5P GAIN MUTATED                     1
  5P GAIN WILD-TYPE                   0
D6V11, multiclass
                         clus
vv                        5P GAIN MUTATED 5P GAIN WILD-TYPE
  MINIMAL (T3)                          4               128
  MODERATE/ADVANCED (T4A)               2                16
  NONE                                 14               316
  VERY ADVANCED (T4B)                   1                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED    15   4   0   2
  5P GAIN WILD-TYPE 368  47   4  28
D6V12, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              15               368
  R1               4                47
  R2               0                 4
  RX               2                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, continuous
D6V14, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     8  13
  5P GAIN WILD-TYPE 217 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      8   13
  5P GAIN WILD-TYPE  217  251
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  MULTIFOCAL               8               217
  UNIFOCAL                13               251
[1] 2 2
[1] FALSE
D6V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0     0
  5P GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           0    13
  5P GAIN WILD-TYPE                        27   316
D6V16, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                         13               316
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V17, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1  12
  5P GAIN WILD-TYPE  37 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   12
  5P GAIN WILD-TYPE   37  348
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                37
  NOT HISPANIC OR LATINO              12               348
[1] 2 2
[1] FALSE

Clustering(7) Variable = 5Q GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    15   2
  5Q GAIN WILD-TYPE 467  14
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               17               481 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                14 
$`5Q GAIN MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EL-A3ZM TCGA-EL-A4KI TCGA-EM-A1YC 
       20.58        20.48         5.72        36.03        23.90        78.61 
TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY 
       57.01        10.65         6.05        32.32        22.52        13.51 
TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       37.25       123.32        33.63         7.82        29.10 

$`5Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
       11.31        30.97        11.08        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       12.82        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       21.63        50.17        37.64        27.32        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        52.27        43.17        52.37         8.32        48.07 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       30.58        35.41        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
      107.47        66.90        82.82        89.56        91.17        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       62.30        53.06        72.69        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        61.02 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       47.84        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        48.49        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        44.52         8.35 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        27.02        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.95        29.85        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       88.41        58.75        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW 
       79.10        76.64         5.79        87.62        77.82        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       66.77       112.80        39.95        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       48.10       116.09         1.25        20.42        17.82        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
       21.63        17.06        17.36        15.16        23.87        22.49 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04        13.81        14.04        21.60        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46        11.01        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       24.69        22.29         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV 
       40.37         9.50        36.10        32.45        30.21        12.89 
TCGA-E8-A418 
        3.02 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             5.72              0.20 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           123.32            178.29 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            23.90             31.27 
[1] "5.7 - 123.3 (23.9)" "0.2 - 178.3 (31.3)"
[1] "hr=" "5.2"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  5Q GAIN MUTATED         5        5         5        1         1         0
  5Q GAIN WILD-TYPE     277       45       106        1        45         6
D7V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 5               277
  STAGE II                5                45
  STAGE III               5               106
  STAGE IV                1                 1
  STAGE IVA               1                45
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  5Q GAIN MUTATED     3   6   6   2
  5Q GAIN WILD-TYPE 139 159 161  21
D7V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               3               139
  T2               6               159
  T3               6               161
  T4               2                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    11   2
  5Q GAIN WILD-TYPE 214 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11    2
  5Q GAIN WILD-TYPE  214  222
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              11               214
  1               2               222
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     2   0
  5Q GAIN WILD-TYPE 276   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    0
  5Q GAIN WILD-TYPE  276    9
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               2               276
  1               0                 9
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    11   6
  5Q GAIN WILD-TYPE 354 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11    6
  5Q GAIN WILD-TYPE  354  128
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              11               354
  MALE                 6               128
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     4  10
  5Q GAIN WILD-TYPE 176 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4   10
  5Q GAIN WILD-TYPE  176  293
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                4               176
  YES              10               293
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  5Q GAIN MUTATED                0
  5Q GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  5Q GAIN MUTATED                                               9
  5Q GAIN WILD-TYPE                                           347
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  5Q GAIN MUTATED                                                                        8
  5Q GAIN WILD-TYPE                                                                     92
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  5Q GAIN MUTATED                                                                     0
  5Q GAIN WILD-TYPE                                                                  36
D7V9, multiclass
                                                                        clus
vv                                                                       5Q GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        9
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       5Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                92
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    16   0
  5Q GAIN WILD-TYPE 404  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     16    0
  5Q GAIN WILD-TYPE  404   17
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               16               404
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  5Q GAIN MUTATED              2                       1   13
  5Q GAIN WILD-TYPE          130                      17  317
                   vv
clus                VERY ADVANCED (T4B)
  5Q GAIN MUTATED                     1
  5Q GAIN WILD-TYPE                   0
D7V11, multiclass
                         clus
vv                        5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  MINIMAL (T3)                          2               130
  MODERATE/ADVANCED (T4A)               1                17
  NONE                                 13               317
  VERY ADVANCED (T4B)                   1                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    12   3   0   2
  5Q GAIN WILD-TYPE 371  48   4  28
D7V12, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              12               371
  R1               3                48
  R2               0                 4
  RX               2                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, continuous
D7V14, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     8   9
  5Q GAIN WILD-TYPE 217 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      8    9
  5Q GAIN WILD-TYPE  217  255
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  MULTIFOCAL               8               217
  UNIFOCAL                 9               255
[1] 2 2
[1] FALSE
D7V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     0
  5Q GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           0    10
  5Q GAIN WILD-TYPE                        27   319
D7V16, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                         10               319
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V17, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  10
  5Q GAIN WILD-TYPE  38 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   10
  5Q GAIN WILD-TYPE   38  350
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO              10               350
[1] 2 2
[1] FALSE

Clustering(8) Variable = 7P GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    17   1
  7P GAIN WILD-TYPE 465  15
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18               480 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                1                15 
$`7P GAIN MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-BJ-A45E TCGA-DJ-A2Q0 TCGA-EL-A3T9 TCGA-EL-A3ZM 
       20.58        20.48        21.01        34.36         5.72        36.03 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI 
       78.61        57.01        10.65         6.05        32.32        22.52 
TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 TCGA-FY-A3NM 
        9.24        13.51        37.25       123.32         7.82        29.10 

$`7P GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
       11.31        30.97        11.08        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       12.82        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        7.99        10.88         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 
       11.38        10.68        15.02        12.43        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        27.32        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       52.27        43.17        52.37         8.32        48.07       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.99        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       35.41        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
       28.96         8.78         8.42        37.74        43.96        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       33.53        35.18        39.95        36.92        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        36.33 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        35.87        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       40.70        18.97         9.60        35.67        36.43        23.44 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        30.12        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       63.19        52.44        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 
       31.50        31.04        31.30        30.84        25.45        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       31.27        31.33        14.96        39.88        33.50        31.00 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       30.15        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ 
       60.95       157.15        37.94        57.01       106.62        79.50 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR 
       98.53        69.57       108.36        64.87        49.51       115.10 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       136.01        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      108.66        57.63        52.50        29.65       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       132.07        98.24        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        89.56        91.17        51.78        62.30        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       72.69        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        61.02        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        53.36        44.15        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       24.30        27.06        23.90        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I 
       48.49        18.05        19.79        19.46        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P 
       14.50        15.75        10.45        14.53        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP 
       14.24        47.57        17.88        13.18        23.51         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ 
       33.96        17.59        17.46        17.29        14.60        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR 
       15.68        14.14        33.07        44.52         8.35        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
       12.53        27.02        38.66        38.86        29.95        29.85 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 
      116.09         1.25        20.42        17.82        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
        9.50        36.10        32.45        30.21        12.89         3.02 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             5.72              0.20 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           123.32            178.29 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           21.765            31.285 
[1] "5.7 - 123.3 (21.8)" "0.2 - 178.3 (31.3)"
[1] "hr=" "2.4"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  7P GAIN MUTATED         7        6         3        1         1         0
  7P GAIN WILD-TYPE     275       44       108        1        45         6
D8V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 7               275
  STAGE II                6                44
  STAGE III               3               108
  STAGE IV                1                 1
  STAGE IVA               1                45
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  7P GAIN MUTATED     4   7   5   2
  7P GAIN WILD-TYPE 138 158 162  21
D8V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               4               138
  T2               7               158
  T3               5               162
  T4               2                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    12   2
  7P GAIN WILD-TYPE 213 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     12    2
  7P GAIN WILD-TYPE  213  222
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              12               213
  1               2               222
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     4   0
  7P GAIN WILD-TYPE 274   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4    0
  7P GAIN WILD-TYPE  274    9
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0               4               274
  1               0                 9
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    13   5
  7P GAIN WILD-TYPE 352 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     13    5
  7P GAIN WILD-TYPE  352  129
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              13               352
  MALE                 5               129
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     6   9
  7P GAIN WILD-TYPE 174 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6    9
  7P GAIN WILD-TYPE  174  294
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                6               174
  YES               9               294
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  7P GAIN MUTATED                0
  7P GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  7P GAIN MUTATED                                               9
  7P GAIN WILD-TYPE                                           347
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  7P GAIN MUTATED                                                                        9
  7P GAIN WILD-TYPE                                                                     91
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  7P GAIN MUTATED                                                                     0
  7P GAIN WILD-TYPE                                                                  36
D8V9, multiclass
                                                                        clus
vv                                                                       7P GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        9
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       7P GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    16   0
  7P GAIN WILD-TYPE 404  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     16    0
  7P GAIN WILD-TYPE  404   17
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               16               404
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  7P GAIN MUTATED              1                       1   14
  7P GAIN WILD-TYPE          131                      17  316
                   vv
clus                VERY ADVANCED (T4B)
  7P GAIN MUTATED                     1
  7P GAIN WILD-TYPE                   0
D8V11, multiclass
                         clus
vv                        7P GAIN MUTATED 7P GAIN WILD-TYPE
  MINIMAL (T3)                          1               131
  MODERATE/ADVANCED (T4A)               1                17
  NONE                                 14               316
  VERY ADVANCED (T4B)                   1                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED    12   3   0   2
  7P GAIN WILD-TYPE 371  48   4  28
D8V12, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              12               371
  R1               3                48
  R2               0                 4
  RX               2                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, continuous
D8V14, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     8  10
  7P GAIN WILD-TYPE 217 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8   10
  7P GAIN WILD-TYPE  217  254
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  MULTIFOCAL               8               217
  UNIFOCAL                10               254
[1] 2 2
[1] FALSE
D8V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  0     0
  7P GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                           0    10
  7P GAIN WILD-TYPE                        27   319
D8V16, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                         10               319
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V17, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     0  10
  7P GAIN WILD-TYPE  38 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      0   10
  7P GAIN WILD-TYPE   38  350
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO              10               350
[1] 2 2
[1] FALSE

Clustering(9) Variable = 7Q GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    19   1
  7Q GAIN WILD-TYPE 463  15
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               20               478 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                1                15 
$`7Q GAIN MUTATED`
TCGA-BJ-A190 TCGA-BJ-A192 TCGA-BJ-A2N9 TCGA-BJ-A45E TCGA-DJ-A2Q0 TCGA-EL-A3T9 
       20.58        44.35        20.48        21.01        34.36         5.72 
TCGA-EL-A3ZM TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CJ TCGA-EM-A2CO 
       36.03        78.61        57.01        10.65        47.57         6.05 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       32.32        22.52         9.24        13.51        37.25       123.32 
TCGA-FY-A3I5 TCGA-FY-A3NM 
        7.82        29.10 

$`7Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
        4.83        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.97        11.08        18.38        16.57        18.97        12.82 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
       10.88         3.45        23.84        28.44        15.45        21.63 
TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       19.43        23.47        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       10.68        15.02        12.43        12.66        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        27.32        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12        14.70        14.27         2.76        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        52.27 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        48.07       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.99        30.58        35.41 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42        37.74        43.96        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       37.48        36.46        35.11        39.09        35.90        33.53 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        39.95        36.92        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX 
       16.41        19.56        36.33        32.81        36.33        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 
       35.87        40.96        36.99        20.22        30.61        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        40.70 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         9.60        35.67        36.43        23.44        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       30.87        30.12        33.04        34.78        27.06        26.93 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       35.54         3.12        15.81        35.38        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        92.55        47.21        66.38        80.52        63.19 
TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       52.44        31.23        35.67        31.27        29.98        31.50 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 
       31.04        31.30        30.84        25.45        30.61        31.27 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       31.33        14.96        39.88        33.50        31.00        30.15 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT 
       31.66        26.73       155.54        97.74       158.83        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 
      157.15        37.94        57.01       106.62        79.50        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS 
       69.57       108.36        64.87        49.51       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW 
       49.32        43.36        49.71        83.57       139.00       108.66 
TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       57.63        52.50        29.65       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB 
      132.07        98.24        41.29       107.47        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO 
       89.56        91.17        51.78        62.30        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       18.05        19.79        19.46        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       15.75        10.45        14.53        44.19        41.29        14.24 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       17.88        13.18        23.51         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        40.34        19.73        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.46        17.29        14.60        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        15.06         7.33        12.53        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        63.45        88.41        58.75        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        4.11        22.03         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       20.42        17.82        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08        23.31        21.63        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 
       15.16        23.87        22.49        19.04        13.81        14.04 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       21.83        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       32.45        30.21        12.89         3.02 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             5.72              0.20 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           123.32            178.29 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            25.81             31.27 
[1] "5.7 - 123.3 (25.8)" "0.2 - 178.3 (31.3)"
[1] "hr=" "2.1"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  7Q GAIN MUTATED         8        6         4        1         1         0
  7Q GAIN WILD-TYPE     274       44       107        1        45         6
D9V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 8               274
  STAGE II                6                44
  STAGE III               4               107
  STAGE IV                1                 1
  STAGE IVA               1                45
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  7Q GAIN MUTATED     5   7   6   2
  7Q GAIN WILD-TYPE 137 158 161  21
D9V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               5               137
  T2               7               158
  T3               6               161
  T4               2                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    12   2
  7Q GAIN WILD-TYPE 213 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     12    2
  7Q GAIN WILD-TYPE  213  222
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              12               213
  1               2               222
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     5   0
  7Q GAIN WILD-TYPE 273   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5    0
  7Q GAIN WILD-TYPE  273    9
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0               5               273
  1               0                 9
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    15   5
  7Q GAIN WILD-TYPE 350 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     15    5
  7Q GAIN WILD-TYPE  350  129
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              15               350
  MALE                 5               129
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     8   9
  7Q GAIN WILD-TYPE 172 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8    9
  7Q GAIN WILD-TYPE  172  294
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                8               172
  YES               9               294
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  7Q GAIN MUTATED                0
  7Q GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  7Q GAIN MUTATED                                              10
  7Q GAIN WILD-TYPE                                           346
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  7Q GAIN MUTATED                                                                       10
  7Q GAIN WILD-TYPE                                                                     90
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  7Q GAIN MUTATED                                                                     0
  7Q GAIN WILD-TYPE                                                                  36
D9V9, multiclass
                                                                        clus
vv                                                                       7Q GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       10
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              10
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       7Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        346
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                90
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    18   0
  7Q GAIN WILD-TYPE 402  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     18    0
  7Q GAIN WILD-TYPE  402   17
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               18               402
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  7Q GAIN MUTATED              2                       1   15
  7Q GAIN WILD-TYPE          130                      17  315
                   vv
clus                VERY ADVANCED (T4B)
  7Q GAIN MUTATED                     1
  7Q GAIN WILD-TYPE                   0
D9V11, multiclass
                         clus
vv                        7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  MINIMAL (T3)                          2               130
  MODERATE/ADVANCED (T4A)               1                17
  NONE                                 15               315
  VERY ADVANCED (T4B)                   1                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED    13   3   0   3
  7Q GAIN WILD-TYPE 370  48   4  27
D9V12, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              13               370
  R1               3                48
  R2               0                 4
  RX               3                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, continuous
D9V14, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     9  11
  7Q GAIN WILD-TYPE 216 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      9   11
  7Q GAIN WILD-TYPE  216  253
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  MULTIFOCAL               9               216
  UNIFOCAL                11               253
[1] 2 2
[1] FALSE
D9V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0     0
  7Q GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                           0    11
  7Q GAIN WILD-TYPE                        27   318
D9V16, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                         11               318
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V17, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     0  10
  7Q GAIN WILD-TYPE  38 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      0   10
  7Q GAIN WILD-TYPE   38  350
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO              10               350
[1] 2 2
[1] FALSE

Clustering(10) Variable = 8P GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED     6   0
  8P GAIN WILD-TYPE 476  16
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6               492 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                0                16 
$`8P GAIN MUTATED`
TCGA-ET-A3BV TCGA-EM-A2CO TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 TCGA-L6-A4EP 
       75.42         6.05        37.25       123.32         7.82        33.40 

$`8P GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET 
       50.40         1.05         1.68        17.23         2.60        21.83 
TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       23.93         4.24        24.79        13.78        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 
       25.48        15.12        42.08        51.39        41.52        20.58 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        78.61        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
       23.51         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       27.02        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
      116.09         1.25        20.42        17.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
       21.63        17.06        17.36        15.16        23.87        22.49 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04        13.81        14.04        21.60        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46        11.01        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       24.69        22.29         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EQ 
       32.45        87.39        84.72        35.28        33.24        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
        9.50        36.10        32.45        30.21        12.89         3.02 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             6.05              0.20 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           123.32            178.29 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           35.325            31.165 
[1] "6.0 - 123.3 (35.3)" "0.2 - 178.3 (31.2)"
[1] "hr="     "9100000"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  8P GAIN MUTATED         3        1         2        0         0         0
  8P GAIN WILD-TYPE     279       49       109        2        46         6
D10V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 3               279
  STAGE II                1                49
  STAGE III               2               109
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  8P GAIN MUTATED     1   3   2   0
  8P GAIN WILD-TYPE 141 162 165  23
D10V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               1               141
  T2               3               162
  T3               2               165
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     3   1
  8P GAIN WILD-TYPE 222 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3    1
  8P GAIN WILD-TYPE  222  223
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               3               222
  1               1               223
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1   0
  8P GAIN WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1    0
  8P GAIN WILD-TYPE  277    9
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               1               277
  1               0                 9
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     5   1
  8P GAIN WILD-TYPE 360 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    1
  8P GAIN WILD-TYPE  360  133
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               5               360
  MALE                 1               133
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1   4
  8P GAIN WILD-TYPE 179 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1    4
  8P GAIN WILD-TYPE  179  299
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                1               179
  YES               4               299
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  8P GAIN MUTATED                0
  8P GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  8P GAIN MUTATED                                               4
  8P GAIN WILD-TYPE                                           352
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  8P GAIN MUTATED                                                                        2
  8P GAIN WILD-TYPE                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  8P GAIN MUTATED                                                                     0
  8P GAIN WILD-TYPE                                                                  36
D10V9, multiclass
                                                                        clus
vv                                                                       8P GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       8P GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     5   0
  8P GAIN WILD-TYPE 415  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    0
  8P GAIN WILD-TYPE  415   17
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                5               415
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  8P GAIN MUTATED              0                       0    6
  8P GAIN WILD-TYPE          132                      18  324
                   vv
clus                VERY ADVANCED (T4B)
  8P GAIN MUTATED                     0
  8P GAIN WILD-TYPE                   1
D10V11, multiclass
                         clus
vv                        8P GAIN MUTATED 8P GAIN WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  6               324
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED     5   0   0   1
  8P GAIN WILD-TYPE 378  51   4  29
D10V12, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0               5               378
  R1               0                51
  R2               0                 4
  RX               1                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, continuous
D10V14, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1   5
  8P GAIN WILD-TYPE 224 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1    5
  8P GAIN WILD-TYPE  224  259
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  MULTIFOCAL               1               224
  UNIFOCAL                 5               259
[1] 2 2
[1] FALSE
D10V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     1
  8P GAIN WILD-TYPE                                1    51
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           0     4
  8P GAIN WILD-TYPE                        27   325
D10V16, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                51
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                          4               325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V17, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     0   5
  8P GAIN WILD-TYPE  38 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0    5
  8P GAIN WILD-TYPE   38  355
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               5               355
[1] 2 2
[1] FALSE

Clustering(11) Variable = 8Q GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED     6   1
  8Q GAIN WILD-TYPE 476  15
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7               491 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                15 
$`8Q GAIN MUTATED`
TCGA-ET-A3BV TCGA-EL-A3T9 TCGA-EM-A2CO TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       75.42         5.72         6.05        37.25       123.32         7.82 
TCGA-L6-A4EP 
       33.40 

$`8Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET 
       50.40         1.05         1.68        17.23         2.60        21.83 
TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       23.93         4.24        24.79        13.78        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 
       25.48        15.12        42.08        51.39        41.52        20.58 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29       107.47        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       65.29        18.38        63.45        88.41        58.75        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EQ TCGA-L6-A4EU 
       87.39        84.72        35.28        33.24        40.37         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       36.10        32.45        30.21        12.89         3.02 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             5.72              0.20 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           123.32            178.29 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            33.40             31.23 
[1] "5.7 - 123.3 (33.4)" "0.2 - 178.3 (31.2)"
[1] "hr=" "4.2"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  8Q GAIN MUTATED         3        1         2        1         0         0
  8Q GAIN WILD-TYPE     279       49       109        1        46         6
D11V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 3               279
  STAGE II                1                49
  STAGE III               2               109
  STAGE IV                1                 1
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  8Q GAIN MUTATED     1   3   2   1
  8Q GAIN WILD-TYPE 141 162 165  22
D11V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               1               141
  T2               3               162
  T3               2               165
  T4               1                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"
D11V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     3   2
  8Q GAIN WILD-TYPE 222 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3    2
  8Q GAIN WILD-TYPE  222  222
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0               3               222
  1               2               222
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     1   0
  8Q GAIN WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1    0
  8Q GAIN WILD-TYPE  277    9
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0               1               277
  1               0                 9
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     6   1
  8Q GAIN WILD-TYPE 359 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6    1
  8Q GAIN WILD-TYPE  359  133
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               6               359
  MALE                 1               133
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     1   4
  8Q GAIN WILD-TYPE 179 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1    4
  8Q GAIN WILD-TYPE  179  299
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                1               179
  YES               4               299
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  8Q GAIN MUTATED                0
  8Q GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  8Q GAIN MUTATED                                               5
  8Q GAIN WILD-TYPE                                           351
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  8Q GAIN MUTATED                                                                        2
  8Q GAIN WILD-TYPE                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  8Q GAIN MUTATED                                                                     0
  8Q GAIN WILD-TYPE                                                                  36
D11V9, multiclass
                                                                        clus
vv                                                                       8Q GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       8Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     6   0
  8Q GAIN WILD-TYPE 414  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6    0
  8Q GAIN WILD-TYPE  414   17
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                6               414
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  8Q GAIN MUTATED              0                       0    6
  8Q GAIN WILD-TYPE          132                      18  324
                   vv
clus                VERY ADVANCED (T4B)
  8Q GAIN MUTATED                     1
  8Q GAIN WILD-TYPE                   0
D11V11, multiclass
                         clus
vv                        8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  6               324
  VERY ADVANCED (T4B)                   1                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED     5   1   0   1
  8Q GAIN WILD-TYPE 378  50   4  29
D11V12, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0               5               378
  R1               1                50
  R2               0                 4
  RX               1                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, continuous
D11V14, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     1   6
  8Q GAIN WILD-TYPE 224 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1    6
  8Q GAIN WILD-TYPE  224  258
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  MULTIFOCAL               1               224
  UNIFOCAL                 6               258
[1] 2 2
[1] FALSE
D11V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     1
  8Q GAIN WILD-TYPE                                1    51
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           0     5
  8Q GAIN WILD-TYPE                        27   324
D11V16, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                51
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                          5               324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V17, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     0   6
  8Q GAIN WILD-TYPE  38 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      0    6
  8Q GAIN WILD-TYPE   38  354
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               6               354
[1] 2 2
[1] FALSE

Clustering(12) Variable = 9P GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     3   0
  9P GAIN WILD-TYPE 479  16
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               495 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                16 
$`9P GAIN MUTATED`
TCGA-EL-A4K9 TCGA-EM-A1YD TCGA-FY-A3I5 
       47.84        57.01         7.82 

$`9P GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       31.30        30.84        25.45        30.61        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 
       37.94        57.01       106.62        79.50        98.53        69.57 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        49.51       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX 
       43.36        49.71        83.57       139.00       108.66        57.63 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       52.50        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        91.17        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       72.69        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        61.02        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG 
       30.51        53.36        44.15        41.13        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I 
       18.05        19.79        19.46        78.61        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       27.02        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       33.24       106.09       107.41       108.46        84.89       123.32 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW 
       79.10        76.64         5.79        87.62        77.82        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77       112.80        39.95        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE 
       85.15        85.68        78.77        71.08         4.11        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       29.10        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08        23.31        21.63        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 
       23.87        22.49        19.04        13.81        14.04        21.60 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
       31.10         8.22        25.64        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.24        33.40        40.37         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             7.82              0.20 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            57.01            178.29 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            47.84             31.23 
[1] "7.8 - 57.0 (47.8)"  "0.2 - 178.3 (31.2)"
[1] "hr="     "3300000"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  9P GAIN MUTATED         0        2         1        0         0         0
  9P GAIN WILD-TYPE     282       48       110        2        46         6
D12V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 0               282
  STAGE II                2                48
  STAGE III               1               110
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  9P GAIN MUTATED     0   2   1   0
  9P GAIN WILD-TYPE 142 163 166  23
D12V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               0               142
  T2               2               163
  T3               1               166
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     3   0
  9P GAIN WILD-TYPE 222 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    0
  9P GAIN WILD-TYPE  222  224
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               3               222
  1               0               224
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1   0
  9P GAIN WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1    0
  9P GAIN WILD-TYPE  277    9
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               1               277
  1               0                 9
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2   1
  9P GAIN WILD-TYPE 363 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    1
  9P GAIN WILD-TYPE  363  133
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               2               363
  MALE                 1               133
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1   1
  9P GAIN WILD-TYPE 179 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1    1
  9P GAIN WILD-TYPE  179  302
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                1               179
  YES               1               302
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  9P GAIN MUTATED                0
  9P GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  9P GAIN MUTATED                                               1
  9P GAIN WILD-TYPE                                           355
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  9P GAIN MUTATED                                                                        2
  9P GAIN WILD-TYPE                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  9P GAIN MUTATED                                                                     0
  9P GAIN WILD-TYPE                                                                  36
D12V9, multiclass
                                                                        clus
vv                                                                       9P GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       9P GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        355
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2   0
  9P GAIN WILD-TYPE 418  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    0
  9P GAIN WILD-TYPE  418   17
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                2               418
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  9P GAIN MUTATED              1                       0    2
  9P GAIN WILD-TYPE          131                      18  328
                   vv
clus                VERY ADVANCED (T4B)
  9P GAIN MUTATED                     0
  9P GAIN WILD-TYPE                   1
D12V11, multiclass
                         clus
vv                        9P GAIN MUTATED 9P GAIN WILD-TYPE
  MINIMAL (T3)                          1               131
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  2               328
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED     3   0   0   0
  9P GAIN WILD-TYPE 380  51   4  30
D12V12, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0               3               380
  R1               0                51
  R2               0                 4
  RX               0                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, continuous
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2               384 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A45K        TCGA-CE-A13K 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DJ-A2PR        TCGA-DJ-A3UU        TCGA-DJ-A3UW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3V4        TCGA-DJ-A3VI        TCGA-DJ-A3VK        TCGA-E3-A3E5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CY        TCGA-EL-A3D0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3GQ        TCGA-EL-A3H8        TCGA-EM-A3AQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BV        TCGA-J8-A3NZ        TCGA-J8-A4HW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-4C-A93U        TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZJ        TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A191        TCGA-BJ-A28R        TCGA-BJ-A28T        TCGA-BJ-A28W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A28X        TCGA-BJ-A28Z        TCGA-BJ-A2N8        TCGA-BJ-A2N9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR        TCGA-BJ-A3PU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45G 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A4O8        TCGA-BJ-A4O9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN        TCGA-DE-A4M8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13V        TCGA-DJ-A13W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PO        TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PT        TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PX        TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UM        TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UQ        TCGA-DJ-A3UR        TCGA-DJ-A3UX        TCGA-DJ-A3UZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3V0        TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9        TCGA-DJ-A3VA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3VB        TCGA-DJ-A3VD        TCGA-DJ-A3VF        TCGA-DJ-A3VG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A4UL        TCGA-DJ-A4UP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW        TCGA-DJ-A4V2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A4V5        TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E3-A3E3        TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A414 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A415        TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A436        TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CT        TCGA-EL-A3CU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D6        TCGA-EL-A3GO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3T0        TCGA-EL-A3T1        TCGA-EL-A3T2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3TB        TCGA-EL-A3ZH        TCGA-EL-A3ZK        TCGA-EL-A3ZL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3ZM        TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3ZS        TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4KD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4KG        TCGA-EL-A4KI        TCGA-EM-A1CS        TCGA-EM-A1CT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22N        TCGA-EM-A22O 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A22P        TCGA-EM-A22Q        TCGA-EM-A2CK        TCGA-EM-A2CN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CT        TCGA-EM-A2CU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OX        TCGA-EM-A2OY        TCGA-EM-A2OZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2P0        TCGA-EM-A2P1        TCGA-EM-A2P2        TCGA-EM-A3AJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3AK        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3AR        TCGA-EM-A3FJ        TCGA-EM-A3FK        TCGA-EM-A3FM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O8        TCGA-EM-A3O9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST        TCGA-EM-A3SU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3SX        TCGA-EM-A3SZ        TCGA-EM-A4FF        TCGA-EM-A4FM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ        TCGA-EM-A4FR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G        TCGA-ET-A25I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A2MX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39K        TCGA-ET-A39L        TCGA-ET-A39O        TCGA-ET-A39P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BX        TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A40P        TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A40T        TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A3PD        TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FK-A3SG        TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3R6        TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-H2-A3RI        TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IM-A3ED        TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IM-A41Z        TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3O0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I        TCGA-KS-A41J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3        TCGA-KS-A4I5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB        TCGA-KS-A4IC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ        TCGA-L6-A4EU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9        TCGA-QD-A8IV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D12V14, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2   1
  9P GAIN WILD-TYPE 223 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    1
  9P GAIN WILD-TYPE  223  263
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  MULTIFOCAL               2               223
  UNIFOCAL                 1               263
[1] 2 2
[1] FALSE
D12V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     0
  9P GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           0     2
  9P GAIN WILD-TYPE                        27   327
D12V16, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2               407 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A45K        TCGA-CE-A13K 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DJ-A13L        TCGA-DJ-A2PR        TCGA-DJ-A3UU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UW        TCGA-DJ-A3V4        TCGA-DJ-A3VI        TCGA-DJ-A3VK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D5        TCGA-EL-A3GQ        TCGA-EL-A3H2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MY        TCGA-EL-A3N3        TCGA-ET-A3BO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-FK-A3SD        TCGA-FY-A76V        TCGA-J8-A3NZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-L6-A4ET        TCGA-MK-A84Z        TCGA-4C-A93U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A2N7        TCGA-BJ-A2N8        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-BJ-A3PR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A3PT        TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A45E        TCGA-BJ-A45F        TCGA-BJ-A45G        TCGA-BJ-A45H 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A4O8        TCGA-BJ-A4O9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CE-A482        TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL        TCGA-DE-A3KN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA        TCGA-DE-A4MB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J        TCGA-DE-A69K 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13T        TCGA-DJ-A13U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13W        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QI        TCGA-DJ-A1QM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A1QO        TCGA-DJ-A1QQ        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PS        TCGA-DJ-A2PT        TCGA-DJ-A2PU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX        TCGA-DJ-A2PY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q7        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN        TCGA-DJ-A3UO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UQ        TCGA-DJ-A3UR        TCGA-DJ-A3US        TCGA-DJ-A3UT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UX        TCGA-DJ-A3UY        TCGA-DJ-A3UZ        TCGA-DJ-A3V2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3V3        TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3V9        TCGA-DJ-A3VD        TCGA-DJ-A3VE        TCGA-DJ-A3VF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A3VM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A4UL        TCGA-DJ-A4UP        TCGA-DJ-A4UQ        TCGA-DJ-A4UR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A4UT        TCGA-DJ-A4UW        TCGA-DJ-A4V0        TCGA-DJ-A4V4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A4V5        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-DO-A2HM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E8-A242        TCGA-E8-A2EA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A3X7        TCGA-E8-A413        TCGA-E8-A414        TCGA-E8-A415 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A416        TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A432 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A433        TCGA-E8-A434        TCGA-E8-A436        TCGA-E8-A437 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-E8-A44M        TCGA-EL-A3CL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CZ        TCGA-EL-A3D1        TCGA-EL-A3D4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3T0        TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3T3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3T6        TCGA-EL-A3T7        TCGA-EL-A3T8        TCGA-EL-A3T9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3TA        TCGA-EL-A3TB        TCGA-EL-A3ZG        TCGA-EL-A3ZH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3ZK        TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3ZP        TCGA-EL-A3ZQ        TCGA-EL-A3ZR        TCGA-EL-A3ZS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3ZT        TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4KD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4KG        TCGA-EL-A4KH        TCGA-EL-A4KI        TCGA-EM-A22M 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A22O        TCGA-EM-A2OV        TCGA-EM-A3AI        TCGA-ET-A25G 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A25R        TCGA-ET-A2MX        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N3        TCGA-ET-A2N4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39K 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39O        TCGA-ET-A39P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A40P        TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A40T        TCGA-ET-A4KN        TCGA-ET-A4KQ        TCGA-FE-A22Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG        TCGA-FK-A3SH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3I4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6        TCGA-FY-A3R7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA        TCGA-FY-A3TY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3WA        TCGA-FY-A3YR        TCGA-FY-A40K 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6        TCGA-H2-A26U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI        TCGA-H2-A421 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-IM-A3U2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z        TCGA-IM-A420 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IM-A4EB        TCGA-J8-A3O0        TCGA-J8-A3O1        TCGA-J8-A3O2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J8-A3YD        TCGA-J8-A3YE        TCGA-J8-A3YF        TCGA-J8-A3YG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J8-A3YH        TCGA-J8-A42S        TCGA-J8-A4HY        TCGA-KS-A41F 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A41I        TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A4I3        TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A4IB        TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-L6-A4EQ        TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-MK-A4N9        TCGA-QD-A8IV        TCGA-E8-A418 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D12V17, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0   2
  9P GAIN WILD-TYPE  38 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    2
  9P GAIN WILD-TYPE   38  358
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               358
[1] 2 2
[1] FALSE

Clustering(13) Variable = 9Q GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     4   0
  9Q GAIN WILD-TYPE 478  16
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               494 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                16 
$`9Q GAIN MUTATED`
TCGA-DJ-A2PW TCGA-EL-A4K9 TCGA-EM-A1YD TCGA-FY-A3I5 
       34.85        47.84        57.01         7.82 

$`9Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       33.96        31.99        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       53.36        44.15        41.13        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP 
       95.34        94.13        55.10        98.20        28.24        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        87.62        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10       116.09         1.25        20.42        17.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             7.82              0.20 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            57.01            178.29 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           41.345            31.165 
[1] "7.8 - 57.0 (41.3)"  "0.2 - 178.3 (31.2)"
[1] "hr="     "3300000"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  9Q GAIN MUTATED         0        2         2        0         0         0
  9Q GAIN WILD-TYPE     282       48       109        2        46         6
D13V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 0               282
  STAGE II                2                48
  STAGE III               2               109
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  9Q GAIN MUTATED     0   2   2   0
  9Q GAIN WILD-TYPE 142 163 165  23
D13V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               0               142
  T2               2               163
  T3               2               165
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3   1
  9Q GAIN WILD-TYPE 222 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    1
  9Q GAIN WILD-TYPE  222  223
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               3               222
  1               1               223
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2   0
  9Q GAIN WILD-TYPE 276   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    0
  9Q GAIN WILD-TYPE  276    9
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               2               276
  1               0                 9
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2   2
  9Q GAIN WILD-TYPE 363 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    2
  9Q GAIN WILD-TYPE  363  132
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               2               363
  MALE                 2               132
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1   2
  9Q GAIN WILD-TYPE 179 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1    2
  9Q GAIN WILD-TYPE  179  301
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1               179
  YES               2               301
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  9Q GAIN MUTATED                0
  9Q GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  9Q GAIN MUTATED                                               2
  9Q GAIN WILD-TYPE                                           354
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  9Q GAIN MUTATED                                                                        2
  9Q GAIN WILD-TYPE                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  9Q GAIN MUTATED                                                                     0
  9Q GAIN WILD-TYPE                                                                  36
D13V9, multiclass
                                                                        clus
vv                                                                       9Q GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       9Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3   0
  9Q GAIN WILD-TYPE 417  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    0
  9Q GAIN WILD-TYPE  417   17
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                3               417
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  9Q GAIN MUTATED              1                       0    3
  9Q GAIN WILD-TYPE          131                      18  327
                   vv
clus                VERY ADVANCED (T4B)
  9Q GAIN MUTATED                     0
  9Q GAIN WILD-TYPE                   1
D13V11, multiclass
                         clus
vv                        9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  MINIMAL (T3)                          1               131
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  3               327
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED     4   0   0   0
  9Q GAIN WILD-TYPE 379  51   4  30
D13V12, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               4               379
  R1               0                51
  R2               0                 4
  RX               0                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, continuous
D13V14, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3   1
  9Q GAIN WILD-TYPE 222 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    1
  9Q GAIN WILD-TYPE  222  263
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  MULTIFOCAL               3               222
  UNIFOCAL                 1               263
[1] 2 2
[1] FALSE
D13V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     0
  9Q GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           0     3
  9Q GAIN WILD-TYPE                        27   326
D13V16, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                          3               326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V17, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0   3
  9Q GAIN WILD-TYPE  38 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    3
  9Q GAIN WILD-TYPE   38  357
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               357
[1] 2 2
[1] FALSE

Clustering(14) Variable = 11P GAIN MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     6   0
  11P GAIN WILD-TYPE 476  16
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                492 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                 16 
$`11P GAIN MUTATED`
TCGA-EL-A3ZR TCGA-EM-A1YC TCGA-EM-A2P2 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       60.16        78.61        17.29        13.51        37.25       123.32 

$`11P GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       31.30        30.84        25.45        30.61        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 
       37.94        57.01       106.62        79.50        98.53        69.57 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        49.51       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX 
       43.36        49.71        83.57       139.00       108.66        57.63 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       52.50        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        91.17        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       72.69        65.49        61.22         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       18.05        19.79        19.46        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        63.45        88.41        58.75        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        4.11        22.03         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
       20.42        17.82         7.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
        9.50        36.10        32.45        30.21        12.89         3.02 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             13.51               0.20 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            123.32             178.29 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            48.705             31.165 
[1] "13.5 - 123.3 (48.7)" "0.2 - 178.3 (31.2)" 
[1] "hr="     "9200000"
D14V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  11P GAIN MUTATED         3        1         2        0         0         0
  11P GAIN WILD-TYPE     279       49       109        2        46         6
D14V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  3                279
  STAGE II                 1                 49
  STAGE III                2                109
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  11P GAIN MUTATED     2   1   3   0
  11P GAIN WILD-TYPE 140 164 164  23
D14V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                2                140
  T2                1                164
  T3                3                164
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     4   0
  11P GAIN WILD-TYPE 221 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4    0
  11P GAIN WILD-TYPE  221  224
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                4                221
  1                0                224
[1] 2 2
[1] FALSE
D14V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1   0
  11P GAIN WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    0
  11P GAIN WILD-TYPE  277    9
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                1                277
  1                0                  9
[1] 2 2
[1] FALSE
D14V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     3   3
  11P GAIN WILD-TYPE 362 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    3
  11P GAIN WILD-TYPE  362  131
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                3                362
  MALE                  3                131
[1] 2 2
[1] FALSE
D14V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     2   4
  11P GAIN WILD-TYPE 178 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    4
  11P GAIN WILD-TYPE  178  299
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 2                178
  YES                4                299
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  11P GAIN MUTATED                0
  11P GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  11P GAIN MUTATED                                               3
  11P GAIN WILD-TYPE                                           353
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  11P GAIN MUTATED                                                                        3
  11P GAIN WILD-TYPE                                                                     97
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  11P GAIN MUTATED                                                                     0
  11P GAIN WILD-TYPE                                                                  36
D14V9, multiclass
                                                                        clus
vv                                                                       11P GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       11P GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     6   0
  11P GAIN WILD-TYPE 414  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6    0
  11P GAIN WILD-TYPE  414   17
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 6                414
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  11P GAIN MUTATED              0                       0    6
  11P GAIN WILD-TYPE          132                      18  324
                    vv
clus                 VERY ADVANCED (T4B)
  11P GAIN MUTATED                     0
  11P GAIN WILD-TYPE                   1
D14V11, multiclass
                         clus
vv                        11P GAIN MUTATED 11P GAIN WILD-TYPE
  MINIMAL (T3)                           0                132
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   6                324
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED     5   0   0   1
  11P GAIN WILD-TYPE 378  51   4  29
D14V12, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                5                378
  R1                0                 51
  R2                0                  4
  RX                1                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, continuous
D14V14, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1   5
  11P GAIN WILD-TYPE 224 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    5
  11P GAIN WILD-TYPE  224  259
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  MULTIFOCAL                1                224
  UNIFOCAL                  5                259
[1] 2 2
[1] FALSE
D14V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     0
  11P GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           0     3
  11P GAIN WILD-TYPE                        27   326
D14V16, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           3                326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V17, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0   3
  11P GAIN WILD-TYPE  38 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    3
  11P GAIN WILD-TYPE   38  357
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                3                357
[1] 2 2
[1] FALSE

Clustering(15) Variable = 11Q GAIN MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     5   0
  11Q GAIN WILD-TYPE 477  16
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                493 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                 16 
$`11Q GAIN MUTATED`
TCGA-EL-A3ZR TCGA-EM-A1YC TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       60.16        78.61        13.51        37.25       123.32 

$`11Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       31.30        30.84        25.45        30.61        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 
       37.94        57.01       106.62        79.50        98.53        69.57 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        49.51       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX 
       43.36        49.71        83.57       139.00       108.66        57.63 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       52.50        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        91.17        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       72.69        65.49        61.22         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       18.05        19.79        19.46        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       27.02        38.66        38.86        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       65.29        18.38        63.45        88.41        58.75        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25        20.42        17.82         7.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
       21.63        17.06        17.36        15.16        23.87        22.49 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04        13.81        14.04        21.60        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46        11.01        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       24.69        22.29         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV 
       40.37         9.50        36.10        32.45        30.21        12.89 
TCGA-E8-A418 
        3.02 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             13.51               0.20 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            123.32             178.29 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             60.16              31.10 
[1] "13.5 - 123.3 (60.2)" "0.2 - 178.3 (31.1)" 
[1] "hr="     "9200000"
D15V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  11Q GAIN MUTATED         3        1         1        0         0         0
  11Q GAIN WILD-TYPE     279       49       110        2        46         6
D15V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  3                279
  STAGE II                 1                 49
  STAGE III                1                110
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  11Q GAIN MUTATED     2   1   2   0
  11Q GAIN WILD-TYPE 140 164 165  23
D15V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                2                140
  T2                1                164
  T3                2                165
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3   0
  11Q GAIN WILD-TYPE 222 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    0
  11Q GAIN WILD-TYPE  222  224
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                3                222
  1                0                224
[1] 2 2
[1] FALSE
D15V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1   0
  11Q GAIN WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    0
  11Q GAIN WILD-TYPE  277    9
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                1                277
  1                0                  9
[1] 2 2
[1] FALSE
D15V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3   2
  11Q GAIN WILD-TYPE 362 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    2
  11Q GAIN WILD-TYPE  362  132
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                362
  MALE                  2                132
[1] 2 2
[1] FALSE
D15V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     2   3
  11Q GAIN WILD-TYPE 178 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    3
  11Q GAIN WILD-TYPE  178  300
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 2                178
  YES                3                300
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  11Q GAIN MUTATED                0
  11Q GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  11Q GAIN MUTATED                                               3
  11Q GAIN WILD-TYPE                                           353
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  11Q GAIN MUTATED                                                                        2
  11Q GAIN WILD-TYPE                                                                     98
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  11Q GAIN MUTATED                                                                     0
  11Q GAIN WILD-TYPE                                                                  36
D15V9, multiclass
                                                                        clus
vv                                                                       11Q GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       11Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     5   0
  11Q GAIN WILD-TYPE 415  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    0
  11Q GAIN WILD-TYPE  415   17
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 5                415
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  11Q GAIN MUTATED              0                       0    5
  11Q GAIN WILD-TYPE          132                      18  325
                    vv
clus                 VERY ADVANCED (T4B)
  11Q GAIN MUTATED                     0
  11Q GAIN WILD-TYPE                   1
D15V11, multiclass
                         clus
vv                        11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  MINIMAL (T3)                           0                132
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   5                325
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED     4   0   0   1
  11Q GAIN WILD-TYPE 379  51   4  29
D15V12, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                4                379
  R1                0                 51
  R2                0                  4
  RX                1                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                384 
        TCGA-BJ-A290         TCGA-BJ-A291         TCGA-BJ-A45K 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CE-A13K         TCGA-DE-A0XZ         TCGA-DJ-A2PR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UU         TCGA-DJ-A3UW         TCGA-DJ-A3V4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VI         TCGA-DJ-A3VK         TCGA-E3-A3E5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3CR         TCGA-EL-A3CS         TCGA-EL-A3CY 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3D0         TCGA-EL-A3D5         TCGA-EL-A3GQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3H8         TCGA-EM-A3AQ         TCGA-ET-A3BO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-J8-A3NZ         TCGA-J8-A4HW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-4C-A93U         TCGA-BJ-A0Z0         TCGA-BJ-A0Z3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A0Z5         TCGA-BJ-A0Z9         TCGA-BJ-A0ZA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZB         TCGA-BJ-A0ZH         TCGA-BJ-A0ZJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A190 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A191         TCGA-BJ-A28R         TCGA-BJ-A28T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A28W         TCGA-BJ-A28X         TCGA-BJ-A28Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A2N8         TCGA-BJ-A2N9         TCGA-BJ-A2NA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A3EZ         TCGA-BJ-A3PR         TCGA-BJ-A3PU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A45C         TCGA-BJ-A45D         TCGA-BJ-A45E 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A45G         TCGA-BJ-A45I         TCGA-BJ-A45J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A4O8         TCGA-BJ-A4O9         TCGA-CE-A3MD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CE-A483         TCGA-CE-A484         TCGA-CE-A485 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DE-A0Y2         TCGA-DE-A0Y3         TCGA-DE-A3KN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DE-A4M8         TCGA-DE-A4MA         TCGA-DE-A4MB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DE-A4MC         TCGA-DE-A4MD         TCGA-DE-A69K 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DE-A7U5         TCGA-DJ-A13M         TCGA-DJ-A13O 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A13R         TCGA-DJ-A13T         TCGA-DJ-A13V 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A13W         TCGA-DJ-A13X         TCGA-DJ-A1QG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QH         TCGA-DJ-A1QM         TCGA-DJ-A2PO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PP         TCGA-DJ-A2PQ         TCGA-DJ-A2PS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PT         TCGA-DJ-A2PU         TCGA-DJ-A2PV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PW         TCGA-DJ-A2PX         TCGA-DJ-A2PY 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PZ         TCGA-DJ-A2Q0         TCGA-DJ-A2Q1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q2         TCGA-DJ-A2Q3         TCGA-DJ-A2Q4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q8         TCGA-DJ-A2Q9         TCGA-DJ-A2QA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2QB         TCGA-DJ-A3UK         TCGA-DJ-A3UM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UN         TCGA-DJ-A3UO         TCGA-DJ-A3UP 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UQ         TCGA-DJ-A3UR         TCGA-DJ-A3UX 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UZ         TCGA-DJ-A3V0         TCGA-DJ-A3V2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V3         TCGA-DJ-A3V5         TCGA-DJ-A3V7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V8         TCGA-DJ-A3V9         TCGA-DJ-A3VA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VB         TCGA-DJ-A3VD         TCGA-DJ-A3VF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VG         TCGA-DJ-A3VJ         TCGA-DJ-A3VL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A4UL         TCGA-DJ-A4UP         TCGA-DJ-A4UQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A4UR         TCGA-DJ-A4UW         TCGA-DJ-A4V2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A4V5         TCGA-DO-A1K0         TCGA-DO-A2HM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E3-A3DY         TCGA-E3-A3DZ         TCGA-E3-A3E0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E3-A3E1         TCGA-E3-A3E2         TCGA-E3-A3E3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E8-A242         TCGA-E8-A2EA         TCGA-E8-A414 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E8-A415         TCGA-E8-A417         TCGA-E8-A419 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E8-A433         TCGA-E8-A436         TCGA-E8-A438 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E8-A44K         TCGA-EL-A3CM         TCGA-EL-A3CN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3CO         TCGA-EL-A3CT         TCGA-EL-A3CU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D1         TCGA-EL-A3D4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3D6         TCGA-EL-A3GO         TCGA-EL-A3GP 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3GS         TCGA-EL-A3GU         TCGA-EL-A3GV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3GX         TCGA-EL-A3H3         TCGA-EL-A3H4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3MW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3MX         TCGA-EL-A3MZ         TCGA-EL-A3N2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3T0         TCGA-EL-A3T1         TCGA-EL-A3T2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3TB         TCGA-EL-A3ZH         TCGA-EL-A3ZK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZL         TCGA-EL-A3ZM         TCGA-EL-A3ZN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZO         TCGA-EL-A3ZP         TCGA-EL-A3ZS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A4JV         TCGA-EL-A4JW         TCGA-EL-A4JX 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A4JZ         TCGA-EL-A4K0         TCGA-EL-A4K1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A4K2         TCGA-EL-A4K4         TCGA-EL-A4K6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A4K7         TCGA-EL-A4KD         TCGA-EL-A4KG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A4KI         TCGA-EM-A1CS         TCGA-EM-A1CT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A1CU         TCGA-EM-A1CV         TCGA-EM-A1CW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A1YD         TCGA-EM-A1YE         TCGA-EM-A22I 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A22J         TCGA-EM-A22K         TCGA-EM-A22L 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22N         TCGA-EM-A22O 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A22P         TCGA-EM-A22Q         TCGA-EM-A2CK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A2CN         TCGA-EM-A2CP         TCGA-EM-A2CQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A2CT         TCGA-EM-A2CU         TCGA-EM-A2OV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A2OX         TCGA-EM-A2OY         TCGA-EM-A2OZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A2P0         TCGA-EM-A2P1         TCGA-EM-A2P2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3AJ         TCGA-EM-A3AK         TCGA-EM-A3AL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3AN         TCGA-EM-A3AO         TCGA-EM-A3AR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3FJ         TCGA-EM-A3FK         TCGA-EM-A3FM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3FN         TCGA-EM-A3FO         TCGA-EM-A3FP 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3FQ         TCGA-EM-A3FR         TCGA-EM-A3O3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3O8         TCGA-EM-A3O9         TCGA-EM-A3OA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3OB         TCGA-EM-A3ST         TCGA-EM-A3SU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3SX         TCGA-EM-A3SZ         TCGA-EM-A4FF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A4FM         TCGA-EM-A4FN         TCGA-EM-A4FO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A4FQ         TCGA-EM-A4FR         TCGA-EM-A4FV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A4G1         TCGA-ET-A25G         TCGA-ET-A25I 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A25J         TCGA-ET-A25K         TCGA-ET-A25L 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25N         TCGA-ET-A25O 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A25P         TCGA-ET-A2MX         TCGA-ET-A2N0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N4         TCGA-ET-A39K 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A39L         TCGA-ET-A39O         TCGA-ET-A39P 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39S         TCGA-ET-A39T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A3BP         TCGA-ET-A3BQ         TCGA-ET-A3BS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A3BT         TCGA-ET-A3BU         TCGA-ET-A3BX 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A3DQ         TCGA-ET-A3DR         TCGA-ET-A3DS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DU         TCGA-ET-A3DV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-ET-A40P         TCGA-ET-A40Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A40R         TCGA-ET-A40S         TCGA-ET-A40T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A4KN         TCGA-FE-A22Z         TCGA-FE-A230 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FE-A231         TCGA-FE-A232         TCGA-FE-A233 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FE-A234         TCGA-FE-A235         TCGA-FE-A236 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FE-A237         TCGA-FE-A238         TCGA-FE-A239 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FE-A23A         TCGA-FE-A3PB         TCGA-FE-A3PC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FE-A3PD         TCGA-FK-A3S3         TCGA-FK-A3SB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FK-A3SE         TCGA-FK-A3SG         TCGA-FK-A3SH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FK-A4UB         TCGA-FY-A2QD         TCGA-FY-A3I4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FY-A3I5         TCGA-FY-A3NM         TCGA-FY-A3NN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FY-A3ON         TCGA-FY-A3R6         TCGA-FY-A3R7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FY-A3R9         TCGA-FY-A3TY         TCGA-FY-A3W9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FY-A3YR         TCGA-FY-A40K         TCGA-FY-A40L 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FY-A40M         TCGA-FY-A40N         TCGA-FY-A4B3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FY-A4B4         TCGA-GE-A2C6         TCGA-H2-A26U 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-H2-A2K9         TCGA-H2-A3RH         TCGA-H2-A3RI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-H2-A421         TCGA-H2-A422         TCGA-IM-A3EB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IM-A3ED         TCGA-IM-A3U2         TCGA-IM-A3U3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IM-A41Y         TCGA-IM-A41Z         TCGA-IM-A420 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IM-A4EB         TCGA-J8-A3O0         TCGA-J8-A3O1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-J8-A3O2         TCGA-J8-A3YD         TCGA-J8-A3YE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-J8-A3YF         TCGA-J8-A3YG         TCGA-J8-A3YH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-J8-A42S         TCGA-J8-A4HY         TCGA-KS-A41F 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KS-A41I         TCGA-KS-A41J         TCGA-KS-A41L 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KS-A4I1         TCGA-KS-A4I3         TCGA-KS-A4I5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KS-A4I7         TCGA-KS-A4I9         TCGA-KS-A4IB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KS-A4IC         TCGA-KS-A4ID         TCGA-L6-A4EP 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-L6-A4EQ         TCGA-L6-A4EU         TCGA-MK-A4N6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MK-A4N7         TCGA-MK-A4N9         TCGA-QD-A8IV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D15V14, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0   5
  11Q GAIN WILD-TYPE 225 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    5
  11Q GAIN WILD-TYPE  225  259
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  MULTIFOCAL                0                225
  UNIFOCAL                  5                259
[1] 2 2
[1] FALSE
D15V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     0
  11Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           0     3
  11Q GAIN WILD-TYPE                        27   326
D15V16, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           3                326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V17, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0   3
  11Q GAIN WILD-TYPE  38 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    3
  11Q GAIN WILD-TYPE   38  357
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                3                357
[1] 2 2
[1] FALSE

Clustering(16) Variable = 12P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    15   0
  12P GAIN WILD-TYPE 467  16
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                483 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                 16 
$`12P GAIN MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO 
       20.58        20.48        78.61        57.01        10.65         6.05 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-ET-A3DS 
       32.32        22.52        13.51        37.25       123.32        66.84 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3WA 
        7.82        29.10        17.06 

$`12P GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
       11.31        30.97        11.08        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       12.82        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       21.63        50.17        37.64        27.32        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        52.27        43.17        52.37         8.32        48.07 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       30.58        35.41        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       17.88        13.18        23.51         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        40.34        19.73        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.46        17.29        14.60        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       27.02        38.66        38.86        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       65.29        18.38        63.45        88.41        58.75        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       84.85        80.58        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        4.11        22.03         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       20.42        17.82        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3YR TCGA-FY-A40K 
       16.57        18.08        23.31        21.63        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 
       23.87        22.49        19.04        13.81        14.04        21.60 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
       31.10         8.22        25.64        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.24        33.40        40.37         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              6.05               0.20 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            123.32             178.29 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             22.52              31.27 
[1] "6.0 - 123.3 (22.5)" "0.2 - 178.3 (31.3)"
[1] "hr="     "2.5e+07"
D16V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  12P GAIN MUTATED         7        5         3        0         0         0
  12P GAIN WILD-TYPE     275       45       108        2        46         6
D16V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  7                275
  STAGE II                 5                 45
  STAGE III                3                108
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  12P GAIN MUTATED     5   6   4   0
  12P GAIN WILD-TYPE 137 159 163  23
D16V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                5                137
  T2                6                159
  T3                4                163
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    10   0
  12P GAIN WILD-TYPE 215 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     10    0
  12P GAIN WILD-TYPE  215  224
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               10                215
  1                0                224
[1] 2 2
[1] FALSE
D16V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     1   0
  12P GAIN WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    0
  12P GAIN WILD-TYPE  277    9
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                1                277
  1                0                  9
[1] 2 2
[1] FALSE
D16V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    12   3
  12P GAIN WILD-TYPE 353 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     12    3
  12P GAIN WILD-TYPE  353  131
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               12                353
  MALE                  3                131
[1] 2 2
[1] FALSE
D16V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     6   7
  12P GAIN WILD-TYPE 174 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6    7
  12P GAIN WILD-TYPE  174  296
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 6                174
  YES                7                296
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  12P GAIN MUTATED                0
  12P GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  12P GAIN MUTATED                                               6
  12P GAIN WILD-TYPE                                           350
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  12P GAIN MUTATED                                                                        9
  12P GAIN WILD-TYPE                                                                     91
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  12P GAIN MUTATED                                                                     0
  12P GAIN WILD-TYPE                                                                  36
D16V9, multiclass
                                                                        clus
vv                                                                       12P GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       12P GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    14   0
  12P GAIN WILD-TYPE 406  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     14    0
  12P GAIN WILD-TYPE  406   17
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                14                406
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  12P GAIN MUTATED              1                       0   14
  12P GAIN WILD-TYPE          131                      18  316
                    vv
clus                 VERY ADVANCED (T4B)
  12P GAIN MUTATED                     0
  12P GAIN WILD-TYPE                   1
D16V11, multiclass
                         clus
vv                        12P GAIN MUTATED 12P GAIN WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                  14                316
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    12   1   0   2
  12P GAIN WILD-TYPE 371  50   4  28
D16V12, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               12                371
  R1                1                 50
  R2                0                  4
  RX                2                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, continuous
D16V14, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     7   8
  12P GAIN WILD-TYPE 218 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7    8
  12P GAIN WILD-TYPE  218  256
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  MULTIFOCAL                7                218
  UNIFOCAL                  8                256
[1] 2 2
[1] FALSE
D16V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     0
  12P GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                           0     9
  12P GAIN WILD-TYPE                        27   320
D16V16, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           9                320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V17, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0   9
  12P GAIN WILD-TYPE  38 351
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0    9
  12P GAIN WILD-TYPE   38  351
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                9                351
[1] 2 2
[1] FALSE

Clustering(17) Variable = 12Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    15   0
  12Q GAIN WILD-TYPE 467  16
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                483 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                 16 
$`12Q GAIN MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO 
       20.58        20.48        78.61        57.01        10.65         6.05 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-ET-A3DS 
       32.32        22.52        13.51        37.25       123.32        66.84 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3WA 
        7.82        29.10        17.06 

$`12Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
       11.31        30.97        11.08        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       12.82        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       21.63        50.17        37.64        27.32        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        52.27        43.17        52.37         8.32        48.07 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       30.58        35.41        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       17.88        13.18        23.51         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        40.34        19.73        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.46        17.29        14.60        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       27.02        38.66        38.86        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       65.29        18.38        63.45        88.41        58.75        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       84.85        80.58        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        4.11        22.03         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       20.42        17.82        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3YR TCGA-FY-A40K 
       16.57        18.08        23.31        21.63        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 
       23.87        22.49        19.04        13.81        14.04        21.60 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
       31.10         8.22        25.64        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.24        33.40        40.37         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              6.05               0.20 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            123.32             178.29 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             22.52              31.27 
[1] "6.0 - 123.3 (22.5)" "0.2 - 178.3 (31.3)"
[1] "hr="     "2.5e+07"
D17V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  12Q GAIN MUTATED         7        5         3        0         0         0
  12Q GAIN WILD-TYPE     275       45       108        2        46         6
D17V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  7                275
  STAGE II                 5                 45
  STAGE III                3                108
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  12Q GAIN MUTATED     5   6   4   0
  12Q GAIN WILD-TYPE 137 159 163  23
D17V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                5                137
  T2                6                159
  T3                4                163
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    10   0
  12Q GAIN WILD-TYPE 215 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     10    0
  12Q GAIN WILD-TYPE  215  224
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               10                215
  1                0                224
[1] 2 2
[1] FALSE
D17V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1   0
  12Q GAIN WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    0
  12Q GAIN WILD-TYPE  277    9
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                1                277
  1                0                  9
[1] 2 2
[1] FALSE
D17V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    12   3
  12Q GAIN WILD-TYPE 353 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     12    3
  12Q GAIN WILD-TYPE  353  131
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               12                353
  MALE                  3                131
[1] 2 2
[1] FALSE
D17V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     6   7
  12Q GAIN WILD-TYPE 174 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      6    7
  12Q GAIN WILD-TYPE  174  296
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 6                174
  YES                7                296
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  12Q GAIN MUTATED                0
  12Q GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  12Q GAIN MUTATED                                               6
  12Q GAIN WILD-TYPE                                           350
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  12Q GAIN MUTATED                                                                        9
  12Q GAIN WILD-TYPE                                                                     91
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  12Q GAIN MUTATED                                                                     0
  12Q GAIN WILD-TYPE                                                                  36
D17V9, multiclass
                                                                        clus
vv                                                                       12Q GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       12Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    14   0
  12Q GAIN WILD-TYPE 406  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     14    0
  12Q GAIN WILD-TYPE  406   17
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                14                406
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  12Q GAIN MUTATED              1                       0   14
  12Q GAIN WILD-TYPE          131                      18  316
                    vv
clus                 VERY ADVANCED (T4B)
  12Q GAIN MUTATED                     0
  12Q GAIN WILD-TYPE                   1
D17V11, multiclass
                         clus
vv                        12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                  14                316
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    12   1   0   2
  12Q GAIN WILD-TYPE 371  50   4  28
D17V12, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               12                371
  R1                1                 50
  R2                0                  4
  RX                2                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, continuous
D17V14, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     7   8
  12Q GAIN WILD-TYPE 218 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      7    8
  12Q GAIN WILD-TYPE  218  256
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  MULTIFOCAL                7                218
  UNIFOCAL                  8                256
[1] 2 2
[1] FALSE
D17V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     0
  12Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           0     9
  12Q GAIN WILD-TYPE                        27   320
D17V16, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           9                320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V17, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0   9
  12Q GAIN WILD-TYPE  38 351
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0    9
  12Q GAIN WILD-TYPE   38  351
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                9                351
[1] 2 2
[1] FALSE

Clustering(18) Variable = 13Q GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     5   0
  13Q GAIN WILD-TYPE 477  16
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                493 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                 16 
$`13Q GAIN MUTATED`
TCGA-BJ-A45E TCGA-EL-A4KI TCGA-EM-A1YD TCGA-EM-A2CO TCGA-EM-A2OY 
       21.01        23.90        57.01         6.05        32.32 

$`13Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         7.99        10.88         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       27.06        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP 
       14.24        47.57        17.88        13.18        23.51         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        44.52         8.35 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        27.02        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25        20.42        17.82         7.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
       21.63        17.06        17.36        15.16        23.87        22.49 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04        13.81        14.04        21.60        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46        11.01        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       24.69        22.29         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV 
       40.37         9.50        36.10        32.45        30.21        12.89 
TCGA-E8-A418 
        3.02 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              6.05               0.20 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             57.01             178.29 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             23.90              31.27 
[1] "6.0 - 57.0 (23.9)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "3300000"
D18V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  13Q GAIN MUTATED         1        3         1        0         0         0
  13Q GAIN WILD-TYPE     281       47       110        2        46         6
D18V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  1                281
  STAGE II                 3                 47
  STAGE III                1                110
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  13Q GAIN MUTATED     1   3   1   0
  13Q GAIN WILD-TYPE 141 162 166  23
D18V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                1                141
  T2                3                162
  T3                1                166
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   0
  13Q GAIN WILD-TYPE 221 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    0
  13Q GAIN WILD-TYPE  221  224
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                4                221
  1                0                224
[1] 2 2
[1] FALSE
D18V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1   0
  13Q GAIN WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1    0
  13Q GAIN WILD-TYPE  277    9
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                1                277
  1                0                  9
[1] 2 2
[1] FALSE
D18V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   1
  13Q GAIN WILD-TYPE 361 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    1
  13Q GAIN WILD-TYPE  361  133
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                4                361
  MALE                  1                133
[1] 2 2
[1] FALSE
D18V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     2   3
  13Q GAIN WILD-TYPE 178 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    3
  13Q GAIN WILD-TYPE  178  300
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 2                178
  YES                3                300
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  13Q GAIN MUTATED                0
  13Q GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  13Q GAIN MUTATED                                               2
  13Q GAIN WILD-TYPE                                           354
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  13Q GAIN MUTATED                                                                        3
  13Q GAIN WILD-TYPE                                                                     97
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  13Q GAIN MUTATED                                                                     0
  13Q GAIN WILD-TYPE                                                                  36
D18V9, multiclass
                                                                        clus
vv                                                                       13Q GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       13Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   0
  13Q GAIN WILD-TYPE 416  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    0
  13Q GAIN WILD-TYPE  416   17
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 4                416
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  13Q GAIN MUTATED              1                       0    3
  13Q GAIN WILD-TYPE          131                      18  327
                    vv
clus                 VERY ADVANCED (T4B)
  13Q GAIN MUTATED                     0
  13Q GAIN WILD-TYPE                   1
D18V11, multiclass
                         clus
vv                        13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   3                327
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED     4   0   0   0
  13Q GAIN WILD-TYPE 379  51   4  30
D18V12, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0                4                379
  R1                0                 51
  R2                0                  4
  RX                0                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, continuous
D18V14, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     3   2
  13Q GAIN WILD-TYPE 222 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    2
  13Q GAIN WILD-TYPE  222  262
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  MULTIFOCAL                3                222
  UNIFOCAL                  2                262
[1] 2 2
[1] FALSE
D18V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     0
  13Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           0     2
  13Q GAIN WILD-TYPE                        27   327
D18V16, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                407 
        TCGA-BJ-A290         TCGA-BJ-A291         TCGA-BJ-A45K 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CE-A13K         TCGA-DE-A0XZ         TCGA-DJ-A13L 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PR         TCGA-DJ-A3UU         TCGA-DJ-A3UW 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V4         TCGA-DJ-A3VI         TCGA-DJ-A3VK 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E3-A3E5         TCGA-EL-A3CR         TCGA-EL-A3CS 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3CY         TCGA-EL-A3D0         TCGA-EL-A3D5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3GQ         TCGA-EL-A3H2         TCGA-EL-A3H8 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3MY         TCGA-EL-A3N3         TCGA-ET-A3BO 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-FK-A3SD         TCGA-FY-A76V 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A4HW         TCGA-L6-A4ET 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-MK-A84Z         TCGA-4C-A93U         TCGA-BJ-A0YZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A0Z2         TCGA-BJ-A0Z3         TCGA-BJ-A0Z5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A0Z9         TCGA-BJ-A0ZA         TCGA-BJ-A0ZB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZC         TCGA-BJ-A0ZE         TCGA-BJ-A0ZG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZH         TCGA-BJ-A0ZJ         TCGA-BJ-A18Y 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A18Z         TCGA-BJ-A190         TCGA-BJ-A191 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A192         TCGA-BJ-A28R         TCGA-BJ-A28S 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A28T         TCGA-BJ-A28V         TCGA-BJ-A28W 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A28X         TCGA-BJ-A28Z         TCGA-BJ-A2N7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A2N8         TCGA-BJ-A2N9         TCGA-BJ-A2NA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A2P4         TCGA-BJ-A3EZ         TCGA-BJ-A3F0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A3PR         TCGA-BJ-A3PT         TCGA-BJ-A3PU 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A45C         TCGA-BJ-A45D         TCGA-BJ-A45F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A45G         TCGA-BJ-A45H         TCGA-BJ-A45I 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A45J         TCGA-BJ-A4O8         TCGA-BJ-A4O9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CE-A27D         TCGA-CE-A3MD         TCGA-CE-A3ME 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CE-A481         TCGA-CE-A482         TCGA-CE-A483 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CE-A484         TCGA-CE-A485         TCGA-DE-A0Y2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DE-A0Y3         TCGA-DE-A2OL         TCGA-DE-A3KN 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DE-A4M8         TCGA-DE-A4M9         TCGA-DE-A4MA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DE-A4MB         TCGA-DE-A4MC         TCGA-DE-A4MD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DE-A69J         TCGA-DE-A69K         TCGA-DE-A7U5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A13M         TCGA-DJ-A13O         TCGA-DJ-A13P 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A13R         TCGA-DJ-A13S         TCGA-DJ-A13T 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A13U         TCGA-DJ-A13W         TCGA-DJ-A1QD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QE         TCGA-DJ-A1QF         TCGA-DJ-A1QG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QH         TCGA-DJ-A1QI         TCGA-DJ-A1QM 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QO         TCGA-DJ-A1QQ         TCGA-DJ-A2PN 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PO         TCGA-DJ-A2PQ         TCGA-DJ-A2PS 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PT         TCGA-DJ-A2PU         TCGA-DJ-A2PV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PW         TCGA-DJ-A2PX         TCGA-DJ-A2PY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PZ         TCGA-DJ-A2Q0         TCGA-DJ-A2Q1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q2         TCGA-DJ-A2Q3         TCGA-DJ-A2Q4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q9         TCGA-DJ-A2QA         TCGA-DJ-A2QB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UK         TCGA-DJ-A3UM         TCGA-DJ-A3UN 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UO         TCGA-DJ-A3UQ         TCGA-DJ-A3UR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3US         TCGA-DJ-A3UT         TCGA-DJ-A3UX 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UY         TCGA-DJ-A3UZ         TCGA-DJ-A3V2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V3         TCGA-DJ-A3V5         TCGA-DJ-A3V7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V8         TCGA-DJ-A3V9         TCGA-DJ-A3VD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VE         TCGA-DJ-A3VF         TCGA-DJ-A3VG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VJ         TCGA-DJ-A3VL         TCGA-DJ-A3VM 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A4UL         TCGA-DJ-A4UP         TCGA-DJ-A4UQ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A4UR         TCGA-DJ-A4UT         TCGA-DJ-A4UW 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A4V0         TCGA-DJ-A4V4         TCGA-DJ-A4V5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DO-A1JZ         TCGA-DO-A1K0         TCGA-DO-A2HM 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E3-A3DY         TCGA-E3-A3DZ         TCGA-E3-A3E0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E3-A3E1         TCGA-E3-A3E2         TCGA-E3-A3E3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A242         TCGA-E8-A2EA         TCGA-E8-A3X7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A413         TCGA-E8-A414         TCGA-E8-A415 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A416         TCGA-E8-A417         TCGA-E8-A419 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A432         TCGA-E8-A433         TCGA-E8-A434 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A436         TCGA-E8-A437         TCGA-E8-A438 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A44K         TCGA-E8-A44M         TCGA-EL-A3CL 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3CP         TCGA-EL-A3CT         TCGA-EL-A3CU 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D1         TCGA-EL-A3D4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3D6         TCGA-EL-A3GO         TCGA-EL-A3GP 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3GR         TCGA-EL-A3GS         TCGA-EL-A3GU 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GW         TCGA-EL-A3GX 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3GY         TCGA-EL-A3GZ         TCGA-EL-A3H1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3H3         TCGA-EL-A3H4         TCGA-EL-A3H5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3H7         TCGA-EL-A3MW         TCGA-EL-A3MX 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3T0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3T1         TCGA-EL-A3T2         TCGA-EL-A3T3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3T6         TCGA-EL-A3T7         TCGA-EL-A3T8 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3T9         TCGA-EL-A3TA         TCGA-EL-A3TB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZG         TCGA-EL-A3ZH         TCGA-EL-A3ZK 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZL         TCGA-EL-A3ZN         TCGA-EL-A3ZO 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZP         TCGA-EL-A3ZQ         TCGA-EL-A3ZR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZS         TCGA-EL-A3ZT         TCGA-EL-A4JV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4JW         TCGA-EL-A4JX         TCGA-EL-A4JZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4K0         TCGA-EL-A4K1         TCGA-EL-A4K2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4K4         TCGA-EL-A4K6         TCGA-EL-A4K7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4K9         TCGA-EL-A4KD         TCGA-EL-A4KG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4KH         TCGA-EM-A22M         TCGA-EM-A22O 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EM-A2OV         TCGA-EM-A3AI         TCGA-ET-A25G 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A25I         TCGA-ET-A25J         TCGA-ET-A25K 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A25L         TCGA-ET-A25M         TCGA-ET-A25N 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A25O         TCGA-ET-A25P         TCGA-ET-A25R 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A2MX         TCGA-ET-A2MY         TCGA-ET-A2MZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A2N0         TCGA-ET-A2N1         TCGA-ET-A2N3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A2N4         TCGA-ET-A2N5         TCGA-ET-A39I 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A39J         TCGA-ET-A39K         TCGA-ET-A39M 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A39N         TCGA-ET-A39O         TCGA-ET-A39P 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39S         TCGA-ET-A39T 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3BN         TCGA-ET-A3BP         TCGA-ET-A3BQ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3BW         TCGA-ET-A3BX         TCGA-ET-A3DO 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3DP         TCGA-ET-A3DQ         TCGA-ET-A3DR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DU 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3DV         TCGA-ET-A3DW         TCGA-ET-A40P 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A40Q         TCGA-ET-A40R         TCGA-ET-A40S 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A40T         TCGA-ET-A4KN         TCGA-ET-A4KQ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A238         TCGA-FE-A239         TCGA-FE-A23A 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A3PA         TCGA-FE-A3PB         TCGA-FE-A3PC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A3PD         TCGA-FK-A3S3         TCGA-FK-A3SB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FK-A3SE         TCGA-FK-A3SG         TCGA-FK-A3SH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FK-A4UB         TCGA-FY-A2QD         TCGA-FY-A3BL 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A3I4         TCGA-FY-A3I5         TCGA-FY-A3NM 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A3ON         TCGA-FY-A3R6         TCGA-FY-A3R7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A3R8         TCGA-FY-A3R9         TCGA-FY-A3RA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A3TY         TCGA-FY-A3W9         TCGA-FY-A3WA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A3YR         TCGA-FY-A40K         TCGA-FY-A40L 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A40M         TCGA-FY-A40N         TCGA-FY-A4B0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A4B3         TCGA-FY-A4B4         TCGA-GE-A2C6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-H2-A26U         TCGA-H2-A2K9         TCGA-H2-A3RH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-H2-A3RI         TCGA-H2-A421         TCGA-H2-A422 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IM-A3EB         TCGA-IM-A3ED         TCGA-IM-A3U2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IM-A3U3         TCGA-IM-A41Y         TCGA-IM-A41Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IM-A420         TCGA-IM-A4EB         TCGA-J8-A3O0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-J8-A3O1         TCGA-J8-A3O2         TCGA-J8-A3YD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-J8-A3YE         TCGA-J8-A3YF         TCGA-J8-A3YG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-J8-A3YH         TCGA-J8-A42S         TCGA-J8-A4HY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-KS-A41F         TCGA-KS-A41I         TCGA-KS-A41J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-KS-A41L         TCGA-KS-A4I1         TCGA-KS-A4I3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-KS-A4I5         TCGA-KS-A4I7         TCGA-KS-A4I9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-KS-A4IB         TCGA-KS-A4IC         TCGA-KS-A4ID 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-L6-A4EP         TCGA-L6-A4EQ         TCGA-L6-A4EU 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-MK-A4N6         TCGA-MK-A4N7         TCGA-MK-A4N9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-QD-A8IV         TCGA-E8-A418 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D18V17, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0   2
  13Q GAIN WILD-TYPE  38 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    2
  13Q GAIN WILD-TYPE   38  358
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                2                358
[1] 2 2
[1] FALSE

Clustering(19) Variable = 14Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    11   0
  14Q GAIN WILD-TYPE 471  16
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                487 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 0                 16 
$`14Q GAIN MUTATED`
TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY 
       60.16        23.90        57.01        10.65         6.05        32.32 
TCGA-EM-A3AI TCGA-ET-A39N TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-J8-A3YG 
       22.52       123.32         7.82        29.10        22.29 

$`14Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       31.30        30.84        25.45        30.61        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 
       37.94        57.01       106.62        79.50        98.53        69.57 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        49.51       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX 
       43.36        49.71        83.57       139.00       108.66        57.63 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       52.50        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        91.17        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       72.69        65.49        61.22         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       27.06        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       15.75        10.45        14.53        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       47.57        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       48.46        13.15        22.16        40.34        19.73        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.59        17.46        17.29        14.60        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        44.52         8.35        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        27.02        38.66        38.86        29.95        29.85 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       58.75        37.25        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW 
       79.10        76.64         5.79        87.62        77.82        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77       112.80        39.95        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE 
       85.15        85.68        78.77        71.08         4.11        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       27.85        24.69         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV 
       40.37         9.50        36.10        32.45        30.21        12.89 
TCGA-E8-A418 
        3.02 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              6.05               0.20 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            123.32             178.29 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             23.90              31.27 
[1] "6.0 - 123.3 (23.9)" "0.2 - 178.3 (31.3)"
[1] "hr="     "9200000"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  14Q GAIN MUTATED         2        5         4        0         0         0
  14Q GAIN WILD-TYPE     280       45       107        2        46         6
D19V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  2                280
  STAGE II                 5                 45
  STAGE III                4                107
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  14Q GAIN MUTATED     1   6   4   0
  14Q GAIN WILD-TYPE 141 159 163  23
D19V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                1                141
  T2                6                159
  T3                4                163
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     7   1
  14Q GAIN WILD-TYPE 218 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      7    1
  14Q GAIN WILD-TYPE  218  223
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                7                218
  1                1                223
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2   0
  14Q GAIN WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    0
  14Q GAIN WILD-TYPE  276    9
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                2                276
  1                0                  9
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    10   1
  14Q GAIN WILD-TYPE 355 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     10    1
  14Q GAIN WILD-TYPE  355  133
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               10                355
  MALE                  1                133
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1   8
  14Q GAIN WILD-TYPE 179 295
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    8
  14Q GAIN WILD-TYPE  179  295
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 1                179
  YES                8                295
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  14Q GAIN MUTATED                0
  14Q GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  14Q GAIN MUTATED                                               5
  14Q GAIN WILD-TYPE                                           351
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  14Q GAIN MUTATED                                                                        6
  14Q GAIN WILD-TYPE                                                                     94
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  14Q GAIN MUTATED                                                                     0
  14Q GAIN WILD-TYPE                                                                  36
D19V9, multiclass
                                                                        clus
vv                                                                       14Q GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                6
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       14Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 94
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    10   0
  14Q GAIN WILD-TYPE 410  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     10    0
  14Q GAIN WILD-TYPE  410   17
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                10                410
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  14Q GAIN MUTATED              2                       0    9
  14Q GAIN WILD-TYPE          130                      18  321
                    vv
clus                 VERY ADVANCED (T4B)
  14Q GAIN MUTATED                     0
  14Q GAIN WILD-TYPE                   1
D19V11, multiclass
                         clus
vv                        14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  MINIMAL (T3)                           2                130
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   9                321
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    10   0   0   1
  14Q GAIN WILD-TYPE 373  51   4  29
D19V12, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               10                373
  R1                0                 51
  R2                0                  4
  RX                1                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, continuous
D19V14, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     8   3
  14Q GAIN WILD-TYPE 217 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      8    3
  14Q GAIN WILD-TYPE  217  261
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  MULTIFOCAL                8                217
  UNIFOCAL                  3                261
[1] 2 2
[1] FALSE
D19V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     0
  14Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           0     7
  14Q GAIN WILD-TYPE                        27   322
D19V16, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           7                322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V17, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0   6
  14Q GAIN WILD-TYPE  38 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    6
  14Q GAIN WILD-TYPE   38  354
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                354
[1] 2 2
[1] FALSE

Clustering(20) Variable = 16P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    14   1
  16P GAIN WILD-TYPE 468  15
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                483 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 15 
$`16P GAIN MUTATED`
TCGA-BJ-A192 TCGA-BJ-A2N9 TCGA-DJ-A2Q0 TCGA-EL-A3T9 TCGA-EM-A1YD TCGA-EM-A22N 
       44.35        20.48        34.36         5.72        57.01        10.65 
TCGA-EM-A2CO TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
        6.05        22.52         9.24        13.51        37.25       123.32 
TCGA-ET-A3DS TCGA-FY-A3I5 TCGA-FY-A3NM 
       66.84         7.82        29.10 

$`16P GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
       20.58         4.83        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
       11.31        30.97        11.08        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       12.82        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       21.63        50.17        37.64        27.32        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        52.27        43.17        52.37         8.32        48.07 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       30.58        35.41        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       34.85        28.96         8.78         8.42        37.74        43.96 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        39.95        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       36.33        11.34        35.87        40.96        36.99        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       30.61        19.20        23.21        21.27        20.48        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        40.70        18.97         9.60        35.67        36.43 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       23.44        27.62        30.87        30.12        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       80.52        63.19        52.44        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 
       29.98        31.50        31.04        31.30        30.84        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       30.61        31.27        31.33        14.96        39.88        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       31.00        30.15        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
      158.83        60.95       157.15        37.94        57.01       106.62 
TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       79.50        98.53        69.57       108.36        64.87        49.51 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      101.13       139.99        49.32        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 
      139.00       108.66        57.63        52.50        29.65       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        91.17        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        72.69        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        61.02 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       78.61        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       13.18        23.51         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.46        17.29        14.60        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        15.06         7.33        12.53        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        63.45        88.41        58.75        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       80.58        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       17.82        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08        23.31        21.63        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 
       23.87        22.49        19.04        13.81        14.04        21.60 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
       31.10         8.22        25.64        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.24        33.40        40.37         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              5.72               0.20 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            123.32             178.29 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             22.52              31.27 
[1] "5.7 - 123.3 (22.5)" "0.2 - 178.3 (31.3)"
[1] "hr=" "2.6"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  16P GAIN MUTATED         7        4         3        1         0         0
  16P GAIN WILD-TYPE     275       46       108        1        46         6
D20V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  7                275
  STAGE II                 4                 46
  STAGE III                3                108
  STAGE IV                 1                  1
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  16P GAIN MUTATED     4   5   5   1
  16P GAIN WILD-TYPE 138 160 162  22
D20V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                4                138
  T2                5                160
  T3                5                162
  T4                1                 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"
D20V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     9   1
  16P GAIN WILD-TYPE 216 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9    1
  16P GAIN WILD-TYPE  216  223
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                9                216
  1                1                223
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     3   0
  16P GAIN WILD-TYPE 275   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    0
  16P GAIN WILD-TYPE  275    9
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                3                275
  1                0                  9
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    12   3
  16P GAIN WILD-TYPE 353 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     12    3
  16P GAIN WILD-TYPE  353  131
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               12                353
  MALE                  3                131
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     7   5
  16P GAIN WILD-TYPE 173 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      7    5
  16P GAIN WILD-TYPE  173  298
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 7                173
  YES                5                298
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  16P GAIN MUTATED                0
  16P GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  16P GAIN MUTATED                                               8
  16P GAIN WILD-TYPE                                           348
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  16P GAIN MUTATED                                                                        7
  16P GAIN WILD-TYPE                                                                     93
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  16P GAIN MUTATED                                                                     0
  16P GAIN WILD-TYPE                                                                  36
D20V9, multiclass
                                                                        clus
vv                                                                       16P GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         8
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       16P GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    14   0
  16P GAIN WILD-TYPE 406  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     14    0
  16P GAIN WILD-TYPE  406   17
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                14                406
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  16P GAIN MUTATED              2                       0   12
  16P GAIN WILD-TYPE          130                      18  318
                    vv
clus                 VERY ADVANCED (T4B)
  16P GAIN MUTATED                     1
  16P GAIN WILD-TYPE                   0
D20V11, multiclass
                         clus
vv                        16P GAIN MUTATED 16P GAIN WILD-TYPE
  MINIMAL (T3)                           2                130
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                  12                318
  VERY ADVANCED (T4B)                    1                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    10   2   0   3
  16P GAIN WILD-TYPE 373  49   4  27
D20V12, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               10                373
  R1                2                 49
  R2                0                  4
  RX                3                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, continuous
D20V14, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     6   9
  16P GAIN WILD-TYPE 219 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      6    9
  16P GAIN WILD-TYPE  219  255
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  MULTIFOCAL                6                219
  UNIFOCAL                  9                255
[1] 2 2
[1] FALSE
D20V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  0     0
  16P GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                           0    10
  16P GAIN WILD-TYPE                        27   319
D20V16, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                          10                319
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V17, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0   9
  16P GAIN WILD-TYPE  38 351
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0    9
  16P GAIN WILD-TYPE   38  351
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                9                351
[1] 2 2
[1] FALSE

Clustering(21) Variable = 16Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    12   1
  16Q GAIN WILD-TYPE 470  15
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                485 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 15 
$`16Q GAIN MUTATED`
TCGA-BJ-A2N9 TCGA-DJ-A2Q0 TCGA-EL-A3T9 TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO 
       20.48        34.36         5.72        57.01        10.65         6.05 
TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       22.52         9.24        13.51        37.25       123.32         7.82 
TCGA-FY-A3NM 
       29.10 

$`16Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
      107.47        66.90        82.82        89.56        91.17        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        72.69        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       61.02        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        78.61        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       17.88        13.18        23.51         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.59        17.46        17.29        14.60        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        44.52         8.35        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33        12.53 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       27.02        38.66        38.86        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       65.29        18.38        63.45        88.41        58.75        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.25        20.42        17.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08        23.31        21.63        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 
       17.36        15.16        23.87        22.49        19.04        13.81 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       14.04        21.60        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       11.01        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 
       16.90        21.83        31.10         8.22        25.64        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        5.75         2.47         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU 
       84.72        35.28        33.24        33.40        40.37         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       36.10        32.45        30.21        12.89         3.02 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              5.72               0.20 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            123.32             178.29 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             20.48              31.30 
[1] "5.7 - 123.3 (20.5)" "0.2 - 178.3 (31.3)"
[1] "hr=" "3.6"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  16Q GAIN MUTATED         6        4         2        1         0         0
  16Q GAIN WILD-TYPE     276       46       109        1        46         6
D21V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  6                276
  STAGE II                 4                 46
  STAGE III                2                109
  STAGE IV                 1                  1
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  16Q GAIN MUTATED     3   5   4   1
  16Q GAIN WILD-TYPE 139 160 163  22
D21V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                3                139
  T2                5                160
  T3                4                163
  T4                1                 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"
D21V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     8   1
  16Q GAIN WILD-TYPE 217 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      8    1
  16Q GAIN WILD-TYPE  217  223
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                8                217
  1                1                223
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2   0
  16Q GAIN WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2    0
  16Q GAIN WILD-TYPE  276    9
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                2                276
  1                0                  9
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    10   3
  16Q GAIN WILD-TYPE 355 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     10    3
  16Q GAIN WILD-TYPE  355  131
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               10                355
  MALE                  3                131
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     5   5
  16Q GAIN WILD-TYPE 175 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5    5
  16Q GAIN WILD-TYPE  175  298
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 5                175
  YES                5                298
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  16Q GAIN MUTATED                0
  16Q GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  16Q GAIN MUTATED                                               6
  16Q GAIN WILD-TYPE                                           350
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  16Q GAIN MUTATED                                                                        7
  16Q GAIN WILD-TYPE                                                                     93
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  16Q GAIN MUTATED                                                                     0
  16Q GAIN WILD-TYPE                                                                  36
D21V9, multiclass
                                                                        clus
vv                                                                       16Q GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       16Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    12   0
  16Q GAIN WILD-TYPE 408  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     12    0
  16Q GAIN WILD-TYPE  408   17
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                12                408
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  16Q GAIN MUTATED              1                       0   11
  16Q GAIN WILD-TYPE          131                      18  319
                    vv
clus                 VERY ADVANCED (T4B)
  16Q GAIN MUTATED                     1
  16Q GAIN WILD-TYPE                   0
D21V11, multiclass
                         clus
vv                        16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                  11                319
  VERY ADVANCED (T4B)                    1                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED     9   2   0   2
  16Q GAIN WILD-TYPE 374  49   4  28
D21V12, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                9                374
  R1                2                 49
  R2                0                  4
  RX                2                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, continuous
D21V14, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     6   7
  16Q GAIN WILD-TYPE 219 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      6    7
  16Q GAIN WILD-TYPE  219  257
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  MULTIFOCAL                6                219
  UNIFOCAL                  7                257
[1] 2 2
[1] FALSE
D21V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     0
  16Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                           0     8
  16Q GAIN WILD-TYPE                        27   321
D21V16, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           8                321
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V17, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0   8
  16Q GAIN WILD-TYPE  38 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0    8
  16Q GAIN WILD-TYPE   38  352
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                8                352
[1] 2 2
[1] FALSE

Clustering(22) Variable = 17P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    16   0
  17P GAIN WILD-TYPE 466  16
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                482 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 0                 16 
$`17P GAIN MUTATED`
TCGA-DJ-A2Q0 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1YC 
       34.36        91.17        60.16        44.15        23.90        78.61 
TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY 
       57.01        10.65         6.05        32.32        22.52        13.51 
TCGA-ET-A25P TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       18.38        37.25       123.32         7.82 

$`17P GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       61.22         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 
       61.02        31.04        34.39        30.51        53.36        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       47.84        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        48.49        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        44.52         8.35 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        27.02        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.95        29.85        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MX 
       56.58        60.20        63.39        65.29        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       58.75        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       33.24       106.09       107.41       108.46        84.89       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP 
       95.34        94.13        55.10        98.20        28.24        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        87.62        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10       116.09         1.25        20.42        17.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              6.05               0.20 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            123.32             178.29 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            33.340             31.165 
[1] "6.0 - 123.3 (33.3)" "0.2 - 178.3 (31.2)"
[1] "hr="     "2.6e+07"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  17P GAIN MUTATED         6        6         3        1         0         0
  17P GAIN WILD-TYPE     276       44       108        1        46         6
D22V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  6                276
  STAGE II                 6                 44
  STAGE III                3                108
  STAGE IV                 1                  1
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  17P GAIN MUTATED     4   6   5   1
  17P GAIN WILD-TYPE 138 159 162  22
D22V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                4                138
  T2                6                159
  T3                5                162
  T4                1                 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"
D22V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    10   2
  17P GAIN WILD-TYPE 215 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     10    2
  17P GAIN WILD-TYPE  215  222
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               10                215
  1                2                222
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     3   0
  17P GAIN WILD-TYPE 275   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    0
  17P GAIN WILD-TYPE  275    9
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                3                275
  1                0                  9
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    12   4
  17P GAIN WILD-TYPE 353 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     12    4
  17P GAIN WILD-TYPE  353  130
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               12                353
  MALE                  4                130
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     4  10
  17P GAIN WILD-TYPE 176 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4   10
  17P GAIN WILD-TYPE  176  293
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 4                176
  YES               10                293
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  17P GAIN MUTATED                0
  17P GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  17P GAIN MUTATED                                               8
  17P GAIN WILD-TYPE                                           348
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  17P GAIN MUTATED                                                                        8
  17P GAIN WILD-TYPE                                                                     92
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  17P GAIN MUTATED                                                                     0
  17P GAIN WILD-TYPE                                                                  36
D22V9, multiclass
                                                                        clus
vv                                                                       17P GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         8
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       17P GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 92
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    15   0
  17P GAIN WILD-TYPE 405  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     15    0
  17P GAIN WILD-TYPE  405   17
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                15                405
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  17P GAIN MUTATED              3                       0   13
  17P GAIN WILD-TYPE          129                      18  317
                    vv
clus                 VERY ADVANCED (T4B)
  17P GAIN MUTATED                     0
  17P GAIN WILD-TYPE                   1
D22V11, multiclass
                         clus
vv                        17P GAIN MUTATED 17P GAIN WILD-TYPE
  MINIMAL (T3)                           3                129
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                  13                317
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    14   0   0   2
  17P GAIN WILD-TYPE 369  51   4  28
D22V12, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               14                369
  R1                0                 51
  R2                0                  4
  RX                2                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, continuous
D22V14, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     7   9
  17P GAIN WILD-TYPE 218 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      7    9
  17P GAIN WILD-TYPE  218  255
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  MULTIFOCAL                7                218
  UNIFOCAL                  9                255
[1] 2 2
[1] FALSE
D22V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     1
  17P GAIN WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           0     9
  17P GAIN WILD-TYPE                        27   320
D22V16, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 51
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           9                320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V17, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  10
  17P GAIN WILD-TYPE  38 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   10
  17P GAIN WILD-TYPE   38  350
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO               10                350
[1] 2 2
[1] FALSE

Clustering(23) Variable = 17Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    18   0
  17Q GAIN WILD-TYPE 464  16
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                480 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 0                 16 
$`17Q GAIN MUTATED`
TCGA-DJ-A2Q0 TCGA-EL-A3ZH TCGA-EL-A3ZM TCGA-EL-A3ZR TCGA-EL-A4K6 TCGA-EL-A4KI 
       34.36        91.17        36.03        60.16        44.15        23.90 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI 
       78.61        57.01        10.65         6.05        32.32        22.52 
TCGA-EM-A3SY TCGA-ET-A25P TCGA-ET-A2MZ TCGA-ET-A39N TCGA-ET-A3DS TCGA-FY-A3I5 
       13.51        18.38        37.25       123.32        66.84         7.82 

$`17Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       51.78        62.30        53.06        72.69        65.49        61.22 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        61.02 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 
       31.04        34.39        30.51        53.36        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       43.59        24.30        27.06        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I 
       48.49        18.05        19.79        19.46        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P 
       14.50        15.75        10.45        14.53        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP 
       14.24        47.57        17.88        13.18        23.51         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ 
       33.96        17.59        17.46        17.29        14.60        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR 
       15.68        14.14        33.07        44.52         8.35        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        27.02        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       29.85        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       60.20        63.39        65.29        63.45        88.41        58.75 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       94.59        84.85        80.58        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
        9.50        36.10        32.45        30.21        12.89         3.02 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              6.05               0.20 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            123.32             178.29 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            35.195             31.070 
[1] "6.0 - 123.3 (35.2)" "0.2 - 178.3 (31.1)"
[1] "hr="     "2.6e+07"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  17Q GAIN MUTATED         7        6         3        1         1         0
  17Q GAIN WILD-TYPE     275       44       108        1        45         6
D23V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  7                275
  STAGE II                 6                 44
  STAGE III                3                108
  STAGE IV                 1                  1
  STAGE IVA                1                 45
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  17Q GAIN MUTATED     5   6   5   2
  17Q GAIN WILD-TYPE 137 159 162  21
D23V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                5                137
  T2                6                159
  T3                5                162
  T4                2                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    11   3
  17Q GAIN WILD-TYPE 214 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     11    3
  17Q GAIN WILD-TYPE  214  221
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               11                214
  1                3                221
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     4   0
  17Q GAIN WILD-TYPE 274   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4    0
  17Q GAIN WILD-TYPE  274    9
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                4                274
  1                0                  9
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    13   5
  17Q GAIN WILD-TYPE 352 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     13    5
  17Q GAIN WILD-TYPE  352  129
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               13                352
  MALE                  5                129
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     5  11
  17Q GAIN WILD-TYPE 175 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5   11
  17Q GAIN WILD-TYPE  175  292
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 5                175
  YES               11                292
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  17Q GAIN MUTATED                0
  17Q GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  17Q GAIN MUTATED                                              10
  17Q GAIN WILD-TYPE                                           346
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  17Q GAIN MUTATED                                                                        8
  17Q GAIN WILD-TYPE                                                                     92
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  17Q GAIN MUTATED                                                                     0
  17Q GAIN WILD-TYPE                                                                  36
D23V9, multiclass
                                                                        clus
vv                                                                       17Q GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        10
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       17Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         346
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 92
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    17   0
  17Q GAIN WILD-TYPE 403  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     17    0
  17Q GAIN WILD-TYPE  403   17
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                17                403
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  17Q GAIN MUTATED              3                       1   14
  17Q GAIN WILD-TYPE          129                      17  316
                    vv
clus                 VERY ADVANCED (T4B)
  17Q GAIN MUTATED                     0
  17Q GAIN WILD-TYPE                   1
D23V11, multiclass
                         clus
vv                        17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  MINIMAL (T3)                           3                129
  MODERATE/ADVANCED (T4A)                1                 17
  NONE                                  14                316
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    15   1   0   2
  17Q GAIN WILD-TYPE 368  50   4  28
D23V12, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               15                368
  R1                1                 50
  R2                0                  4
  RX                2                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, continuous
D23V14, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     7  11
  17Q GAIN WILD-TYPE 218 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7   11
  17Q GAIN WILD-TYPE  218  253
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  MULTIFOCAL                7                218
  UNIFOCAL                 11                253
[1] 2 2
[1] FALSE
D23V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     1
  17Q GAIN WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           0    10
  17Q GAIN WILD-TYPE                        27   319
D23V16, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 51
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                          10                319
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V17, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  11
  17Q GAIN WILD-TYPE  38 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   11
  17Q GAIN WILD-TYPE   38  349
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO               11                349
[1] 2 2
[1] FALSE

Clustering(24) Variable = 18P GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     6   0
  18P GAIN WILD-TYPE 476  16
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                492 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                 16 
$`18P GAIN MUTATED`
TCGA-BJ-A45E TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       21.01        60.16        23.90        37.25       123.32         7.82 

$`18P GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         7.99        10.88         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       65.49        61.22         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.46        78.61        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       65.29        18.38        63.45        88.41        58.75        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
        9.50        36.10        32.45        30.21        12.89         3.02 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              7.82               0.20 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            123.32             178.29 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            30.575             31.250 
[1] "7.8 - 123.3 (30.6)" "0.2 - 178.3 (31.2)"
[1] "hr="     "9100000"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  18P GAIN MUTATED         3        1         2        0         0         0
  18P GAIN WILD-TYPE     279       49       109        2        46         6
D24V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  3                279
  STAGE II                 1                 49
  STAGE III                2                109
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  18P GAIN MUTATED     2   1   3   0
  18P GAIN WILD-TYPE 140 164 164  23
D24V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                2                140
  T2                1                164
  T3                3                164
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     5   0
  18P GAIN WILD-TYPE 220 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5    0
  18P GAIN WILD-TYPE  220  224
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                5                220
  1                0                224
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2   0
  18P GAIN WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    0
  18P GAIN WILD-TYPE  276    9
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                2                276
  1                0                  9
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4   2
  18P GAIN WILD-TYPE 361 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    2
  18P GAIN WILD-TYPE  361  132
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                4                361
  MALE                  2                132
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2   3
  18P GAIN WILD-TYPE 178 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    3
  18P GAIN WILD-TYPE  178  300
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 2                178
  YES                3                300
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  18P GAIN MUTATED                0
  18P GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  18P GAIN MUTATED                                               5
  18P GAIN WILD-TYPE                                           351
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  18P GAIN MUTATED                                                                        1
  18P GAIN WILD-TYPE                                                                     99
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  18P GAIN MUTATED                                                                     0
  18P GAIN WILD-TYPE                                                                  36
D24V9, multiclass
                                                                        clus
vv                                                                       18P GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       18P GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4   0
  18P GAIN WILD-TYPE 416  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    0
  18P GAIN WILD-TYPE  416   17
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 4                416
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  18P GAIN MUTATED              1                       0    4
  18P GAIN WILD-TYPE          131                      18  326
                    vv
clus                 VERY ADVANCED (T4B)
  18P GAIN MUTATED                     0
  18P GAIN WILD-TYPE                   1
D24V11, multiclass
                         clus
vv                        18P GAIN MUTATED 18P GAIN WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   4                326
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED     4   0   0   1
  18P GAIN WILD-TYPE 379  51   4  29
D24V12, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                4                379
  R1                0                 51
  R2                0                  4
  RX                1                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, continuous
D24V14, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2   4
  18P GAIN WILD-TYPE 223 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    4
  18P GAIN WILD-TYPE  223  260
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  MULTIFOCAL                2                223
  UNIFOCAL                  4                260
[1] 2 2
[1] FALSE
D24V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     0
  18P GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           0     6
  18P GAIN WILD-TYPE                        27   323
D24V16, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           6                323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V17, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0   6
  18P GAIN WILD-TYPE  38 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0    6
  18P GAIN WILD-TYPE   38  354
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                354
[1] 2 2
[1] FALSE

Clustering(25) Variable = 18Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     6   0
  18Q GAIN WILD-TYPE 476  16
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                492 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                 16 
$`18Q GAIN MUTATED`
TCGA-BJ-A45E TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       21.01        60.16        23.90        37.25       123.32         7.82 

$`18Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         7.99        10.88         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       65.49        61.22         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.46        78.61        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       65.29        18.38        63.45        88.41        58.75        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
        9.50        36.10        32.45        30.21        12.89         3.02 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              7.82               0.20 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            123.32             178.29 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            30.575             31.250 
[1] "7.8 - 123.3 (30.6)" "0.2 - 178.3 (31.2)"
[1] "hr="     "9100000"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  18Q GAIN MUTATED         3        1         2        0         0         0
  18Q GAIN WILD-TYPE     279       49       109        2        46         6
D25V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  3                279
  STAGE II                 1                 49
  STAGE III                2                109
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  18Q GAIN MUTATED     2   1   3   0
  18Q GAIN WILD-TYPE 140 164 164  23
D25V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                2                140
  T2                1                164
  T3                3                164
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     5   0
  18Q GAIN WILD-TYPE 220 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    0
  18Q GAIN WILD-TYPE  220  224
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                5                220
  1                0                224
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2   0
  18Q GAIN WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    0
  18Q GAIN WILD-TYPE  276    9
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                2                276
  1                0                  9
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     4   2
  18Q GAIN WILD-TYPE 361 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    2
  18Q GAIN WILD-TYPE  361  132
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                361
  MALE                  2                132
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2   3
  18Q GAIN WILD-TYPE 178 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    3
  18Q GAIN WILD-TYPE  178  300
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 2                178
  YES                3                300
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  18Q GAIN MUTATED                0
  18Q GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  18Q GAIN MUTATED                                               5
  18Q GAIN WILD-TYPE                                           351
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  18Q GAIN MUTATED                                                                        1
  18Q GAIN WILD-TYPE                                                                     99
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  18Q GAIN MUTATED                                                                     0
  18Q GAIN WILD-TYPE                                                                  36
D25V9, multiclass
                                                                        clus
vv                                                                       18Q GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       18Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     4   0
  18Q GAIN WILD-TYPE 416  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    0
  18Q GAIN WILD-TYPE  416   17
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 4                416
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  18Q GAIN MUTATED              1                       0    4
  18Q GAIN WILD-TYPE          131                      18  326
                    vv
clus                 VERY ADVANCED (T4B)
  18Q GAIN MUTATED                     0
  18Q GAIN WILD-TYPE                   1
D25V11, multiclass
                         clus
vv                        18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   4                326
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED     4   0   0   1
  18Q GAIN WILD-TYPE 379  51   4  29
D25V12, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                4                379
  R1                0                 51
  R2                0                  4
  RX                1                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, continuous
D25V14, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2   4
  18Q GAIN WILD-TYPE 223 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    4
  18Q GAIN WILD-TYPE  223  260
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  MULTIFOCAL                2                223
  UNIFOCAL                  4                260
[1] 2 2
[1] FALSE
D25V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           0     6
  18Q GAIN WILD-TYPE                        27   323
D25V16, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           6                323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V17, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0   6
  18Q GAIN WILD-TYPE  38 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    6
  18Q GAIN WILD-TYPE   38  354
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                354
[1] 2 2
[1] FALSE

Clustering(26) Variable = 19P GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED     8   0
  19P GAIN WILD-TYPE 474  16
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 8                490 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                 16 
$`19P GAIN MUTATED`
TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A22N TCGA-EM-A2OY TCGA-EM-A3O9 TCGA-EM-A3SY 
       23.90        78.61        10.65        32.32         9.24        13.51 
TCGA-FY-A3I5 TCGA-FY-A4B0 
        7.82        13.81 

$`19P GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       31.30        30.84        25.45        30.61        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 
       37.94        57.01       106.62        79.50        98.53        69.57 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        49.51       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX 
       43.36        49.71        83.57       139.00       108.66        57.63 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       52.50        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        91.17        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       72.69        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        61.02        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        53.36        44.15        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       24.30        27.06        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       18.05        19.79        19.46        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P 
       14.50        15.75        10.45        14.53        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        44.52 
TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
        8.35        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
       15.06         7.33        12.53        27.02        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.95        29.85        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        4.11        22.03         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82        29.10        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08        23.31        21.63        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16        23.87        22.49        19.04        14.04 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       21.83        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       32.45        30.21        12.89         3.02 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              7.82               0.20 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             78.61             178.29 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            13.660             31.285 
[1] "7.8 - 78.6 (13.7)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "3300000"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  19P GAIN MUTATED         4        1         3        0         0         0
  19P GAIN WILD-TYPE     278       49       108        2        46         6
D26V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  4                278
  STAGE II                 1                 49
  STAGE III                3                108
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  19P GAIN MUTATED     3   1   4   0
  19P GAIN WILD-TYPE 139 164 163  23
D26V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                3                139
  T2                1                164
  T3                4                163
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     6   0
  19P GAIN WILD-TYPE 219 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6    0
  19P GAIN WILD-TYPE  219  224
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                6                219
  1                0                224
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0   0
  19P GAIN WILD-TYPE 278   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    0
  19P GAIN WILD-TYPE  278    9
D26V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     4   4
  19P GAIN WILD-TYPE 361 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      4    4
  19P GAIN WILD-TYPE  361  130
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                4                361
  MALE                  4                130
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1   6
  19P GAIN WILD-TYPE 179 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    6
  19P GAIN WILD-TYPE  179  297
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 1                179
  YES                6                297
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  19P GAIN MUTATED                0
  19P GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  19P GAIN MUTATED                                               2
  19P GAIN WILD-TYPE                                           354
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  19P GAIN MUTATED                                                                        6
  19P GAIN WILD-TYPE                                                                     94
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  19P GAIN MUTATED                                                                     0
  19P GAIN WILD-TYPE                                                                  36
D26V9, multiclass
                                                                        clus
vv                                                                       19P GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                6
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       19P GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 94
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     7   0
  19P GAIN WILD-TYPE 413  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7    0
  19P GAIN WILD-TYPE  413   17
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 7                413
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  19P GAIN MUTATED              1                       0    7
  19P GAIN WILD-TYPE          131                      18  323
                    vv
clus                 VERY ADVANCED (T4B)
  19P GAIN MUTATED                     0
  19P GAIN WILD-TYPE                   1
D26V11, multiclass
                         clus
vv                        19P GAIN MUTATED 19P GAIN WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   7                323
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED     6   1   0   1
  19P GAIN WILD-TYPE 377  50   4  29
D26V12, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                6                377
  R1                1                 50
  R2                0                  4
  RX                1                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, continuous
D26V14, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     6   2
  19P GAIN WILD-TYPE 219 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6    2
  19P GAIN WILD-TYPE  219  262
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  MULTIFOCAL                6                219
  UNIFOCAL                  2                262
[1] 2 2
[1] FALSE
D26V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     0
  19P GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           0     3
  19P GAIN WILD-TYPE                        27   326
D26V16, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           3                326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V17, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0   3
  19P GAIN WILD-TYPE  38 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    3
  19P GAIN WILD-TYPE   38  357
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                3                357
[1] 2 2
[1] FALSE

Clustering(27) Variable = 19Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED     9   1
  19Q GAIN WILD-TYPE 473  15
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                488 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 15 
$`19Q GAIN MUTATED`
TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A22N TCGA-EM-A2OY TCGA-EM-A3O9 TCGA-EM-A3SY 
       23.90        78.61        10.65        32.32         9.24        13.51 
TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3WA TCGA-FY-A4B0 
       33.63         7.82        17.06        13.81 

$`19Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       31.30        30.84        25.45        30.61        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 
       37.94        57.01       106.62        79.50        98.53        69.57 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        49.51       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX 
       43.36        49.71        83.57       139.00       108.66        57.63 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       52.50        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        91.17        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       72.69        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        61.02        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        53.36        44.15        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       24.30        27.06        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       18.05        19.79        19.46        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P 
       14.50        15.75        10.45        14.53        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        44.52 
TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
        8.35        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
       15.06         7.33        12.53        27.02        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.95        29.85        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A 
       68.22       117.40        66.77       112.80        39.95        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82        29.10        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3YR TCGA-FY-A40K 
       16.57        18.08        23.31        21.63        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       23.87        22.49        19.04        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              7.82               0.20 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             78.61             178.29 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            15.435             31.285 
[1] "7.8 - 78.6 (15.4)"  "0.2 - 178.3 (31.3)"
[1] "hr=" "6.1"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  19Q GAIN MUTATED         5        1         4        0         0         0
  19Q GAIN WILD-TYPE     277       49       107        2        46         6
D27V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  5                277
  STAGE II                 1                 49
  STAGE III                4                107
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  19Q GAIN MUTATED     4   1   5   0
  19Q GAIN WILD-TYPE 138 164 162  23
D27V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                4                138
  T2                1                164
  T3                5                162
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     7   0
  19Q GAIN WILD-TYPE 218 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      7    0
  19Q GAIN WILD-TYPE  218  224
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                7                218
  1                0                224
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0   0
  19Q GAIN WILD-TYPE 278   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    0
  19Q GAIN WILD-TYPE  278    9
D27V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     5   5
  19Q GAIN WILD-TYPE 360 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      5    5
  19Q GAIN WILD-TYPE  360  129
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                5                360
  MALE                  5                129
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2   7
  19Q GAIN WILD-TYPE 178 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    7
  19Q GAIN WILD-TYPE  178  296
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 2                178
  YES                7                296
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  19Q GAIN MUTATED                0
  19Q GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  19Q GAIN MUTATED                                               3
  19Q GAIN WILD-TYPE                                           353
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  19Q GAIN MUTATED                                                                        7
  19Q GAIN WILD-TYPE                                                                     93
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  19Q GAIN MUTATED                                                                     0
  19Q GAIN WILD-TYPE                                                                  36
D27V9, multiclass
                                                                        clus
vv                                                                       19Q GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       19Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     9   0
  19Q GAIN WILD-TYPE 411  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      9    0
  19Q GAIN WILD-TYPE  411   17
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 9                411
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  19Q GAIN MUTATED              1                       0    9
  19Q GAIN WILD-TYPE          131                      18  321
                    vv
clus                 VERY ADVANCED (T4B)
  19Q GAIN MUTATED                     0
  19Q GAIN WILD-TYPE                   1
D27V11, multiclass
                         clus
vv                        19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   9                321
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED     8   1   0   1
  19Q GAIN WILD-TYPE 375  50   4  29
D27V12, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0                8                375
  R1                1                 50
  R2                0                  4
  RX                1                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, continuous
D27V14, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     6   4
  19Q GAIN WILD-TYPE 219 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      6    4
  19Q GAIN WILD-TYPE  219  260
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  MULTIFOCAL                6                219
  UNIFOCAL                  4                260
[1] 2 2
[1] FALSE
D27V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     0
  19Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           0     5
  19Q GAIN WILD-TYPE                        27   324
D27V16, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           5                324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V17, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0   5
  19Q GAIN WILD-TYPE  38 355
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    5
  19Q GAIN WILD-TYPE   38  355
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                355
[1] 2 2
[1] FALSE

Clustering(28) Variable = 20P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    11   1
  20P GAIN WILD-TYPE 471  15
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                486 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                 15 
$`20P GAIN MUTATED`
TCGA-EL-A3T9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A2CO TCGA-EM-A2OY 
        5.72        23.90        78.61        57.01         6.05        32.32 
TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       22.52         9.24        13.51        37.25       123.32         7.82 

$`20P GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       31.30        30.84        25.45        30.61        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 
       37.94        57.01       106.62        79.50        98.53        69.57 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        49.51       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX 
       43.36        49.71        83.57       139.00       108.66        57.63 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       52.50        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       98.24        41.29       107.47        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       27.06        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       47.57        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       48.46        13.15        22.16        40.34        19.73        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.59        17.46        17.29        14.60        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        44.52         8.35        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33        12.53 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       27.02        38.66        38.86        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       65.29        18.38        63.45        88.41        58.75        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
        9.50        36.10        32.45        30.21        12.89         3.02 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              5.72               0.20 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            123.32             178.29 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             23.21              31.27 
[1] "5.7 - 123.3 (23.2)" "0.2 - 178.3 (31.3)"
[1] "hr=" "3.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  20P GAIN MUTATED         4        4         3        1         0         0
  20P GAIN WILD-TYPE     278       46       108        1        46         6
D28V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  4                278
  STAGE II                 4                 46
  STAGE III                3                108
  STAGE IV                 1                  1
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  20P GAIN MUTATED     2   4   5   1
  20P GAIN WILD-TYPE 140 161 162  22
D28V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                2                140
  T2                4                161
  T3                5                162
  T4                1                 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"
D28V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     7   1
  20P GAIN WILD-TYPE 218 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7    1
  20P GAIN WILD-TYPE  218  223
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0                7                218
  1                1                223
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     0   0
  20P GAIN WILD-TYPE 278   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      0    0
  20P GAIN WILD-TYPE  278    9
D28V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     8   4
  20P GAIN WILD-TYPE 357 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      8    4
  20P GAIN WILD-TYPE  357  130
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                8                357
  MALE                  4                130
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     3   7
  20P GAIN WILD-TYPE 177 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3    7
  20P GAIN WILD-TYPE  177  296
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 3                177
  YES                7                296
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  20P GAIN MUTATED                0
  20P GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  20P GAIN MUTATED                                               4
  20P GAIN WILD-TYPE                                           352
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  20P GAIN MUTATED                                                                        8
  20P GAIN WILD-TYPE                                                                     92
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  20P GAIN MUTATED                                                                     0
  20P GAIN WILD-TYPE                                                                  36
D28V9, multiclass
                                                                        clus
vv                                                                       20P GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       20P GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 92
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    11   0
  20P GAIN WILD-TYPE 409  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     11    0
  20P GAIN WILD-TYPE  409   17
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                11                409
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  20P GAIN MUTATED              1                       0   10
  20P GAIN WILD-TYPE          131                      18  320
                    vv
clus                 VERY ADVANCED (T4B)
  20P GAIN MUTATED                     1
  20P GAIN WILD-TYPE                   0
D28V11, multiclass
                         clus
vv                        20P GAIN MUTATED 20P GAIN WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                  10                320
  VERY ADVANCED (T4B)                    1                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED    10   1   0   1
  20P GAIN WILD-TYPE 373  50   4  29
D28V12, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               10                373
  R1                1                 50
  R2                0                  4
  RX                1                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, continuous
D28V14, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     6   6
  20P GAIN WILD-TYPE 219 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      6    6
  20P GAIN WILD-TYPE  219  258
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  MULTIFOCAL                6                219
  UNIFOCAL                  6                258
[1] 2 2
[1] FALSE
D28V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     0
  20P GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                           0     6
  20P GAIN WILD-TYPE                        27   323
D28V16, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           6                323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V17, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     0   6
  20P GAIN WILD-TYPE  38 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      0    6
  20P GAIN WILD-TYPE   38  354
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                354
[1] 2 2
[1] FALSE

Clustering(29) Variable = 20Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    11   1
  20Q GAIN WILD-TYPE 471  15
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                486 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                 15 
$`20Q GAIN MUTATED`
TCGA-EL-A3T9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A2CO TCGA-EM-A2OY 
        5.72        23.90        78.61        57.01         6.05        32.32 
TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       22.52         9.24        13.51        37.25       123.32         7.82 

$`20Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       31.30        30.84        25.45        30.61        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 
       37.94        57.01       106.62        79.50        98.53        69.57 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        49.51       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX 
       43.36        49.71        83.57       139.00       108.66        57.63 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       52.50        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       98.24        41.29       107.47        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       27.06        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       47.57        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       48.46        13.15        22.16        40.34        19.73        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.59        17.46        17.29        14.60        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        44.52         8.35        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33        12.53 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       27.02        38.66        38.86        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       65.29        18.38        63.45        88.41        58.75        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
        9.50        36.10        32.45        30.21        12.89         3.02 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              5.72               0.20 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            123.32             178.29 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             23.21              31.27 
[1] "5.7 - 123.3 (23.2)" "0.2 - 178.3 (31.3)"
[1] "hr=" "3.1"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  20Q GAIN MUTATED         4        4         3        1         0         0
  20Q GAIN WILD-TYPE     278       46       108        1        46         6
D29V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  4                278
  STAGE II                 4                 46
  STAGE III                3                108
  STAGE IV                 1                  1
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  20Q GAIN MUTATED     2   4   5   1
  20Q GAIN WILD-TYPE 140 161 162  22
D29V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                2                140
  T2                4                161
  T3                5                162
  T4                1                 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"
D29V5, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     7   1
  20Q GAIN WILD-TYPE 218 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      7    1
  20Q GAIN WILD-TYPE  218  223
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0                7                218
  1                1                223
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     0   0
  20Q GAIN WILD-TYPE 278   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0    0
  20Q GAIN WILD-TYPE  278    9
D29V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     8   4
  20Q GAIN WILD-TYPE 357 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8    4
  20Q GAIN WILD-TYPE  357  130
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                8                357
  MALE                  4                130
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     3   7
  20Q GAIN WILD-TYPE 177 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3    7
  20Q GAIN WILD-TYPE  177  296
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 3                177
  YES                7                296
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  20Q GAIN MUTATED                0
  20Q GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  20Q GAIN MUTATED                                               4
  20Q GAIN WILD-TYPE                                           352
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  20Q GAIN MUTATED                                                                        8
  20Q GAIN WILD-TYPE                                                                     92
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  20Q GAIN MUTATED                                                                     0
  20Q GAIN WILD-TYPE                                                                  36
D29V9, multiclass
                                                                        clus
vv                                                                       20Q GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       20Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 92
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    11   0
  20Q GAIN WILD-TYPE 409  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     11    0
  20Q GAIN WILD-TYPE  409   17
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                11                409
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  20Q GAIN MUTATED              1                       0   10
  20Q GAIN WILD-TYPE          131                      18  320
                    vv
clus                 VERY ADVANCED (T4B)
  20Q GAIN MUTATED                     1
  20Q GAIN WILD-TYPE                   0
D29V11, multiclass
                         clus
vv                        20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                  10                320
  VERY ADVANCED (T4B)                    1                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED    10   1   0   1
  20Q GAIN WILD-TYPE 373  50   4  29
D29V12, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               10                373
  R1                1                 50
  R2                0                  4
  RX                1                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, continuous
D29V14, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     6   6
  20Q GAIN WILD-TYPE 219 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6    6
  20Q GAIN WILD-TYPE  219  258
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  MULTIFOCAL                6                219
  UNIFOCAL                  6                258
[1] 2 2
[1] FALSE
D29V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     0
  20Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                           0     6
  20Q GAIN WILD-TYPE                        27   323
D29V16, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           6                323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V17, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     0   6
  20Q GAIN WILD-TYPE  38 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0    6
  20Q GAIN WILD-TYPE   38  354
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                354
[1] 2 2
[1] FALSE

Clustering(30) Variable = 21Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED     5   0
  21Q GAIN WILD-TYPE 477  16
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                493 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                 16 
$`21Q GAIN MUTATED`
TCGA-BJ-A45E TCGA-EL-A3ZR TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       21.01        60.16        13.51        37.25       123.32 

$`21Q GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         7.99        10.88         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       65.49        61.22         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       27.02        38.66        38.86        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       65.29        18.38        63.45        88.41        58.75        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25        20.42        17.82         7.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
       21.63        17.06        17.36        15.16        23.87        22.49 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04        13.81        14.04        21.60        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46        11.01        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       24.69        22.29         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV 
       40.37         9.50        36.10        32.45        30.21        12.89 
TCGA-E8-A418 
        3.02 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             13.51               0.20 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            123.32             178.29 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             37.25              31.23 
[1] "13.5 - 123.3 (37.2)" "0.2 - 178.3 (31.2)" 
[1] "hr="     "9100000"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  21Q GAIN MUTATED         4        1         0        0         0         0
  21Q GAIN WILD-TYPE     278       49       111        2        46         6
D30V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  4                278
  STAGE II                 1                 49
  STAGE III                0                111
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  21Q GAIN MUTATED     3   1   1   0
  21Q GAIN WILD-TYPE 139 164 166  23
D30V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                139
  T2                1                164
  T3                1                166
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3   0
  21Q GAIN WILD-TYPE 222 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    0
  21Q GAIN WILD-TYPE  222  224
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                3                222
  1                0                224
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     2   0
  21Q GAIN WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    0
  21Q GAIN WILD-TYPE  276    9
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                2                276
  1                0                  9
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3   2
  21Q GAIN WILD-TYPE 362 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    2
  21Q GAIN WILD-TYPE  362  132
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                3                362
  MALE                  2                132
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3   2
  21Q GAIN WILD-TYPE 177 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    2
  21Q GAIN WILD-TYPE  177  301
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 3                177
  YES                2                301
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  21Q GAIN MUTATED                0
  21Q GAIN WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  21Q GAIN MUTATED                                               4
  21Q GAIN WILD-TYPE                                           352
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  21Q GAIN MUTATED                                                                        1
  21Q GAIN WILD-TYPE                                                                     99
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  21Q GAIN MUTATED                                                                     0
  21Q GAIN WILD-TYPE                                                                  36
D30V9, multiclass
                                                                        clus
vv                                                                       21Q GAIN MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       21Q GAIN WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     4   0
  21Q GAIN WILD-TYPE 416  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4    0
  21Q GAIN WILD-TYPE  416   17
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 4                416
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  21Q GAIN MUTATED              0                       0    4
  21Q GAIN WILD-TYPE          132                      18  326
                    vv
clus                 VERY ADVANCED (T4B)
  21Q GAIN MUTATED                     0
  21Q GAIN WILD-TYPE                   1
D30V11, multiclass
                         clus
vv                        21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  MINIMAL (T3)                           0                132
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   4                326
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED     3   0   0   1
  21Q GAIN WILD-TYPE 380  51   4  29
D30V12, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0                3                380
  R1                0                 51
  R2                0                  4
  RX                1                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                384 
        TCGA-BJ-A290         TCGA-BJ-A291         TCGA-BJ-A45K 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CE-A13K         TCGA-DE-A0XZ         TCGA-DJ-A2PR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UU         TCGA-DJ-A3UW         TCGA-DJ-A3V4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VI         TCGA-DJ-A3VK         TCGA-E3-A3E5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CR         TCGA-EL-A3CS         TCGA-EL-A3CY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3D0         TCGA-EL-A3D5         TCGA-EL-A3GQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3H8         TCGA-EM-A3AQ         TCGA-ET-A3BO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-J8-A3NZ         TCGA-J8-A4HW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-4C-A93U         TCGA-BJ-A0Z0         TCGA-BJ-A0Z3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A0Z5         TCGA-BJ-A0Z9         TCGA-BJ-A0ZA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZB         TCGA-BJ-A0ZH         TCGA-BJ-A0ZJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A190 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A191         TCGA-BJ-A28R         TCGA-BJ-A28T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A28W         TCGA-BJ-A28X         TCGA-BJ-A28Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A2N8         TCGA-BJ-A2N9         TCGA-BJ-A2NA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A3EZ         TCGA-BJ-A3PR         TCGA-BJ-A3PU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A45C         TCGA-BJ-A45D         TCGA-BJ-A45G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A45I         TCGA-BJ-A45J         TCGA-BJ-A4O8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A4O9         TCGA-CE-A3MD         TCGA-CE-A483 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CE-A484         TCGA-CE-A485         TCGA-DE-A0Y2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DE-A0Y3         TCGA-DE-A3KN         TCGA-DE-A4M8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DE-A4MA         TCGA-DE-A4MB         TCGA-DE-A4MC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DE-A4MD         TCGA-DE-A69K         TCGA-DE-A7U5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A13M         TCGA-DJ-A13O         TCGA-DJ-A13R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A13T         TCGA-DJ-A13V         TCGA-DJ-A13W 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A13X         TCGA-DJ-A1QG         TCGA-DJ-A1QH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A2PO         TCGA-DJ-A2PP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PQ         TCGA-DJ-A2PS         TCGA-DJ-A2PT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PU         TCGA-DJ-A2PV         TCGA-DJ-A2PW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PX         TCGA-DJ-A2PY         TCGA-DJ-A2PZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q0         TCGA-DJ-A2Q1         TCGA-DJ-A2Q2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q3         TCGA-DJ-A2Q4         TCGA-DJ-A2Q5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q6         TCGA-DJ-A2Q7         TCGA-DJ-A2Q8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q9         TCGA-DJ-A2QA         TCGA-DJ-A2QB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UK         TCGA-DJ-A3UM         TCGA-DJ-A3UN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UO         TCGA-DJ-A3UP         TCGA-DJ-A3UQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UR         TCGA-DJ-A3UX         TCGA-DJ-A3UZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V0         TCGA-DJ-A3V2         TCGA-DJ-A3V3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V5         TCGA-DJ-A3V7         TCGA-DJ-A3V8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V9         TCGA-DJ-A3VA         TCGA-DJ-A3VB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VD         TCGA-DJ-A3VF         TCGA-DJ-A3VG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VJ         TCGA-DJ-A3VL         TCGA-DJ-A4UL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A4UP         TCGA-DJ-A4UQ         TCGA-DJ-A4UR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A4UW         TCGA-DJ-A4V2         TCGA-DJ-A4V5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-DO-A2HM         TCGA-E3-A3DY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E3-A3DZ         TCGA-E3-A3E0         TCGA-E3-A3E1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E3-A3E2         TCGA-E3-A3E3         TCGA-E8-A242 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E8-A2EA         TCGA-E8-A414         TCGA-E8-A415 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E8-A417         TCGA-E8-A419         TCGA-E8-A433 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E8-A436         TCGA-E8-A438         TCGA-E8-A44K 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3D1         TCGA-EL-A3D4         TCGA-EL-A3D6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GU         TCGA-EL-A3GV         TCGA-EL-A3GX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3H3         TCGA-EL-A3H4         TCGA-EL-A3H5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3H7         TCGA-EL-A3MW         TCGA-EL-A3MX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3T0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3T1         TCGA-EL-A3T2         TCGA-EL-A3TB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZH         TCGA-EL-A3ZK         TCGA-EL-A3ZL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZM         TCGA-EL-A3ZN         TCGA-EL-A3ZO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZP         TCGA-EL-A3ZS         TCGA-EL-A4JV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A4JW         TCGA-EL-A4JX         TCGA-EL-A4JZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A4K0         TCGA-EL-A4K1         TCGA-EL-A4K2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A4K4         TCGA-EL-A4K6         TCGA-EL-A4K7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A4KD         TCGA-EL-A4KG         TCGA-EL-A4KI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1CS         TCGA-EM-A1CT         TCGA-EM-A1CU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1CV         TCGA-EM-A1CW         TCGA-EM-A1YC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1YD         TCGA-EM-A1YE         TCGA-EM-A22I 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A22J         TCGA-EM-A22K         TCGA-EM-A22L 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22N         TCGA-EM-A22O 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A22P         TCGA-EM-A22Q         TCGA-EM-A2CK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CN         TCGA-EM-A2CP         TCGA-EM-A2CQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CT         TCGA-EM-A2CU         TCGA-EM-A2OV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2OX         TCGA-EM-A2OY         TCGA-EM-A2OZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2P0         TCGA-EM-A2P1         TCGA-EM-A2P2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3AJ         TCGA-EM-A3AK         TCGA-EM-A3AL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3AN         TCGA-EM-A3AO         TCGA-EM-A3AR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3FJ         TCGA-EM-A3FK         TCGA-EM-A3FM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3FN         TCGA-EM-A3FO         TCGA-EM-A3FP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3FQ         TCGA-EM-A3FR         TCGA-EM-A3O3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3O8         TCGA-EM-A3O9         TCGA-EM-A3OA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3OB         TCGA-EM-A3ST         TCGA-EM-A3SU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3SX         TCGA-EM-A3SZ         TCGA-EM-A4FF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A4FM         TCGA-EM-A4FN         TCGA-EM-A4FO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A4FQ         TCGA-EM-A4FR         TCGA-EM-A4FV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A4G1         TCGA-ET-A25G         TCGA-ET-A25I 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A25J         TCGA-ET-A25K         TCGA-ET-A25L 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25N         TCGA-ET-A25O 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A25P         TCGA-ET-A2MX         TCGA-ET-A2N0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N4         TCGA-ET-A39K 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A39L         TCGA-ET-A39O         TCGA-ET-A39P 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39S         TCGA-ET-A39T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3BP         TCGA-ET-A3BQ         TCGA-ET-A3BS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3BT         TCGA-ET-A3BU         TCGA-ET-A3BX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3DQ         TCGA-ET-A3DR         TCGA-ET-A3DS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DU         TCGA-ET-A3DV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-ET-A40P         TCGA-ET-A40Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A40R         TCGA-ET-A40S         TCGA-ET-A40T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A4KN         TCGA-FE-A22Z         TCGA-FE-A230 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A231         TCGA-FE-A232         TCGA-FE-A233 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A234         TCGA-FE-A235         TCGA-FE-A236 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A237         TCGA-FE-A238         TCGA-FE-A239 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A23A         TCGA-FE-A3PB         TCGA-FE-A3PC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A3PD         TCGA-FK-A3S3         TCGA-FK-A3SB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FK-A3SE         TCGA-FK-A3SG         TCGA-FK-A3SH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FK-A4UB         TCGA-FY-A2QD         TCGA-FY-A3I4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A3I5         TCGA-FY-A3NM         TCGA-FY-A3NN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A3ON         TCGA-FY-A3R6         TCGA-FY-A3R7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A3R9         TCGA-FY-A3TY         TCGA-FY-A3W9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A3YR         TCGA-FY-A40K         TCGA-FY-A40L 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A40M         TCGA-FY-A40N         TCGA-FY-A4B3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A4B4         TCGA-GE-A2C6         TCGA-H2-A26U 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-H2-A2K9         TCGA-H2-A3RH         TCGA-H2-A3RI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-H2-A421         TCGA-H2-A422         TCGA-IM-A3EB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IM-A3ED         TCGA-IM-A3U2         TCGA-IM-A3U3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IM-A41Y         TCGA-IM-A41Z         TCGA-IM-A420 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IM-A4EB         TCGA-J8-A3O0         TCGA-J8-A3O1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-J8-A3O2         TCGA-J8-A3YD         TCGA-J8-A3YE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-J8-A3YF         TCGA-J8-A3YG         TCGA-J8-A3YH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-J8-A42S         TCGA-J8-A4HY         TCGA-KS-A41F 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KS-A41I         TCGA-KS-A41J         TCGA-KS-A41L 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KS-A4I1         TCGA-KS-A4I3         TCGA-KS-A4I5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KS-A4I7         TCGA-KS-A4I9         TCGA-KS-A4IB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KS-A4IC         TCGA-KS-A4ID         TCGA-L6-A4EP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-L6-A4EQ         TCGA-L6-A4EU         TCGA-MK-A4N6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-MK-A4N7         TCGA-MK-A4N9         TCGA-QD-A8IV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D30V14, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0   5
  21Q GAIN WILD-TYPE 225 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    5
  21Q GAIN WILD-TYPE  225  259
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  MULTIFOCAL                0                225
  UNIFOCAL                  5                259
[1] 2 2
[1] FALSE
D30V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     0
  21Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           0     4
  21Q GAIN WILD-TYPE                        27   325
D30V16, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           4                325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V17, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0   4
  21Q GAIN WILD-TYPE  38 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    4
  21Q GAIN WILD-TYPE   38  356
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                4                356
[1] 2 2
[1] FALSE

Clustering(31) Variable = XP GAIN MUTATION ANALYSIS
D31V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED     7   1
  XP GAIN WILD-TYPE 475  15
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                8               490 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                15 
$`XP GAIN MUTATED`
TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A3AI 
       20.48         5.72        78.61        57.01        10.65        22.52 
TCGA-ET-A40S TCGA-FY-A3NM 
       40.21        29.10 

$`XP GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29       107.47        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ 
       33.96        17.59        17.46        17.29        14.60        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR 
       15.68        14.14        33.07        44.52         8.35        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        27.02        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       43.99        46.26        44.38        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         7.82        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08        23.31        21.63        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 
       15.16        23.87        22.49        19.04        13.81        14.04 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       21.83        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       32.45        30.21        12.89         3.02 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             5.72              0.20 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            78.61            178.29 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            25.81             31.27 
[1] "5.7 - 78.6 (25.8)"  "0.2 - 178.3 (31.3)"
[1] "hr=" "4.9"
D31V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  XP GAIN MUTATED         2        3         2        1         0         0
  XP GAIN WILD-TYPE     280       47       109        1        46         6
D31V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 2               280
  STAGE II                3                47
  STAGE III               2               109
  STAGE IV                1                 1
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  XP GAIN MUTATED     1   4   2   1
  XP GAIN WILD-TYPE 141 161 165  22
D31V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               1               141
  T2               4               161
  T3               2               165
  T4               1                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"
D31V5, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     6   1
  XP GAIN WILD-TYPE 219 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      6    1
  XP GAIN WILD-TYPE  219  223
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0               6               219
  1               1               223
[1] 2 2
[1] FALSE
D31V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     1   0
  XP GAIN WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1    0
  XP GAIN WILD-TYPE  277    9
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0               1               277
  1               0                 9
[1] 2 2
[1] FALSE
D31V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     7   1
  XP GAIN WILD-TYPE 358 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      7    1
  XP GAIN WILD-TYPE  358  133
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               7               358
  MALE                 1               133
[1] 2 2
[1] FALSE
D31V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     2   4
  XP GAIN WILD-TYPE 178 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2    4
  XP GAIN WILD-TYPE  178  299
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                2               178
  YES               4               299
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  XP GAIN MUTATED                0
  XP GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  XP GAIN MUTATED                                               4
  XP GAIN WILD-TYPE                                           352
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  XP GAIN MUTATED                                                                        4
  XP GAIN WILD-TYPE                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  XP GAIN MUTATED                                                                     0
  XP GAIN WILD-TYPE                                                                  36
D31V9, multiclass
                                                                        clus
vv                                                                       XP GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       XP GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     7   1
  XP GAIN WILD-TYPE 413  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      7    1
  XP GAIN WILD-TYPE  413   16
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                7               413
  YES               1                16
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  XP GAIN MUTATED              1                       0    6
  XP GAIN WILD-TYPE          131                      18  324
                   vv
clus                VERY ADVANCED (T4B)
  XP GAIN MUTATED                     1
  XP GAIN WILD-TYPE                   0
D31V11, multiclass
                         clus
vv                        XP GAIN MUTATED XP GAIN WILD-TYPE
  MINIMAL (T3)                          1               131
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  6               324
  VERY ADVANCED (T4B)                   1                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED     4   2   0   2
  XP GAIN WILD-TYPE 379  49   4  28
D31V12, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0               4               379
  R1               2                49
  R2               0                 4
  RX               2                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, continuous
D31V14, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     5   3
  XP GAIN WILD-TYPE 220 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      5    3
  XP GAIN WILD-TYPE  220  261
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  MULTIFOCAL               5               220
  UNIFOCAL                 3               261
[1] 2 2
[1] FALSE
D31V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  0     0
  XP GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                           0     5
  XP GAIN WILD-TYPE                        27   324
D31V16, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                          5               324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V17, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0   5
  XP GAIN WILD-TYPE  38 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0    5
  XP GAIN WILD-TYPE   38  355
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               5               355
[1] 2 2
[1] FALSE

Clustering(32) Variable = XQ GAIN MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     6   1
  XQ GAIN WILD-TYPE 476  15
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7               491 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                15 
$`XQ GAIN MUTATED`
TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A3AI 
       20.48         5.72        78.61        57.01        10.65        22.52 
TCGA-FY-A3NM 
       29.10 

$`XQ GAIN WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29       107.47        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ 
       33.96        17.59        17.46        17.29        14.60        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR 
       15.68        14.14        33.07        44.52         8.35        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        27.02        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        4.11        22.03         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82         7.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08        23.31        21.63        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 
       17.36        15.16        23.87        22.49        19.04        13.81 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       14.04        21.60        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       11.01        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 
       16.90        21.83        31.10         8.22        25.64        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        5.75         2.47         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU 
       84.72        35.28        33.24        33.40        40.37         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       36.10        32.45        30.21        12.89         3.02 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             5.72              0.20 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            78.61            178.29 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            22.52             31.27 
[1] "5.7 - 78.6 (22.5)"  "0.2 - 178.3 (31.3)"
[1] "hr=" "5.7"
D32V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  XQ GAIN MUTATED         2        2         2        1         0         0
  XQ GAIN WILD-TYPE     280       48       109        1        46         6
D32V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 2               280
  STAGE II                2                48
  STAGE III               2               109
  STAGE IV                1                 1
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  XQ GAIN MUTATED     1   3   2   1
  XQ GAIN WILD-TYPE 141 162 165  22
D32V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               1               141
  T2               3               162
  T3               2               165
  T4               1                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"
D32V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     5   1
  XQ GAIN WILD-TYPE 220 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      5    1
  XQ GAIN WILD-TYPE  220  223
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               5               220
  1               1               223
[1] 2 2
[1] FALSE
D32V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1   0
  XQ GAIN WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1    0
  XQ GAIN WILD-TYPE  277    9
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               1               277
  1               0                 9
[1] 2 2
[1] FALSE
D32V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     7   0
  XQ GAIN WILD-TYPE 358 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      7    0
  XQ GAIN WILD-TYPE  358  134
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               7               358
  MALE                 0               134
[1] 2 2
[1] FALSE
D32V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     2   3
  XQ GAIN WILD-TYPE 178 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    3
  XQ GAIN WILD-TYPE  178  300
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                2               178
  YES               3               300
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  XQ GAIN MUTATED                0
  XQ GAIN WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  XQ GAIN MUTATED                                               3
  XQ GAIN WILD-TYPE                                           353
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  XQ GAIN MUTATED                                                                        4
  XQ GAIN WILD-TYPE                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  XQ GAIN MUTATED                                                                     0
  XQ GAIN WILD-TYPE                                                                  36
D32V9, multiclass
                                                                        clus
vv                                                                       XQ GAIN MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       XQ GAIN WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     7   0
  XQ GAIN WILD-TYPE 413  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      7    0
  XQ GAIN WILD-TYPE  413   17
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                7               413
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  XQ GAIN MUTATED              1                       0    5
  XQ GAIN WILD-TYPE          131                      18  325
                   vv
clus                VERY ADVANCED (T4B)
  XQ GAIN MUTATED                     1
  XQ GAIN WILD-TYPE                   0
D32V11, multiclass
                         clus
vv                        XQ GAIN MUTATED XQ GAIN WILD-TYPE
  MINIMAL (T3)                          1               131
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  5               325
  VERY ADVANCED (T4B)                   1                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED     4   2   0   1
  XQ GAIN WILD-TYPE 379  49   4  29
D32V12, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0               4               379
  R1               2                49
  R2               0                 4
  RX               1                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, continuous
D32V14, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     4   3
  XQ GAIN WILD-TYPE 221 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4    3
  XQ GAIN WILD-TYPE  221  261
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  MULTIFOCAL               4               221
  UNIFOCAL                 3               261
[1] 2 2
[1] FALSE
D32V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     0
  XQ GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           0     4
  XQ GAIN WILD-TYPE                        27   325
D32V16, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                          4               325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V17, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0   4
  XQ GAIN WILD-TYPE  38 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    4
  XQ GAIN WILD-TYPE   38  356
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               4               356
[1] 2 2
[1] FALSE

Clustering(33) Variable = 1P LOSS MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED     4   0
  1P LOSS WILD-TYPE 478  16
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               494 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                0                16 
$`1P LOSS MUTATED`
TCGA-E8-A432 TCGA-EM-A1YE TCGA-ET-A39N TCGA-FY-A3I5 
       30.61        54.08       123.32         7.82 

$`1P LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       31.30        30.84        25.45        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I 
       18.05        19.79        19.46        78.61        57.01        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       27.02        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       33.24       106.09       107.41       108.46        84.89       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP 
       95.34        94.13        55.10        98.20        28.24        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        87.62        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10       116.09         1.25        20.42        17.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             7.82              0.20 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           123.32            178.29 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           42.345            31.250 
[1] "7.8 - 123.3 (42.3)" "0.2 - 178.3 (31.2)"
[1] "hr="     "9100000"
D33V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  1P LOSS MUTATED         1        2         1        0         0         0
  1P LOSS WILD-TYPE     281       48       110        2        46         6
D33V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 1               281
  STAGE II                2                48
  STAGE III               1               110
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  1P LOSS MUTATED     0   2   2   0
  1P LOSS WILD-TYPE 142 163 165  23
D33V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               0               142
  T2               2               163
  T3               2               165
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3   0
  1P LOSS WILD-TYPE 222 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    0
  1P LOSS WILD-TYPE  222  224
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0               3               222
  1               0               224
[1] 2 2
[1] FALSE
D33V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1   0
  1P LOSS WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    0
  1P LOSS WILD-TYPE  277    9
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0               1               277
  1               0                 9
[1] 2 2
[1] FALSE
D33V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     4   0
  1P LOSS WILD-TYPE 361 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4    0
  1P LOSS WILD-TYPE  361  134
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               4               361
  MALE                 0               134
[1] 2 2
[1] FALSE
D33V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1   2
  1P LOSS WILD-TYPE 179 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    2
  1P LOSS WILD-TYPE  179  301
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                1               179
  YES               2               301
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  1P LOSS MUTATED                0
  1P LOSS WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  1P LOSS MUTATED                                               2
  1P LOSS WILD-TYPE                                           354
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  1P LOSS MUTATED                                                                        2
  1P LOSS WILD-TYPE                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  1P LOSS MUTATED                                                                     0
  1P LOSS WILD-TYPE                                                                  36
D33V9, multiclass
                                                                        clus
vv                                                                       1P LOSS MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       1P LOSS WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3   0
  1P LOSS WILD-TYPE 417  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    0
  1P LOSS WILD-TYPE  417   17
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                3               417
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  1P LOSS MUTATED              0                       0    4
  1P LOSS WILD-TYPE          132                      18  326
                   vv
clus                VERY ADVANCED (T4B)
  1P LOSS MUTATED                     0
  1P LOSS WILD-TYPE                   1
D33V11, multiclass
                         clus
vv                        1P LOSS MUTATED 1P LOSS WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  4               326
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED     4   0   0   0
  1P LOSS WILD-TYPE 379  51   4  30
D33V12, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0               4               379
  R1               0                51
  R2               0                 4
  RX               0                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2               384 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A45K        TCGA-CE-A13K 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DJ-A2PR        TCGA-DJ-A3UU        TCGA-DJ-A3UW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3V4        TCGA-DJ-A3VI        TCGA-DJ-A3VK        TCGA-E3-A3E5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CY        TCGA-EL-A3D0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3GQ        TCGA-EL-A3H8        TCGA-EM-A3AQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BV        TCGA-J8-A3NZ        TCGA-J8-A4HW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-4C-A93U        TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZJ        TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A191        TCGA-BJ-A28R        TCGA-BJ-A28T        TCGA-BJ-A28W 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A28X        TCGA-BJ-A28Z        TCGA-BJ-A2N8        TCGA-BJ-A2N9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR        TCGA-BJ-A3PU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A4O8        TCGA-BJ-A4O9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN        TCGA-DE-A4M8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13V        TCGA-DJ-A13W 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PO        TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PT        TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PX        TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3UM        TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3UQ        TCGA-DJ-A3UR        TCGA-DJ-A3UX        TCGA-DJ-A3UZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3V0        TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9        TCGA-DJ-A3VA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3VB        TCGA-DJ-A3VD        TCGA-DJ-A3VF        TCGA-DJ-A3VG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A4UL        TCGA-DJ-A4UP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW        TCGA-DJ-A4V2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A4V5        TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E3-A3E3        TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A414 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E8-A415        TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E8-A436        TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CT        TCGA-EL-A3CU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D6        TCGA-EL-A3GO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3T0        TCGA-EL-A3T1        TCGA-EL-A3T2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3TB        TCGA-EL-A3ZH        TCGA-EL-A3ZK        TCGA-EL-A3ZL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3ZM        TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3ZS        TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4KD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A4KG        TCGA-EL-A4KI        TCGA-EM-A1CS        TCGA-EM-A1CT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A1YD        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22N        TCGA-EM-A22O 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A22P        TCGA-EM-A22Q        TCGA-EM-A2CK        TCGA-EM-A2CN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CT        TCGA-EM-A2CU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OX        TCGA-EM-A2OY        TCGA-EM-A2OZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2P0        TCGA-EM-A2P1        TCGA-EM-A2P2        TCGA-EM-A3AJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3AK        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3AR        TCGA-EM-A3FJ        TCGA-EM-A3FK        TCGA-EM-A3FM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O8        TCGA-EM-A3O9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST        TCGA-EM-A3SU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3SX        TCGA-EM-A3SZ        TCGA-EM-A4FF        TCGA-EM-A4FM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ        TCGA-EM-A4FR 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G        TCGA-ET-A25I 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A2MX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A39K        TCGA-ET-A39L        TCGA-ET-A39O        TCGA-ET-A39P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BX        TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A40P        TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A40T        TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A3PD        TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FK-A3SG        TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FY-A3R6        TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-H2-A3RI        TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IM-A3ED        TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IM-A41Z        TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3O0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I        TCGA-KS-A41J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3        TCGA-KS-A4I5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB        TCGA-KS-A4IC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ        TCGA-L6-A4EU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9        TCGA-QD-A8IV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D33V14, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1   3
  1P LOSS WILD-TYPE 224 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    3
  1P LOSS WILD-TYPE  224  261
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  MULTIFOCAL               1               224
  UNIFOCAL                 3               261
[1] 2 2
[1] FALSE
D33V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     1
  1P LOSS WILD-TYPE                                1    51
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           0     2
  1P LOSS WILD-TYPE                        27   327
D33V16, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                51
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                          2               327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V17, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0   3
  1P LOSS WILD-TYPE  38 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0    3
  1P LOSS WILD-TYPE   38  357
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               357
[1] 2 2
[1] FALSE

Clustering(34) Variable = 1Q LOSS MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED     3   0
  1Q LOSS WILD-TYPE 479  16
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               495 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                0                16 
$`1Q LOSS MUTATED`
TCGA-EM-A1YE TCGA-ET-A39N TCGA-FY-A3I5 
       54.08       123.32         7.82 

$`1Q LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       31.30        30.84        25.45        30.61        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 
       37.94        57.01       106.62        79.50        98.53        69.57 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        49.51       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX 
       43.36        49.71        83.57       139.00       108.66        57.63 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       52.50        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        91.17        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       72.69        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        61.02        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        53.36        44.15        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       24.30        27.06        23.90        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       48.49        18.05        19.79        19.46        78.61        57.01 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        44.52         8.35        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        27.02        38.66        38.86        29.95        29.85 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       58.75        37.25        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW 
       79.10        76.64         5.79        87.62        77.82        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77       112.80        39.95        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE 
       85.15        85.68        78.77        71.08         4.11        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       29.10        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08        23.31        21.63        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 
       23.87        22.49        19.04        13.81        14.04        21.60 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
       31.10         8.22        25.64        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.24        33.40        40.37         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             7.82              0.20 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           123.32            178.29 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            54.08             31.23 
[1] "7.8 - 123.3 (54.1)" "0.2 - 178.3 (31.2)"
[1] "hr="     "9100000"
D34V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  1Q LOSS MUTATED         1        1         1        0         0         0
  1Q LOSS WILD-TYPE     281       49       110        2        46         6
D34V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 1               281
  STAGE II                1                49
  STAGE III               1               110
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  1Q LOSS MUTATED     0   1   2   0
  1Q LOSS WILD-TYPE 142 164 165  23
D34V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               0               142
  T2               1               164
  T3               2               165
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2   0
  1Q LOSS WILD-TYPE 223 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    0
  1Q LOSS WILD-TYPE  223  224
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               2               223
  1               0               224
[1] 2 2
[1] FALSE
D34V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   0
  1Q LOSS WILD-TYPE 278   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    0
  1Q LOSS WILD-TYPE  278    9
D34V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3   0
  1Q LOSS WILD-TYPE 362 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    0
  1Q LOSS WILD-TYPE  362  134
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               3               362
  MALE                 0               134
[1] 2 2
[1] FALSE
D34V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   2
  1Q LOSS WILD-TYPE 180 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    2
  1Q LOSS WILD-TYPE  180  301
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                0               180
  YES               2               301
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  1Q LOSS MUTATED                0
  1Q LOSS WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  1Q LOSS MUTATED                                               1
  1Q LOSS WILD-TYPE                                           355
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  1Q LOSS MUTATED                                                                        2
  1Q LOSS WILD-TYPE                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  1Q LOSS MUTATED                                                                     0
  1Q LOSS WILD-TYPE                                                                  36
D34V9, multiclass
                                                                        clus
vv                                                                       1Q LOSS MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       1Q LOSS WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        355
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2   0
  1Q LOSS WILD-TYPE 418  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    0
  1Q LOSS WILD-TYPE  418   17
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                2               418
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  1Q LOSS MUTATED              0                       0    3
  1Q LOSS WILD-TYPE          132                      18  327
                   vv
clus                VERY ADVANCED (T4B)
  1Q LOSS MUTATED                     0
  1Q LOSS WILD-TYPE                   1
D34V11, multiclass
                         clus
vv                        1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  3               327
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED     3   0   0   0
  1Q LOSS WILD-TYPE 380  51   4  30
D34V12, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               3               380
  R1               0                51
  R2               0                 4
  RX               0                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, continuous
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2               384 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A45K        TCGA-CE-A13K 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DJ-A2PR        TCGA-DJ-A3UU        TCGA-DJ-A3UW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V4        TCGA-DJ-A3VI        TCGA-DJ-A3VK        TCGA-E3-A3E5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CY        TCGA-EL-A3D0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3GQ        TCGA-EL-A3H8        TCGA-EM-A3AQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BV        TCGA-J8-A3NZ        TCGA-J8-A4HW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-4C-A93U        TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0ZJ        TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A191        TCGA-BJ-A28R        TCGA-BJ-A28T        TCGA-BJ-A28W 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A28X        TCGA-BJ-A28Z        TCGA-BJ-A2N8        TCGA-BJ-A2N9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR        TCGA-BJ-A3PU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A4O8        TCGA-BJ-A4O9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN        TCGA-DE-A4M8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13V        TCGA-DJ-A13W 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PO        TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PT        TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PX        TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UM        TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UQ        TCGA-DJ-A3UR        TCGA-DJ-A3UX        TCGA-DJ-A3UZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V0        TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9        TCGA-DJ-A3VA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3VB        TCGA-DJ-A3VD        TCGA-DJ-A3VF        TCGA-DJ-A3VG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A4UL        TCGA-DJ-A4UP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW        TCGA-DJ-A4V2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A4V5        TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E3-A3E3        TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A414 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A415        TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A436        TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CT        TCGA-EL-A3CU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D6        TCGA-EL-A3GO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3T0        TCGA-EL-A3T1        TCGA-EL-A3T2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3TB        TCGA-EL-A3ZH        TCGA-EL-A3ZK        TCGA-EL-A3ZL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZM        TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZS        TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4KD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4KG        TCGA-EL-A4KI        TCGA-EM-A1CS        TCGA-EM-A1CT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A1YD        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22N        TCGA-EM-A22O 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A22P        TCGA-EM-A22Q        TCGA-EM-A2CK        TCGA-EM-A2CN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CT        TCGA-EM-A2CU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OX        TCGA-EM-A2OY        TCGA-EM-A2OZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2P0        TCGA-EM-A2P1        TCGA-EM-A2P2        TCGA-EM-A3AJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3AK        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3AR        TCGA-EM-A3FJ        TCGA-EM-A3FK        TCGA-EM-A3FM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O8        TCGA-EM-A3O9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST        TCGA-EM-A3SU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3SX        TCGA-EM-A3SZ        TCGA-EM-A4FF        TCGA-EM-A4FM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ        TCGA-EM-A4FR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G        TCGA-ET-A25I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A2MX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A39K        TCGA-ET-A39L        TCGA-ET-A39O        TCGA-ET-A39P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BX        TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A40P        TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A40T        TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A3PD        TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FK-A3SG        TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3R6        TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-H2-A3RI        TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IM-A3ED        TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IM-A41Z        TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3O0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I        TCGA-KS-A41J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3        TCGA-KS-A4I5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB        TCGA-KS-A4IC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ        TCGA-L6-A4EU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9        TCGA-QD-A8IV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D34V14, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1   2
  1Q LOSS WILD-TYPE 224 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    2
  1Q LOSS WILD-TYPE  224  262
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  MULTIFOCAL               1               224
  UNIFOCAL                 2               262
[1] 2 2
[1] FALSE
D34V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     0
  1Q LOSS WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           0     2
  1Q LOSS WILD-TYPE                        27   327
D34V16, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2               407 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A45K        TCGA-CE-A13K 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DJ-A13L        TCGA-DJ-A2PR        TCGA-DJ-A3UU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UW        TCGA-DJ-A3V4        TCGA-DJ-A3VI        TCGA-DJ-A3VK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D5        TCGA-EL-A3GQ        TCGA-EL-A3H2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MY        TCGA-EL-A3N3        TCGA-ET-A3BO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-FK-A3SD        TCGA-FY-A76V        TCGA-J8-A3NZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-L6-A4ET        TCGA-MK-A84Z        TCGA-4C-A93U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A2N7        TCGA-BJ-A2N8        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-BJ-A3PR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A3PT        TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A45E        TCGA-BJ-A45F        TCGA-BJ-A45G        TCGA-BJ-A45H 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A4O8        TCGA-BJ-A4O9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CE-A482        TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL        TCGA-DE-A3KN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA        TCGA-DE-A4MB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J        TCGA-DE-A69K 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13T        TCGA-DJ-A13U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13W        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QI        TCGA-DJ-A1QM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QO        TCGA-DJ-A1QQ        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PS        TCGA-DJ-A2PT        TCGA-DJ-A2PU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX        TCGA-DJ-A2PY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q7        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN        TCGA-DJ-A3UO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UQ        TCGA-DJ-A3UR        TCGA-DJ-A3US        TCGA-DJ-A3UT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UX        TCGA-DJ-A3UY        TCGA-DJ-A3UZ        TCGA-DJ-A3V2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V3        TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V9        TCGA-DJ-A3VD        TCGA-DJ-A3VE        TCGA-DJ-A3VF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A3VM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A4UL        TCGA-DJ-A4UP        TCGA-DJ-A4UQ        TCGA-DJ-A4UR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A4UT        TCGA-DJ-A4UW        TCGA-DJ-A4V0        TCGA-DJ-A4V4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A4V5        TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-DO-A2HM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E8-A242        TCGA-E8-A2EA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A3X7        TCGA-E8-A413        TCGA-E8-A414        TCGA-E8-A415 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A416        TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A432 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A433        TCGA-E8-A434        TCGA-E8-A436        TCGA-E8-A437 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-E8-A44M        TCGA-EL-A3CL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CZ        TCGA-EL-A3D1        TCGA-EL-A3D4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3T0        TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3T3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3T6        TCGA-EL-A3T7        TCGA-EL-A3T8        TCGA-EL-A3T9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3TA        TCGA-EL-A3TB        TCGA-EL-A3ZG        TCGA-EL-A3ZH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZK        TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZP        TCGA-EL-A3ZQ        TCGA-EL-A3ZR        TCGA-EL-A3ZS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZT        TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4K9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4KD        TCGA-EL-A4KG        TCGA-EL-A4KH        TCGA-EL-A4KI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A2OV        TCGA-EM-A3AI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25P        TCGA-ET-A25R        TCGA-ET-A2MX        TCGA-ET-A2MY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A39K        TCGA-ET-A39M        TCGA-ET-A39O        TCGA-ET-A39P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A40P        TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A40T        TCGA-ET-A4KN        TCGA-ET-A4KQ        TCGA-FE-A22Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG        TCGA-FK-A3SH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3I4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6        TCGA-FY-A3R7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA        TCGA-FY-A3TY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3WA        TCGA-FY-A3YR        TCGA-FY-A40K 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6        TCGA-H2-A26U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI        TCGA-H2-A421 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-IM-A3U2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z        TCGA-IM-A420 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IM-A4EB        TCGA-J8-A3O0        TCGA-J8-A3O1        TCGA-J8-A3O2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A3YD        TCGA-J8-A3YE        TCGA-J8-A3YF        TCGA-J8-A3YG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A3YH        TCGA-J8-A42S        TCGA-J8-A4HY        TCGA-KS-A41F 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A41I        TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A4I3        TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A4IB        TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-L6-A4EQ        TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-MK-A4N9        TCGA-QD-A8IV        TCGA-E8-A418 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D34V17, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   2
  1Q LOSS WILD-TYPE  38 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    2
  1Q LOSS WILD-TYPE   38  358
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               358
[1] 2 2
[1] FALSE

Clustering(35) Variable = 2P LOSS MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    10   0
  2P LOSS WILD-TYPE 472  16
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               488 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                16 
$`2P LOSS MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A1YE TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY 
       20.58        34.36        54.08        10.65         6.05        32.32 
TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A3DS TCGA-FY-A3I5 
        9.24        13.51        66.84         7.82 

$`2P LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        57.01        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       15.75        10.45        14.53        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       47.57        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       48.46        13.15        22.16        40.34        19.73        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR 
       15.68        14.14        33.07        44.52         8.35        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
       12.53        27.02        38.66        38.86        29.95        29.85 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       33.24       106.09       107.41       108.46        84.89       123.32 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW 
       79.10        76.64         5.79        87.62        77.82        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT 
       52.47       116.78        94.59        84.85        80.58        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10       116.09         1.25        20.42        17.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             6.05              0.20 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            66.84            178.29 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           17.045            31.270 
[1] "6.0 - 66.8 (17.0)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "9100000"
D35V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  2P LOSS MUTATED         4        5         1        0         0         0
  2P LOSS WILD-TYPE     278       45       110        2        46         6
D35V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 4               278
  STAGE II                5                45
  STAGE III               1               110
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  2P LOSS MUTATED     3   5   2   0
  2P LOSS WILD-TYPE 139 160 165  23
D35V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               3               139
  T2               5               160
  T3               2               165
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     8   0
  2P LOSS WILD-TYPE 217 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      8    0
  2P LOSS WILD-TYPE  217  224
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               8               217
  1               0               224
[1] 2 2
[1] FALSE
D35V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1   0
  2P LOSS WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1    0
  2P LOSS WILD-TYPE  277    9
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               1               277
  1               0                 9
[1] 2 2
[1] FALSE
D35V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     7   3
  2P LOSS WILD-TYPE 358 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7    3
  2P LOSS WILD-TYPE  358  131
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               7               358
  MALE                 3               131
[1] 2 2
[1] FALSE
D35V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     3   6
  2P LOSS WILD-TYPE 177 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    6
  2P LOSS WILD-TYPE  177  297
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                3               177
  YES               6               297
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  2P LOSS MUTATED                0
  2P LOSS WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  2P LOSS MUTATED                                               3
  2P LOSS WILD-TYPE                                           353
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  2P LOSS MUTATED                                                                        7
  2P LOSS WILD-TYPE                                                                     93
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  2P LOSS MUTATED                                                                     0
  2P LOSS WILD-TYPE                                                                  36
D35V9, multiclass
                                                                        clus
vv                                                                       2P LOSS MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       2P LOSS WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     9   0
  2P LOSS WILD-TYPE 411  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      9    0
  2P LOSS WILD-TYPE  411   17
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                9               411
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  2P LOSS MUTATED              0                       0   10
  2P LOSS WILD-TYPE          132                      18  320
                   vv
clus                VERY ADVANCED (T4B)
  2P LOSS MUTATED                     0
  2P LOSS WILD-TYPE                   1
D35V11, multiclass
                         clus
vv                        2P LOSS MUTATED 2P LOSS WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                 10               320
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     9   0   0   1
  2P LOSS WILD-TYPE 374  51   4  29
D35V12, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               9               374
  R1               0                51
  R2               0                 4
  RX               1                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, continuous
D35V14, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     5   5
  2P LOSS WILD-TYPE 220 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    5
  2P LOSS WILD-TYPE  220  259
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  MULTIFOCAL               5               220
  UNIFOCAL                 5               259
[1] 2 2
[1] FALSE
D35V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     0
  2P LOSS WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           0     4
  2P LOSS WILD-TYPE                        27   325
D35V16, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                          4               325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V17, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0   4
  2P LOSS WILD-TYPE  38 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    4
  2P LOSS WILD-TYPE   38  356
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               4               356
[1] 2 2
[1] FALSE

Clustering(36) Variable = 2Q LOSS MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    10   0
  2Q LOSS WILD-TYPE 472  16
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               488 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                0                16 
$`2Q LOSS MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A1YE TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY 
       20.58        34.36        54.08        10.65         6.05        32.32 
TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N TCGA-FY-A3I5 
        9.24        13.51       123.32         7.82 

$`2Q LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        57.01        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       15.75        10.45        14.53        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       47.57        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       48.46        13.15        22.16        40.34        19.73        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR 
       15.68        14.14        33.07        44.52         8.35        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
       12.53        27.02        38.66        38.86        29.95        29.85 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       33.24       106.09       107.41       108.46        84.89       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP 
       95.34        94.13        55.10        98.20        28.24        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        87.62        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10       116.09         1.25        20.42        17.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             6.05              0.20 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           123.32            178.29 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           17.045            31.270 
[1] "6.0 - 123.3 (17.0)" "0.2 - 178.3 (31.3)"
[1] "hr="     "9100000"
D36V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  2Q LOSS MUTATED         4        5         1        0         0         0
  2Q LOSS WILD-TYPE     278       45       110        2        46         6
D36V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 4               278
  STAGE II                5                45
  STAGE III               1               110
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  2Q LOSS MUTATED     2   5   3   0
  2Q LOSS WILD-TYPE 140 160 164  23
D36V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               2               140
  T2               5               160
  T3               3               164
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7   0
  2Q LOSS WILD-TYPE 218 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    0
  2Q LOSS WILD-TYPE  218  224
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               7               218
  1               0               224
[1] 2 2
[1] FALSE
D36V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1   0
  2Q LOSS WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    0
  2Q LOSS WILD-TYPE  277    9
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               1               277
  1               0                 9
[1] 2 2
[1] FALSE
D36V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7   3
  2Q LOSS WILD-TYPE 358 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    3
  2Q LOSS WILD-TYPE  358  131
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               7               358
  MALE                 3               131
[1] 2 2
[1] FALSE
D36V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2   7
  2Q LOSS WILD-TYPE 178 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    7
  2Q LOSS WILD-TYPE  178  296
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                2               178
  YES               7               296
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  2Q LOSS MUTATED                0
  2Q LOSS WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  2Q LOSS MUTATED                                               3
  2Q LOSS WILD-TYPE                                           353
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  2Q LOSS MUTATED                                                                        7
  2Q LOSS WILD-TYPE                                                                     93
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  2Q LOSS MUTATED                                                                     0
  2Q LOSS WILD-TYPE                                                                  36
D36V9, multiclass
                                                                        clus
vv                                                                       2Q LOSS MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       2Q LOSS WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     9   0
  2Q LOSS WILD-TYPE 411  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      9    0
  2Q LOSS WILD-TYPE  411   17
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                9               411
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  2Q LOSS MUTATED              0                       0   10
  2Q LOSS WILD-TYPE          132                      18  320
                   vv
clus                VERY ADVANCED (T4B)
  2Q LOSS MUTATED                     0
  2Q LOSS WILD-TYPE                   1
D36V11, multiclass
                         clus
vv                        2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                 10               320
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED     9   0   0   1
  2Q LOSS WILD-TYPE 374  51   4  29
D36V12, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               9               374
  R1               0                51
  R2               0                 4
  RX               1                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, continuous
D36V14, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     5   5
  2Q LOSS WILD-TYPE 220 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    5
  2Q LOSS WILD-TYPE  220  259
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  MULTIFOCAL               5               220
  UNIFOCAL                 5               259
[1] 2 2
[1] FALSE
D36V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     0
  2Q LOSS WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           0     4
  2Q LOSS WILD-TYPE                        27   325
D36V16, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                          4               325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V17, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0   4
  2Q LOSS WILD-TYPE  38 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    4
  2Q LOSS WILD-TYPE   38  356
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               4               356
[1] 2 2
[1] FALSE

Clustering(37) Variable = 3P LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED     3   0
  3P LOSS WILD-TYPE 479  16
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               495 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                0                16 
$`3P LOSS MUTATED`
TCGA-BJ-A190 TCGA-ET-A39N TCGA-FY-A3I5 
       20.58       123.32         7.82 

$`3P LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        78.61        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        44.52         8.35        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        27.02        38.66        38.86        29.95        29.85 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       58.75        37.25        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW 
       79.10        76.64         5.79        87.62        77.82        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77       112.80        39.95        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE 
       85.15        85.68        78.77        71.08         4.11        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       29.10        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08        23.31        21.63        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 
       23.87        22.49        19.04        13.81        14.04        21.60 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
       31.10         8.22        25.64        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.24        33.40        40.37         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             7.82              0.20 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           123.32            178.29 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            20.58             31.27 
[1] "7.8 - 123.3 (20.6)" "0.2 - 178.3 (31.3)"
[1] "hr="     "3300000"
D37V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  3P LOSS MUTATED         1        1         1        0         0         0
  3P LOSS WILD-TYPE     281       49       110        2        46         6
D37V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 1               281
  STAGE II                1                49
  STAGE III               1               110
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  3P LOSS MUTATED     0   1   2   0
  3P LOSS WILD-TYPE 142 164 165  23
D37V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               0               142
  T2               1               164
  T3               2               165
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2   0
  3P LOSS WILD-TYPE 223 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    0
  3P LOSS WILD-TYPE  223  224
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               2               223
  1               0               224
[1] 2 2
[1] FALSE
D37V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0   0
  3P LOSS WILD-TYPE 278   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    0
  3P LOSS WILD-TYPE  278    9
D37V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2   1
  3P LOSS WILD-TYPE 363 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    1
  3P LOSS WILD-TYPE  363  133
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               2               363
  MALE                 1               133
[1] 2 2
[1] FALSE
D37V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0   2
  3P LOSS WILD-TYPE 180 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    2
  3P LOSS WILD-TYPE  180  301
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                0               180
  YES               2               301
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  3P LOSS MUTATED                0
  3P LOSS WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  3P LOSS MUTATED                                               2
  3P LOSS WILD-TYPE                                           354
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  3P LOSS MUTATED                                                                        1
  3P LOSS WILD-TYPE                                                                     99
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  3P LOSS MUTATED                                                                     0
  3P LOSS WILD-TYPE                                                                  36
D37V9, multiclass
                                                                        clus
vv                                                                       3P LOSS MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       3P LOSS WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2   0
  3P LOSS WILD-TYPE 418  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    0
  3P LOSS WILD-TYPE  418   17
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                2               418
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  3P LOSS MUTATED              0                       0    3
  3P LOSS WILD-TYPE          132                      18  327
                   vv
clus                VERY ADVANCED (T4B)
  3P LOSS MUTATED                     0
  3P LOSS WILD-TYPE                   1
D37V11, multiclass
                         clus
vv                        3P LOSS MUTATED 3P LOSS WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  3               327
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED     3   0   0   0
  3P LOSS WILD-TYPE 380  51   4  30
D37V12, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               3               380
  R1               0                51
  R2               0                 4
  RX               0                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, continuous
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2               384 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A45K        TCGA-CE-A13K 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DJ-A2PR        TCGA-DJ-A3UU        TCGA-DJ-A3UW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3V4        TCGA-DJ-A3VI        TCGA-DJ-A3VK        TCGA-E3-A3E5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CY        TCGA-EL-A3D0 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3GQ        TCGA-EL-A3H8        TCGA-EM-A3AQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BV        TCGA-J8-A3NZ        TCGA-J8-A4HW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-4C-A93U        TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZH 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZJ        TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28T        TCGA-BJ-A28W        TCGA-BJ-A28X 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A28Z        TCGA-BJ-A2N8        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3PR        TCGA-BJ-A3PU        TCGA-BJ-A45C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45G        TCGA-BJ-A45I 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A45J        TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A3MD 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485        TCGA-DE-A0Y2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DE-A0Y3        TCGA-DE-A3KN        TCGA-DE-A4M8        TCGA-DE-A4MA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69K 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13R 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A13T        TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QM        TCGA-DJ-A2PO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PS        TCGA-DJ-A2PT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3UR        TCGA-DJ-A3UX        TCGA-DJ-A3UZ        TCGA-DJ-A3V0 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V5        TCGA-DJ-A3V7 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3V8        TCGA-DJ-A3V9        TCGA-DJ-A3VA        TCGA-DJ-A3VB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3VD        TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3VL        TCGA-DJ-A4UL        TCGA-DJ-A4UP        TCGA-DJ-A4UQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A4UR        TCGA-DJ-A4UW        TCGA-DJ-A4V2        TCGA-DJ-A4V5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY        TCGA-E3-A3DZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2        TCGA-E3-A3E3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A414        TCGA-E8-A415 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433        TCGA-E8-A436 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM        TCGA-EL-A3CN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CZ        TCGA-EL-A3D1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3T0        TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3TB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3ZH        TCGA-EL-A3ZK        TCGA-EL-A3ZL        TCGA-EL-A3ZM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP        TCGA-EL-A3ZS 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4KD        TCGA-EL-A4KG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A4KI        TCGA-EM-A1CS        TCGA-EM-A1CT        TCGA-EM-A1CU 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YC        TCGA-EM-A1YD 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22N        TCGA-EM-A22O 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A22P        TCGA-EM-A22Q        TCGA-EM-A2CK        TCGA-EM-A2CN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CT        TCGA-EM-A2CU 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OX        TCGA-EM-A2OY        TCGA-EM-A2OZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2P0        TCGA-EM-A2P1        TCGA-EM-A2P2        TCGA-EM-A3AJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3AK        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3AR        TCGA-EM-A3FJ        TCGA-EM-A3FK        TCGA-EM-A3FM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O8        TCGA-EM-A3O9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST        TCGA-EM-A3SU 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3SX        TCGA-EM-A3SZ        TCGA-EM-A4FF        TCGA-EM-A4FM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ        TCGA-EM-A4FR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G        TCGA-ET-A25I 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A2MX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A39K        TCGA-ET-A39L        TCGA-ET-A39O        TCGA-ET-A39P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BX        TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A40P        TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A40T        TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A3PD        TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FK-A3SG        TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FY-A3R6        TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-H2-A3RI        TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-IM-A3ED        TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-IM-A41Z        TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3O0 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I        TCGA-KS-A41J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3        TCGA-KS-A4I5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB        TCGA-KS-A4IC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ        TCGA-L6-A4EU 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9        TCGA-QD-A8IV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D37V14, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2   1
  3P LOSS WILD-TYPE 223 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    1
  3P LOSS WILD-TYPE  223  263
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  MULTIFOCAL               2               223
  UNIFOCAL                 1               263
[1] 2 2
[1] FALSE
D37V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     0
  3P LOSS WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           0     3
  3P LOSS WILD-TYPE                        27   326
D37V16, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                          3               326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V17, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0   3
  3P LOSS WILD-TYPE  38 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    3
  3P LOSS WILD-TYPE   38  357
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               357
[1] 2 2
[1] FALSE

Clustering(38) Variable = 3Q LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     4   0
  3Q LOSS WILD-TYPE 478  16
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               494 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                16 
$`3Q LOSS MUTATED`
TCGA-BJ-A190 TCGA-EM-A1YE TCGA-ET-A39N TCGA-FY-A3I5 
       20.58        54.08       123.32         7.82 

$`3Q LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I 
       18.05        19.79        19.46        78.61        57.01        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       27.02        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       33.24       106.09       107.41       108.46        84.89       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP 
       95.34        94.13        55.10        98.20        28.24        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        87.62        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10       116.09         1.25        20.42        17.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             7.82              0.20 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           123.32            178.29 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            37.33             31.25 
[1] "7.8 - 123.3 (37.3)" "0.2 - 178.3 (31.2)"
[1] "hr="     "9100000"
D38V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  3Q LOSS MUTATED         1        2         1        0         0         0
  3Q LOSS WILD-TYPE     281       48       110        2        46         6
D38V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 1               281
  STAGE II                2                48
  STAGE III               1               110
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  3Q LOSS MUTATED     0   2   2   0
  3Q LOSS WILD-TYPE 142 163 165  23
D38V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0               142
  T2               2               163
  T3               2               165
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3   0
  3Q LOSS WILD-TYPE 222 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    0
  3Q LOSS WILD-TYPE  222  224
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               3               222
  1               0               224
[1] 2 2
[1] FALSE
D38V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   0
  3Q LOSS WILD-TYPE 278   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    0
  3Q LOSS WILD-TYPE  278    9
D38V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3   1
  3Q LOSS WILD-TYPE 362 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    1
  3Q LOSS WILD-TYPE  362  133
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               3               362
  MALE                 1               133
[1] 2 2
[1] FALSE
D38V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   3
  3Q LOSS WILD-TYPE 180 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    3
  3Q LOSS WILD-TYPE  180  300
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                0               180
  YES               3               300
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  3Q LOSS MUTATED                0
  3Q LOSS WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  3Q LOSS MUTATED                                               2
  3Q LOSS WILD-TYPE                                           354
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  3Q LOSS MUTATED                                                                        2
  3Q LOSS WILD-TYPE                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  3Q LOSS MUTATED                                                                     0
  3Q LOSS WILD-TYPE                                                                  36
D38V9, multiclass
                                                                        clus
vv                                                                       3Q LOSS MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       3Q LOSS WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3   0
  3Q LOSS WILD-TYPE 417  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    0
  3Q LOSS WILD-TYPE  417   17
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                3               417
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  3Q LOSS MUTATED              0                       0    4
  3Q LOSS WILD-TYPE          132                      18  326
                   vv
clus                VERY ADVANCED (T4B)
  3Q LOSS MUTATED                     0
  3Q LOSS WILD-TYPE                   1
D38V11, multiclass
                         clus
vv                        3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  4               326
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED     4   0   0   0
  3Q LOSS WILD-TYPE 379  51   4  30
D38V12, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               4               379
  R1               0                51
  R2               0                 4
  RX               0                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, continuous
D38V14, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2   2
  3Q LOSS WILD-TYPE 223 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    2
  3Q LOSS WILD-TYPE  223  262
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  MULTIFOCAL               2               223
  UNIFOCAL                 2               262
[1] 2 2
[1] FALSE
D38V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           0     3
  3Q LOSS WILD-TYPE                        27   326
D38V16, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                          3               326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V17, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   3
  3Q LOSS WILD-TYPE  38 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    3
  3Q LOSS WILD-TYPE   38  357
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               357
[1] 2 2
[1] FALSE

Clustering(39) Variable = 6P LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED     4   0
  6P LOSS WILD-TYPE 478  16
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4               494 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                0                16 
$`6P LOSS MUTATED`
TCGA-ET-A3BV TCGA-ET-A39N TCGA-FY-A3I5 TCGA-FY-A4B0 
       75.42       123.32         7.82        13.81 

$`6P LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET 
       50.40         1.05         1.68        17.23         2.60        21.83 
TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       23.93         4.24        24.79        13.78        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 
       25.48        15.12        42.08        51.39        41.52        20.58 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        78.61        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        44.52         8.35        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        27.02        38.66        38.86        29.95        29.85 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       58.75        37.25        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW 
       79.10        76.64         5.79        87.62        77.82        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77       112.80        39.95        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE 
       85.15        85.68        78.77        71.08         4.11        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       29.10        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08        23.31        21.63        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       23.87        22.49        19.04        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             7.82              0.20 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           123.32            178.29 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           44.615            31.250 
[1] "7.8 - 123.3 (44.6)" "0.2 - 178.3 (31.2)"
[1] "hr="     "9100000"
D39V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  6P LOSS MUTATED         2        0         2        0         0         0
  6P LOSS WILD-TYPE     280       50       109        2        46         6
D39V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 2               280
  STAGE II                0                50
  STAGE III               2               109
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  6P LOSS MUTATED     1   1   2   0
  6P LOSS WILD-TYPE 141 164 165  23
D39V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               1               141
  T2               1               164
  T3               2               165
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1   1
  6P LOSS WILD-TYPE 224 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1    1
  6P LOSS WILD-TYPE  224  223
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0               1               224
  1               1               223
[1] 2 2
[1] FALSE
D39V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0   0
  6P LOSS WILD-TYPE 278   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    0
  6P LOSS WILD-TYPE  278    9
D39V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     3   1
  6P LOSS WILD-TYPE 362 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3    1
  6P LOSS WILD-TYPE  362  133
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               3               362
  MALE                 1               133
[1] 2 2
[1] FALSE
D39V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0   3
  6P LOSS WILD-TYPE 180 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    3
  6P LOSS WILD-TYPE  180  300
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                0               180
  YES               3               300
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  6P LOSS MUTATED                0
  6P LOSS WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  6P LOSS MUTATED                                               3
  6P LOSS WILD-TYPE                                           353
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  6P LOSS MUTATED                                                                        1
  6P LOSS WILD-TYPE                                                                     99
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  6P LOSS MUTATED                                                                     0
  6P LOSS WILD-TYPE                                                                  36
D39V9, multiclass
                                                                        clus
vv                                                                       6P LOSS MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       6P LOSS WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     3   0
  6P LOSS WILD-TYPE 417  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3    0
  6P LOSS WILD-TYPE  417   17
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                3               417
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  6P LOSS MUTATED              0                       0    4
  6P LOSS WILD-TYPE          132                      18  326
                   vv
clus                VERY ADVANCED (T4B)
  6P LOSS MUTATED                     0
  6P LOSS WILD-TYPE                   1
D39V11, multiclass
                         clus
vv                        6P LOSS MUTATED 6P LOSS WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  4               326
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED     3   1   0   0
  6P LOSS WILD-TYPE 380  50   4  30
D39V12, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0               3               380
  R1               1                50
  R2               0                 4
  RX               0                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, continuous
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2               384 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A45K        TCGA-CE-A13K 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DJ-A2PR        TCGA-DJ-A3UU        TCGA-DJ-A3UW 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3V4        TCGA-DJ-A3VI        TCGA-DJ-A3VK        TCGA-E3-A3E5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CY        TCGA-EL-A3D0 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3GQ        TCGA-EL-A3H8        TCGA-EM-A3AQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-J8-A3NZ        TCGA-J8-A4HW        TCGA-4C-A93U 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5        TCGA-BJ-A0Z9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28T        TCGA-BJ-A28W        TCGA-BJ-A28X 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A28Z        TCGA-BJ-A2N8        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3PR        TCGA-BJ-A3PU        TCGA-BJ-A45C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45G        TCGA-BJ-A45I 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A45J        TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A3MD 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485        TCGA-DE-A0Y2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DE-A0Y3        TCGA-DE-A3KN        TCGA-DE-A4M8        TCGA-DE-A4MA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69K 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13R 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A13T        TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QM        TCGA-DJ-A2PO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PS        TCGA-DJ-A2PT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3UR        TCGA-DJ-A3UX        TCGA-DJ-A3UZ        TCGA-DJ-A3V0 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V5        TCGA-DJ-A3V7 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3V8        TCGA-DJ-A3V9        TCGA-DJ-A3VA        TCGA-DJ-A3VB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3VD        TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3VL        TCGA-DJ-A4UL        TCGA-DJ-A4UP        TCGA-DJ-A4UQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A4UR        TCGA-DJ-A4UW        TCGA-DJ-A4V2        TCGA-DJ-A4V5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY        TCGA-E3-A3DZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2        TCGA-E3-A3E3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A414        TCGA-E8-A415 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433        TCGA-E8-A436 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM        TCGA-EL-A3CN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CZ        TCGA-EL-A3D1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MZ        TCGA-EL-A3N2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3T0        TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3TB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3ZH        TCGA-EL-A3ZK        TCGA-EL-A3ZL        TCGA-EL-A3ZM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP        TCGA-EL-A3ZS 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4KD        TCGA-EL-A4KG 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A4KI        TCGA-EM-A1CS        TCGA-EM-A1CT        TCGA-EM-A1CU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YC        TCGA-EM-A1YD 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22N        TCGA-EM-A22O 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A22P        TCGA-EM-A22Q        TCGA-EM-A2CK        TCGA-EM-A2CN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CT        TCGA-EM-A2CU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OX        TCGA-EM-A2OY        TCGA-EM-A2OZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2P0        TCGA-EM-A2P1        TCGA-EM-A2P2        TCGA-EM-A3AJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3AK        TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3AR        TCGA-EM-A3FJ        TCGA-EM-A3FK        TCGA-EM-A3FM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O8        TCGA-EM-A3O9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST        TCGA-EM-A3SU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3SX        TCGA-EM-A3SZ        TCGA-EM-A4FF        TCGA-EM-A4FM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ        TCGA-EM-A4FR 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G        TCGA-ET-A25I 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A2MX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A39K        TCGA-ET-A39L        TCGA-ET-A39O        TCGA-ET-A39P 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3BX        TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A40P        TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A40T        TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A3PD        TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FK-A3SG        TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FY-A3R6        TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-H2-A3RI        TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IM-A3ED        TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IM-A41Z        TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3O0 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I        TCGA-KS-A41J 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3        TCGA-KS-A4I5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB        TCGA-KS-A4IC 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ        TCGA-L6-A4EU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9        TCGA-QD-A8IV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
D39V14, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     2   2
  6P LOSS WILD-TYPE 223 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2    2
  6P LOSS WILD-TYPE  223  262
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  MULTIFOCAL               2               223
  UNIFOCAL                 2               262
[1] 2 2
[1] FALSE
D39V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     0
  6P LOSS WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           0     4
  6P LOSS WILD-TYPE                        27   325
D39V16, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                          4               325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V17, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0   4
  6P LOSS WILD-TYPE  38 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    4
  6P LOSS WILD-TYPE   38  356
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               4               356
[1] 2 2
[1] FALSE

Clustering(40) Variable = 6Q LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED     5   2
  6Q LOSS WILD-TYPE 477  14
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7               491 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                14 
$`6Q LOSS MUTATED`
TCGA-EL-A3H2 TCGA-ET-A3BV TCGA-EM-A1YE TCGA-ET-A39N TCGA-FE-A239 TCGA-FY-A3I5 
       33.50        75.42        54.08       123.32        33.63         7.82 
TCGA-FY-A4B0 
       13.81 

$`6Q LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO 
       50.24       150.48        17.52       178.29        29.72        50.40 
TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET TCGA-MK-A84Z 
        1.05         1.68        17.23         2.60        21.83        23.93 
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.97        11.08        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       12.82        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       21.63        50.17        37.64        27.32        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        52.27        43.17        52.37         8.32        48.07 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       30.58        35.41        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        57.01        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       39.95        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       14.04        21.60        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       11.01        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 
       16.90        21.83        31.10         8.22        25.64        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        5.75         2.47         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU 
       84.72        35.28        33.24        33.40        40.37         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       36.10        32.45        30.21        12.89         3.02 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             7.82              0.20 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           123.32            178.29 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            33.63             31.10 
[1] "7.8 - 123.3 (33.6)" "0.2 - 178.3 (31.1)"
[1] "hr=" "7.2"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  6Q LOSS MUTATED         2        2         3        0         0         0
  6Q LOSS WILD-TYPE     280       48       108        2        46         6
D40V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 2               280
  STAGE II                2                48
  STAGE III               3               108
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  6Q LOSS MUTATED     1   3   3   0
  6Q LOSS WILD-TYPE 141 162 164  23
D40V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               1               141
  T2               3               162
  T3               3               164
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     4   1
  6Q LOSS WILD-TYPE 221 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    1
  6Q LOSS WILD-TYPE  221  223
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0               4               221
  1               1               223
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     0   0
  6Q LOSS WILD-TYPE 278   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0    0
  6Q LOSS WILD-TYPE  278    9
D40V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     4   3
  6Q LOSS WILD-TYPE 361 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    3
  6Q LOSS WILD-TYPE  361  131
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               4               361
  MALE                 3               131
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     0   6
  6Q LOSS WILD-TYPE 180 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0    6
  6Q LOSS WILD-TYPE  180  297
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                0               180
  YES               6               297
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  6Q LOSS MUTATED                0
  6Q LOSS WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  6Q LOSS MUTATED                                               5
  6Q LOSS WILD-TYPE                                           351
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  6Q LOSS MUTATED                                                                        2
  6Q LOSS WILD-TYPE                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  6Q LOSS MUTATED                                                                     0
  6Q LOSS WILD-TYPE                                                                  36
D40V9, multiclass
                                                                        clus
vv                                                                       6Q LOSS MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       6Q LOSS WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     5   1
  6Q LOSS WILD-TYPE 415  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5    1
  6Q LOSS WILD-TYPE  415   16
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                5               415
  YES               1                16
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  6Q LOSS MUTATED              0                       0    7
  6Q LOSS WILD-TYPE          132                      18  323
                   vv
clus                VERY ADVANCED (T4B)
  6Q LOSS MUTATED                     0
  6Q LOSS WILD-TYPE                   1
D40V11, multiclass
                         clus
vv                        6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  7               323
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED     6   1   0   0
  6Q LOSS WILD-TYPE 377  50   4  30
D40V12, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0               6               377
  R1               1                50
  R2               0                 4
  RX               0                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, continuous
D40V14, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     2   5
  6Q LOSS WILD-TYPE 223 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2    5
  6Q LOSS WILD-TYPE  223  259
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  MULTIFOCAL               2               223
  UNIFOCAL                 5               259
[1] 2 2
[1] FALSE
D40V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     0
  6Q LOSS WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           0     6
  6Q LOSS WILD-TYPE                        27   323
D40V16, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                52
  BLACK OR AFRICAN AMERICAN                      0                27
  WHITE                                          6               323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V17, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     0   6
  6Q LOSS WILD-TYPE  38 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0    6
  6Q LOSS WILD-TYPE   38  354
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               6               354
[1] 2 2
[1] FALSE

Clustering(41) Variable = 8P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED     4   0
  8P LOSS WILD-TYPE 478  16
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4               494 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                16 
$`8P LOSS MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A3O9 TCGA-EM-A3SY 
       20.58        34.36         9.24        13.51 

$`8P LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        15.06         7.33        12.53        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             9.24              0.20 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            34.36            178.29 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           17.045            31.270 
[1] "9.2 - 34.4 (17.0)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "1200000"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  8P LOSS MUTATED         2        2         0        0         0         0
  8P LOSS WILD-TYPE     280       48       111        2        46         6
D41V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 2               280
  STAGE II                2                48
  STAGE III               0               111
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  8P LOSS MUTATED     1   2   1   0
  8P LOSS WILD-TYPE 141 163 166  23
D41V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               1               141
  T2               2               163
  T3               1               166
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     3   0
  8P LOSS WILD-TYPE 222 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    0
  8P LOSS WILD-TYPE  222  224
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               3               222
  1               0               224
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1   0
  8P LOSS WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    0
  8P LOSS WILD-TYPE  277    9
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               1               277
  1               0                 9
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1   3
  8P LOSS WILD-TYPE 364 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    3
  8P LOSS WILD-TYPE  364  131
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               1               364
  MALE                 3               131
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     2   2
  8P LOSS WILD-TYPE 178 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2    2
  8P LOSS WILD-TYPE  178  301
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                2               178
  YES               2               301
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  8P LOSS MUTATED                0
  8P LOSS WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  8P LOSS MUTATED                                               2
  8P LOSS WILD-TYPE                                           354
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  8P LOSS MUTATED                                                                        2
  8P LOSS WILD-TYPE                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  8P LOSS MUTATED                                                                     0
  8P LOSS WILD-TYPE                                                                  36
D41V9, multiclass
                                                                        clus
vv                                                                       8P LOSS MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       8P LOSS WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     4   0
  8P LOSS WILD-TYPE 416  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    0
  8P LOSS WILD-TYPE  416   17
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                4               416
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  8P LOSS MUTATED              0                       0    4
  8P LOSS WILD-TYPE          132                      18  326
                   vv
clus                VERY ADVANCED (T4B)
  8P LOSS MUTATED                     0
  8P LOSS WILD-TYPE                   1
D41V11, multiclass
                         clus
vv                        8P LOSS MUTATED 8P LOSS WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  4               326
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED     4   0   0   0
  8P LOSS WILD-TYPE 379  51   4  30
D41V12, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0               4               379
  R1               0                51
  R2               0                 4
  RX               0                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, continuous
D41V14, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     2   2
  8P LOSS WILD-TYPE 223 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2    2
  8P LOSS WILD-TYPE  223  262
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  MULTIFOCAL               2               223
  UNIFOCAL                 2               262
[1] 2 2
[1] FALSE
D41V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  0     0
  8P LOSS WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                           0     2
  8P LOSS WILD-TYPE                        27   327
D41V16, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2               407 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A45K        TCGA-CE-A13K 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DJ-A13L        TCGA-DJ-A2PR        TCGA-DJ-A3UU 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3UW        TCGA-DJ-A3V4        TCGA-DJ-A3VI        TCGA-DJ-A3VK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D5        TCGA-EL-A3GQ        TCGA-EL-A3H2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MY        TCGA-EL-A3N3        TCGA-ET-A3BO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-FK-A3SD        TCGA-FY-A76V        TCGA-J8-A3NZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-L6-A4ET        TCGA-MK-A84Z        TCGA-4C-A93U 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z        TCGA-BJ-A2N7 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A2N8        TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-BJ-A3PR        TCGA-BJ-A3PT 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A45F        TCGA-BJ-A45G        TCGA-BJ-A45H        TCGA-BJ-A45I 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A45J        TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A27D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481        TCGA-CE-A482 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485        TCGA-DE-A0Y2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DE-A0Y3        TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DE-A4M8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DE-A4M9        TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DE-A4MD        TCGA-DE-A69J        TCGA-DE-A69K        TCGA-DE-A7U5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13P        TCGA-DJ-A13R 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A13S        TCGA-DJ-A13T        TCGA-DJ-A13U        TCGA-DJ-A13W 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A1QH        TCGA-DJ-A1QI        TCGA-DJ-A1QM        TCGA-DJ-A1QO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A1QQ        TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2PS        TCGA-DJ-A2PT        TCGA-DJ-A2PU        TCGA-DJ-A2PV 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2PW        TCGA-DJ-A2PX        TCGA-DJ-A2PY        TCGA-DJ-A2PZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UQ        TCGA-DJ-A3UR 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3US        TCGA-DJ-A3UT        TCGA-DJ-A3UX        TCGA-DJ-A3UY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3UZ        TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9        TCGA-DJ-A3VD 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3VE        TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3VL        TCGA-DJ-A3VM        TCGA-DJ-A4UL        TCGA-DJ-A4UP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UT        TCGA-DJ-A4UW 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A4V0        TCGA-DJ-A4V4        TCGA-DJ-A4V5        TCGA-DO-A1JZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY        TCGA-E3-A3DZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2        TCGA-E3-A3E3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A3X7        TCGA-E8-A413 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A414        TCGA-E8-A415        TCGA-E8-A416        TCGA-E8-A417 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A419        TCGA-E8-A432        TCGA-E8-A433        TCGA-E8-A434 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A436        TCGA-E8-A437        TCGA-E8-A438        TCGA-E8-A44K 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A44M        TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CT        TCGA-EL-A3CU 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D6        TCGA-EL-A3GO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H3        TCGA-EL-A3H4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3MW        TCGA-EL-A3MX 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0        TCGA-EL-A3T1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3T2        TCGA-EL-A3T3        TCGA-EL-A3T6        TCGA-EL-A3T7 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3T8        TCGA-EL-A3T9        TCGA-EL-A3TA        TCGA-EL-A3TB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3ZG        TCGA-EL-A3ZH        TCGA-EL-A3ZK        TCGA-EL-A3ZL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP        TCGA-EL-A3ZQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3ZR        TCGA-EL-A3ZS        TCGA-EL-A3ZT        TCGA-EL-A4JV 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A4K7        TCGA-EL-A4K9        TCGA-EL-A4KD        TCGA-EL-A4KG 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A4KH        TCGA-EL-A4KI        TCGA-EM-A22M        TCGA-EM-A22O 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A3AI        TCGA-ET-A25G        TCGA-ET-A25I 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A25R 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A2MX        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N3        TCGA-ET-A2N4        TCGA-ET-A2N5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39K        TCGA-ET-A39M 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A39N        TCGA-ET-A39O        TCGA-ET-A39P        TCGA-ET-A39R 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-ET-A4KQ        TCGA-FE-A22Z        TCGA-FE-A230 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA        TCGA-FE-A3PB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3        TCGA-FK-A3SB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FK-A3SE        TCGA-FK-A3SG        TCGA-FK-A3SH        TCGA-FK-A4UB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3I4        TCGA-FY-A3I5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6        TCGA-FY-A3R7 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA        TCGA-FY-A3TY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3WA        TCGA-FY-A3YR        TCGA-FY-A40K 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6        TCGA-H2-A26U 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI        TCGA-H2-A421 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-IM-A3U2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z        TCGA-IM-A420 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IM-A4EB        TCGA-J8-A3O0        TCGA-J8-A3O1        TCGA-J8-A3O2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J8-A3YD        TCGA-J8-A3YE        TCGA-J8-A3YF        TCGA-J8-A3YG 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J8-A3YH        TCGA-J8-A42S        TCGA-J8-A4HY        TCGA-KS-A41F 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KS-A41I        TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KS-A4I3        TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KS-A4IB        TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-L6-A4EQ        TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-MK-A4N9        TCGA-QD-A8IV        TCGA-E8-A418 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D41V17, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     0   2
  8P LOSS WILD-TYPE  38 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0    2
  8P LOSS WILD-TYPE   38  358
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               358
[1] 2 2
[1] FALSE

Clustering(42) Variable = 8Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     4   0
  8Q LOSS WILD-TYPE 478  16
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               494 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                16 
$`8Q LOSS MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A3O9 TCGA-EM-A3SY 
       20.58        34.36         9.24        13.51 

$`8Q LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        15.06         7.33        12.53        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             9.24              0.20 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            34.36            178.29 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           17.045            31.270 
[1] "9.2 - 34.4 (17.0)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "1200000"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  8Q LOSS MUTATED         2        2         0        0         0         0
  8Q LOSS WILD-TYPE     280       48       111        2        46         6
D42V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 2               280
  STAGE II                2                48
  STAGE III               0               111
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  8Q LOSS MUTATED     1   2   1   0
  8Q LOSS WILD-TYPE 141 163 166  23
D42V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               1               141
  T2               2               163
  T3               1               166
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     3   0
  8Q LOSS WILD-TYPE 222 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    0
  8Q LOSS WILD-TYPE  222  224
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               3               222
  1               0               224
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1   0
  8Q LOSS WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    0
  8Q LOSS WILD-TYPE  277    9
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               1               277
  1               0                 9
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1   3
  8Q LOSS WILD-TYPE 364 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    3
  8Q LOSS WILD-TYPE  364  131
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               1               364
  MALE                 3               131
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     2   2
  8Q LOSS WILD-TYPE 178 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    2
  8Q LOSS WILD-TYPE  178  301
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                2               178
  YES               2               301
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  8Q LOSS MUTATED                0
  8Q LOSS WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  8Q LOSS MUTATED                                               2
  8Q LOSS WILD-TYPE                                           354
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  8Q LOSS MUTATED                                                                        2
  8Q LOSS WILD-TYPE                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  8Q LOSS MUTATED                                                                     0
  8Q LOSS WILD-TYPE                                                                  36
D42V9, multiclass
                                                                        clus
vv                                                                       8Q LOSS MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       8Q LOSS WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     4   0
  8Q LOSS WILD-TYPE 416  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      4    0
  8Q LOSS WILD-TYPE  416   17
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                4               416
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  8Q LOSS MUTATED              0                       0    4
  8Q LOSS WILD-TYPE          132                      18  326
                   vv
clus                VERY ADVANCED (T4B)
  8Q LOSS MUTATED                     0
  8Q LOSS WILD-TYPE                   1
D42V11, multiclass
                         clus
vv                        8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  4               326
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED     4   0   0   0
  8Q LOSS WILD-TYPE 379  51   4  30
D42V12, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               4               379
  R1               0                51
  R2               0                 4
  RX               0                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, continuous
D42V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     2   2
  8Q LOSS WILD-TYPE 223 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    2
  8Q LOSS WILD-TYPE  223  262
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  MULTIFOCAL               2               223
  UNIFOCAL                 2               262
[1] 2 2
[1] FALSE
D42V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     0
  8Q LOSS WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           0     2
  8Q LOSS WILD-TYPE                        27   327
D42V16, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               407 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A45K        TCGA-CE-A13K 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DJ-A13L        TCGA-DJ-A2PR        TCGA-DJ-A3UU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UW        TCGA-DJ-A3V4        TCGA-DJ-A3VI        TCGA-DJ-A3VK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D5        TCGA-EL-A3GQ        TCGA-EL-A3H2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MY        TCGA-EL-A3N3        TCGA-ET-A3BO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-FK-A3SD        TCGA-FY-A76V        TCGA-J8-A3NZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-L6-A4ET        TCGA-MK-A84Z        TCGA-4C-A93U 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z        TCGA-BJ-A2N7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A2N8        TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-BJ-A3PR        TCGA-BJ-A3PT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A45F        TCGA-BJ-A45G        TCGA-BJ-A45H        TCGA-BJ-A45I 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A45J        TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A27D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481        TCGA-CE-A482 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485        TCGA-DE-A0Y2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DE-A0Y3        TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DE-A4M8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DE-A4M9        TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DE-A4MD        TCGA-DE-A69J        TCGA-DE-A69K        TCGA-DE-A7U5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13P        TCGA-DJ-A13R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A13S        TCGA-DJ-A13T        TCGA-DJ-A13U        TCGA-DJ-A13W 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QH        TCGA-DJ-A1QI        TCGA-DJ-A1QM        TCGA-DJ-A1QO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QQ        TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PS        TCGA-DJ-A2PT        TCGA-DJ-A2PU        TCGA-DJ-A2PV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PW        TCGA-DJ-A2PX        TCGA-DJ-A2PY        TCGA-DJ-A2PZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UQ        TCGA-DJ-A3UR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3US        TCGA-DJ-A3UT        TCGA-DJ-A3UX        TCGA-DJ-A3UY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UZ        TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9        TCGA-DJ-A3VD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3VE        TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3VL        TCGA-DJ-A3VM        TCGA-DJ-A4UL        TCGA-DJ-A4UP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UT        TCGA-DJ-A4UW 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A4V0        TCGA-DJ-A4V4        TCGA-DJ-A4V5        TCGA-DO-A1JZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY        TCGA-E3-A3DZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2        TCGA-E3-A3E3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A3X7        TCGA-E8-A413 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A414        TCGA-E8-A415        TCGA-E8-A416        TCGA-E8-A417 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A419        TCGA-E8-A432        TCGA-E8-A433        TCGA-E8-A434 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A436        TCGA-E8-A437        TCGA-E8-A438        TCGA-E8-A44K 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A44M        TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CT        TCGA-EL-A3CU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D6        TCGA-EL-A3GO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H3        TCGA-EL-A3H4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3MW        TCGA-EL-A3MX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0        TCGA-EL-A3T1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3T2        TCGA-EL-A3T3        TCGA-EL-A3T6        TCGA-EL-A3T7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3T8        TCGA-EL-A3T9        TCGA-EL-A3TA        TCGA-EL-A3TB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZG        TCGA-EL-A3ZH        TCGA-EL-A3ZK        TCGA-EL-A3ZL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP        TCGA-EL-A3ZQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZR        TCGA-EL-A3ZS        TCGA-EL-A3ZT        TCGA-EL-A4JV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A4K7        TCGA-EL-A4K9        TCGA-EL-A4KD        TCGA-EL-A4KG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A4KH        TCGA-EL-A4KI        TCGA-EM-A22M        TCGA-EM-A22O 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A3AI        TCGA-ET-A25G        TCGA-ET-A25I 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A25R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A2MX        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N3        TCGA-ET-A2N4        TCGA-ET-A2N5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39K        TCGA-ET-A39M 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A39N        TCGA-ET-A39O        TCGA-ET-A39P        TCGA-ET-A39R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO        TCGA-ET-A3DP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-ET-A4KQ        TCGA-FE-A22Z        TCGA-FE-A230 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA        TCGA-FE-A3PB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3        TCGA-FK-A3SB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FK-A3SE        TCGA-FK-A3SG        TCGA-FK-A3SH        TCGA-FK-A4UB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3I4        TCGA-FY-A3I5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6        TCGA-FY-A3R7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA        TCGA-FY-A3TY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3WA        TCGA-FY-A3YR        TCGA-FY-A40K 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6        TCGA-H2-A26U 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI        TCGA-H2-A421 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-IM-A3U2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z        TCGA-IM-A420 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IM-A4EB        TCGA-J8-A3O0        TCGA-J8-A3O1        TCGA-J8-A3O2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J8-A3YD        TCGA-J8-A3YE        TCGA-J8-A3YF        TCGA-J8-A3YG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J8-A3YH        TCGA-J8-A42S        TCGA-J8-A4HY        TCGA-KS-A41F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KS-A41I        TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KS-A4I3        TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KS-A4IB        TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-L6-A4EQ        TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-MK-A4N9        TCGA-QD-A8IV        TCGA-E8-A418 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D42V17, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0   2
  8Q LOSS WILD-TYPE  38 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    2
  8Q LOSS WILD-TYPE   38  358
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               358
[1] 2 2
[1] FALSE

Clustering(43) Variable = 9P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    18   1
  9P LOSS WILD-TYPE 464  15
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               19               479 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                1                15 
$`9P LOSS MUTATED`
TCGA-BJ-A2N8 TCGA-DJ-A2Q0 TCGA-DO-A2HM TCGA-E8-A432 TCGA-EL-A3GP TCGA-EL-A3MX 
       16.57        34.36         2.33        30.61        49.51        57.63 
TCGA-EL-A3ZK TCGA-EL-A3ZO TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1YE TCGA-EM-A2OY 
       51.78        72.69        44.15        23.90        54.08        32.32 
TCGA-EM-A3O3 TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N TCGA-FK-A3SG TCGA-FY-A40M 
       14.50         9.24        13.51       123.32         0.92        22.49 
TCGA-FY-A4B0 
       13.81 

$`9P LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N9 
       32.45        11.31        30.97        11.08        18.38        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       35.38        54.90        21.53        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       80.52        63.19        52.44        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 
       29.98        31.50        31.04        31.30        30.84        25.45 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       31.27        31.33        14.96        39.88        33.50        31.00 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       30.15        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ 
       60.95       157.15        37.94        57.01       106.62        79.50 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GR TCGA-EL-A3GS 
       98.53        69.57       108.36        64.87       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW 
       49.32        43.36        49.71        83.57       139.00       108.66 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       52.50        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZP 
       89.56        91.17        62.30        36.03        53.06        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       41.13        47.84        43.59        24.30        27.06        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       78.61        57.01        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       48.46        13.15        22.16        40.34        19.73        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR 
       15.68        14.14        33.07        44.52         8.35        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       17.39        16.18        15.02        15.06         7.33        12.53 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       27.02        38.66        38.86        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FK-A4UB 
       78.77        71.08         4.11        22.03        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25        20.42        17.82         7.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40N 
       21.63        17.06        17.36        15.16        23.87        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       14.04        21.60        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       11.01        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 
       16.90        21.83        31.10         8.22        25.64        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        5.75         2.47         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU 
       84.72        35.28        33.24        33.40        40.37         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       36.10        32.45        30.21        12.89         3.02 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.92              0.20 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           123.32            178.29 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            30.61             31.27 
[1] "0.9 - 123.3 (30.6)" "0.2 - 178.3 (31.3)"
[1] "hr=" "1.9"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  9P LOSS MUTATED         8        4         4        1         1         1
  9P LOSS WILD-TYPE     274       46       107        1        45         5
D43V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 8               274
  STAGE II                4                46
  STAGE III               4               107
  STAGE IV                1                 1
  STAGE IVA               1                45
  STAGE IVC               1                 5
[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                 T1  T2  T3  T4
  9P LOSS MUTATED     5   7   5   2
  9P LOSS WILD-TYPE 137 158 162  21
D43V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               5               137
  T2               7               158
  T3               5               162
  T4               2                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     8   8
  9P LOSS WILD-TYPE 217 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      8    8
  9P LOSS WILD-TYPE  217  216
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0               8               217
  1               8               216
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     6   1
  9P LOSS WILD-TYPE 272   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6    1
  9P LOSS WILD-TYPE  272    8
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0               6               272
  1               1                 8
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    12   7
  9P LOSS WILD-TYPE 353 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     12    7
  9P LOSS WILD-TYPE  353  127
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              12               353
  MALE                 7               127
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     5  12
  9P LOSS WILD-TYPE 175 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      5   12
  9P LOSS WILD-TYPE  175  291
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                5               175
  YES              12               291
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  9P LOSS MUTATED                0
  9P LOSS WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  9P LOSS MUTATED                                              15
  9P LOSS WILD-TYPE                                           341
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  9P LOSS MUTATED                                                                        4
  9P LOSS WILD-TYPE                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  9P LOSS MUTATED                                                                     0
  9P LOSS WILD-TYPE                                                                  36
D43V9, multiclass
                                                                        clus
vv                                                                       9P LOSS MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       15
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       9P LOSS WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        341
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    18   0
  9P LOSS WILD-TYPE 402  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     18    0
  9P LOSS WILD-TYPE  402   17
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               18               402
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  9P LOSS MUTATED              4                       0   14
  9P LOSS WILD-TYPE          128                      18  316
                   vv
clus                VERY ADVANCED (T4B)
  9P LOSS MUTATED                     0
  9P LOSS WILD-TYPE                   1
D43V11, multiclass
                         clus
vv                        9P LOSS MUTATED 9P LOSS WILD-TYPE
  MINIMAL (T3)                          4               128
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                 14               316
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    15   1   0   2
  9P LOSS WILD-TYPE 368  50   4  28
D43V12, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              15               368
  R1               1                50
  R2               0                 4
  RX               2                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, continuous
D43V14, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     7  12
  9P LOSS WILD-TYPE 218 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      7   12
  9P LOSS WILD-TYPE  218  252
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  MULTIFOCAL               7               218
  UNIFOCAL                12               252
[1] 2 2
[1] FALSE
D43V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     1
  9P LOSS WILD-TYPE                                1    51
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           1    12
  9P LOSS WILD-TYPE                        26   317
D43V16, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                51
  BLACK OR AFRICAN AMERICAN                      1                26
  WHITE                                         12               317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V17, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     0  14
  9P LOSS WILD-TYPE  38 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0   14
  9P LOSS WILD-TYPE   38  346
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO              14               346
[1] 2 2
[1] FALSE

Clustering(44) Variable = 9Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    23   2
  9Q LOSS WILD-TYPE 459  14
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               25               473 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                14 
$`9Q LOSS MUTATED`
TCGA-DJ-A13L TCGA-4C-A93U TCGA-BJ-A2N8 TCGA-DE-A4MB TCGA-DJ-A2Q0 TCGA-DO-A2HM 
        9.96         4.24        16.57        11.57        34.36         2.33 
TCGA-E8-A432 TCGA-EL-A3GP TCGA-EL-A3MX TCGA-EL-A3T9 TCGA-EL-A3ZK TCGA-EL-A3ZO 
       30.61        49.51        57.63         5.72        51.78        72.69 
TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A2OY TCGA-EM-A3O3 
       44.15        23.90        19.46        54.08        32.32        14.50 
TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N TCGA-FE-A231 TCGA-FK-A3SG TCGA-FY-A40M 
        9.24        13.51       123.32        31.59         0.92        22.49 
TCGA-FY-A4B0 
       13.81 

$`9Q LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A2PR 
       30.21        22.88        23.18        12.66        35.84        27.45 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK TCGA-E3-A3E5 
       23.44        59.57        42.54         3.12        24.76        39.95 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 TCGA-EL-A3GQ 
        7.66        45.53         4.18       139.86        57.11        50.24 
TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO 
       33.50       150.48        17.52       178.29        29.72        50.40 
TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET 
       75.42         1.05         1.68        17.23         2.60        21.83 
TCGA-MK-A84Z TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
       23.93        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.97        11.08        18.38        20.48        18.97        12.82 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 
       11.38        10.68        15.02        12.43        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        27.32        18.54        18.84        30.12 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12        14.70        14.27         2.76        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        52.27 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        48.07       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.99        30.58        35.41 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42        37.74        43.96        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       37.48        36.46        35.11        39.09        35.90        33.53 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        39.95        36.92        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX 
       16.41        19.56        36.33        32.81        36.33        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 
       35.87        40.96        36.99        20.22        30.61        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        40.70 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         9.60        35.67        36.43        23.44        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       30.87        30.12        33.04        34.78        27.06        26.93 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       35.54         3.12        15.81        35.38        54.90        21.53 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       31.30        30.84        25.45        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       64.87       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 
       83.57       139.00       108.66        52.50        29.65       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZL TCGA-EL-A3ZM 
       66.90        82.82        89.56        91.17        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       53.06        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        61.02        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       30.51        53.36        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       27.06        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.79        78.61        57.01        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        44.52         8.35 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.49        17.39        16.18        15.02        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
       12.53        27.02        38.66        38.86        29.95        29.85 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       33.24       106.09       107.41       108.46        84.89       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP 
       95.34        94.13        55.10        98.20        28.24        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        87.62        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FK-A4UB 
       78.77        71.08         4.11        22.03        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25        20.42        17.82         7.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40N 
       21.63        17.06        17.36        15.16        23.87        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       14.04        21.60        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       11.01        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 
       16.90        21.83        31.10         8.22        25.64        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        5.75         2.47         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU 
       84.72        35.28        33.24        33.40        40.37         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       36.10        32.45        30.21        12.89         3.02 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.92              0.20 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           123.32            178.29 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            22.49             31.30 
[1] "0.9 - 123.3 (22.5)" "0.2 - 178.3 (31.3)"
[1] "hr=" "3.8"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  9Q LOSS MUTATED         9        5         4        2         4         1
  9Q LOSS WILD-TYPE     273       45       107        0        42         5
D44V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 9               273
  STAGE II                5                45
  STAGE III               4               107
  STAGE IV                2                 0
  STAGE IVA               4                42
  STAGE IVC               1                 5
[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                 T1  T2  T3  T4
  9Q LOSS MUTATED     6   8   7   4
  9Q LOSS WILD-TYPE 136 157 160  19
D44V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               6               136
  T2               8               157
  T3               7               160
  T4               4                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"
D44V5, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     9  12
  9Q LOSS WILD-TYPE 216 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9   12
  9Q LOSS WILD-TYPE  216  212
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0               9               216
  1              12               212
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     9   1
  9Q LOSS WILD-TYPE 269   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9    1
  9Q LOSS WILD-TYPE  269    8
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0               9               269
  1               1                 8
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    16   9
  9Q LOSS WILD-TYPE 349 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     16    9
  9Q LOSS WILD-TYPE  349  125
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              16               349
  MALE                 9               125
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     8  14
  9Q LOSS WILD-TYPE 172 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      8   14
  9Q LOSS WILD-TYPE  172  289
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                8               172
  YES              14               289
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  9Q LOSS MUTATED                0
  9Q LOSS WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  9Q LOSS MUTATED                                              19
  9Q LOSS WILD-TYPE                                           337
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  9Q LOSS MUTATED                                                                        5
  9Q LOSS WILD-TYPE                                                                     95
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  9Q LOSS MUTATED                                                                     1
  9Q LOSS WILD-TYPE                                                                  35
D44V9, multiclass
                                                                        clus
vv                                                                       9Q LOSS MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       19
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  1
                                                                        clus
vv                                                                       9Q LOSS WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        337
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    23   1
  9Q LOSS WILD-TYPE 397  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     23    1
  9Q LOSS WILD-TYPE  397   16
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               23               397
  YES               1                16
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  9Q LOSS MUTATED              5                       1   17
  9Q LOSS WILD-TYPE          127                      17  313
                   vv
clus                VERY ADVANCED (T4B)
  9Q LOSS MUTATED                     1
  9Q LOSS WILD-TYPE                   0
D44V11, multiclass
                         clus
vv                        9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  MINIMAL (T3)                          5               127
  MODERATE/ADVANCED (T4A)               1                17
  NONE                                 17               313
  VERY ADVANCED (T4B)                   1                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    19   3   0   2
  9Q LOSS WILD-TYPE 364  48   4  28
D44V12, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              19               364
  R1               3                48
  R2               0                 4
  RX               2                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, continuous
D44V14, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    10  15
  9Q LOSS WILD-TYPE 215 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     10   15
  9Q LOSS WILD-TYPE  215  249
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  MULTIFOCAL              10               215
  UNIFOCAL                15               249
[1] 2 2
[1] FALSE
D44V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     1
  9Q LOSS WILD-TYPE                                1    51
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           2    16
  9Q LOSS WILD-TYPE                        25   313
D44V16, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                51
  BLACK OR AFRICAN AMERICAN                      2                25
  WHITE                                         16               313
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V17, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     1  18
  9Q LOSS WILD-TYPE  37 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   18
  9Q LOSS WILD-TYPE   37  342
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                37
  NOT HISPANIC OR LATINO              18               342
[1] 2 2
[1] FALSE

Clustering(45) Variable = 10P LOSS MUTATION ANALYSIS
D45V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED     7   0
  10P LOSS WILD-TYPE 475  16
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                491 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 0                 16 
$`10P LOSS MUTATED`
TCGA-BJ-A190 TCGA-E8-A432 TCGA-EL-A4KI TCGA-EM-A1YE TCGA-EM-A3O9 TCGA-ET-A39N 
       20.58        30.61        23.90        54.08         9.24       123.32 
TCGA-FY-A3I5 
        7.82 

$`10P LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       30.84        25.45        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        78.61        57.01        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        44.52 
TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
        8.35        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
       15.06         7.33        12.53        27.02        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        4.11        22.03         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82        29.10        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08        23.31        21.63        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 
       17.36        15.16        23.87        22.49        19.04        13.81 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       14.04        21.60        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       11.01        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 
       16.90        21.83        31.10         8.22        25.64        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        5.75         2.47         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU 
       84.72        35.28        33.24        33.40        40.37         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       36.10        32.45        30.21        12.89         3.02 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              7.82               0.20 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            123.32             178.29 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             23.90              31.27 
[1] "7.8 - 123.3 (23.9)" "0.2 - 178.3 (31.3)"
[1] "hr="     "9100000"
D45V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  10P LOSS MUTATED         2        3         2        0         0         0
  10P LOSS WILD-TYPE     280       47       109        2        46         6
D45V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  2                280
  STAGE II                 3                 47
  STAGE III                2                109
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  10P LOSS MUTATED     0   3   4   0
  10P LOSS WILD-TYPE 142 162 163  23
D45V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                0                142
  T2                3                162
  T3                4                163
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     6   0
  10P LOSS WILD-TYPE 219 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6    0
  10P LOSS WILD-TYPE  219  224
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                6                219
  1                0                224
[1] 2 2
[1] FALSE
D45V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1   0
  10P LOSS WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    0
  10P LOSS WILD-TYPE  277    9
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                1                277
  1                0                  9
[1] 2 2
[1] FALSE
D45V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4   3
  10P LOSS WILD-TYPE 361 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4    3
  10P LOSS WILD-TYPE  361  131
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                4                361
  MALE                  3                131
[1] 2 2
[1] FALSE
D45V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1   5
  10P LOSS WILD-TYPE 179 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    5
  10P LOSS WILD-TYPE  179  298
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 1                179
  YES                5                298
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  10P LOSS MUTATED                0
  10P LOSS WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  10P LOSS MUTATED                                               4
  10P LOSS WILD-TYPE                                           352
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  10P LOSS MUTATED                                                                        3
  10P LOSS WILD-TYPE                                                                     97
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  10P LOSS MUTATED                                                                     0
  10P LOSS WILD-TYPE                                                                  36
D45V9, multiclass
                                                                        clus
vv                                                                       10P LOSS MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       10P LOSS WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     6   0
  10P LOSS WILD-TYPE 414  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6    0
  10P LOSS WILD-TYPE  414   17
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 6                414
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  10P LOSS MUTATED              1                       0    6
  10P LOSS WILD-TYPE          131                      18  324
                    vv
clus                 VERY ADVANCED (T4B)
  10P LOSS MUTATED                     0
  10P LOSS WILD-TYPE                   1
D45V11, multiclass
                         clus
vv                        10P LOSS MUTATED 10P LOSS WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   6                324
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED     7   0   0   0
  10P LOSS WILD-TYPE 376  51   4  30
D45V12, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0                7                376
  R1                0                 51
  R2                0                  4
  RX                0                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, continuous
D45V14, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4   3
  10P LOSS WILD-TYPE 221 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4    3
  10P LOSS WILD-TYPE  221  261
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  MULTIFOCAL                4                221
  UNIFOCAL                  3                261
[1] 2 2
[1] FALSE
D45V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     1
  10P LOSS WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           0     4
  10P LOSS WILD-TYPE                        27   325
D45V16, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 51
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           4                325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V17, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     0   5
  10P LOSS WILD-TYPE  38 355
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0    5
  10P LOSS WILD-TYPE   38  355
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                355
[1] 2 2
[1] FALSE

Clustering(46) Variable = 10Q LOSS MUTATION ANALYSIS
D46V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED     6   0
  10Q LOSS WILD-TYPE 476  16
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                492 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 0                 16 
$`10Q LOSS MUTATED`
TCGA-BJ-A190 TCGA-E8-A432 TCGA-EL-A4KI TCGA-EM-A3O9 TCGA-ET-A39N TCGA-FY-A3I5 
       20.58        30.61        23.90         9.24       123.32         7.82 

$`10Q LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       30.84        25.45        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.46        78.61        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33        12.53        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
        9.50        36.10        32.45        30.21        12.89         3.02 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              7.82               0.20 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            123.32             178.29 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            22.240             31.285 
[1] "7.8 - 123.3 (22.2)" "0.2 - 178.3 (31.3)"
[1] "hr="     "3300000"
D46V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  10Q LOSS MUTATED         2        2         2        0         0         0
  10Q LOSS WILD-TYPE     280       48       109        2        46         6
D46V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  2                280
  STAGE II                 2                 48
  STAGE III                2                109
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  10Q LOSS MUTATED     0   2   4   0
  10Q LOSS WILD-TYPE 142 163 163  23
D46V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                0                142
  T2                2                163
  T3                4                163
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     5   0
  10Q LOSS WILD-TYPE 220 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5    0
  10Q LOSS WILD-TYPE  220  224
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                5                220
  1                0                224
[1] 2 2
[1] FALSE
D46V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1   0
  10Q LOSS WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1    0
  10Q LOSS WILD-TYPE  277    9
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                1                277
  1                0                  9
[1] 2 2
[1] FALSE
D46V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     3   3
  10Q LOSS WILD-TYPE 362 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3    3
  10Q LOSS WILD-TYPE  362  131
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                3                362
  MALE                  3                131
[1] 2 2
[1] FALSE
D46V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1   4
  10Q LOSS WILD-TYPE 179 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1    4
  10Q LOSS WILD-TYPE  179  299
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 1                179
  YES                4                299
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  10Q LOSS MUTATED                0
  10Q LOSS WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  10Q LOSS MUTATED                                               4
  10Q LOSS WILD-TYPE                                           352
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  10Q LOSS MUTATED                                                                        2
  10Q LOSS WILD-TYPE                                                                     98
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  10Q LOSS MUTATED                                                                     0
  10Q LOSS WILD-TYPE                                                                  36
D46V9, multiclass
                                                                        clus
vv                                                                       10Q LOSS MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       10Q LOSS WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V10, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     5   0
  10Q LOSS WILD-TYPE 415  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5    0
  10Q LOSS WILD-TYPE  415   17
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 5                415
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  10Q LOSS MUTATED              1                       0    5
  10Q LOSS WILD-TYPE          131                      18  325
                    vv
clus                 VERY ADVANCED (T4B)
  10Q LOSS MUTATED                     0
  10Q LOSS WILD-TYPE                   1
D46V11, multiclass
                         clus
vv                        10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   5                325
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED     6   0   0   0
  10Q LOSS WILD-TYPE 377  51   4  30
D46V12, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0                6                377
  R1                0                 51
  R2                0                  4
  RX                0                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, continuous
D46V14, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     4   2
  10Q LOSS WILD-TYPE 221 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4    2
  10Q LOSS WILD-TYPE  221  262
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  MULTIFOCAL                4                221
  UNIFOCAL                  2                262
[1] 2 2
[1] FALSE
D46V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     1
  10Q LOSS WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                           0     4
  10Q LOSS WILD-TYPE                        27   325
D46V16, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 51
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           4                325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V17, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     0   5
  10Q LOSS WILD-TYPE  38 355
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0    5
  10Q LOSS WILD-TYPE   38  355
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                355
[1] 2 2
[1] FALSE

Clustering(47) Variable = 11P LOSS MUTATION ANALYSIS
D47V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED     6   1
  11P LOSS WILD-TYPE 476  15
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                491 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 15 
$`11P LOSS MUTATED`
TCGA-BJ-A190 TCGA-EL-A3GP TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A22N TCGA-FE-A239 
       20.58        49.51        44.15        23.90        10.65        33.63 
TCGA-FY-A3I5 
        7.82 

$`11P LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       64.87       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       41.13        47.84        43.59        24.30        27.06        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        44.52         8.35 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        27.02        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        4.11        22.03         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82        29.10        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08        23.31        21.63        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 
       17.36        15.16        23.87        22.49        19.04        13.81 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       14.04        21.60        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       11.01        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 
       16.90        21.83        31.10         8.22        25.64        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        5.75         2.47         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU 
       84.72        35.28        33.24        33.40        40.37         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       36.10        32.45        30.21        12.89         3.02 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              7.82               0.20 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             49.51             178.29 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             23.90              31.27 
[1] "7.8 - 49.5 (23.9)"  "0.2 - 178.3 (31.3)"
[1] "hr=" "8.2"
D47V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  11P LOSS MUTATED         1        1         4        1         0         0
  11P LOSS WILD-TYPE     281       49       107        1        46         6
D47V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  1                281
  STAGE II                 1                 49
  STAGE III                4                107
  STAGE IV                 1                  1
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  11P LOSS MUTATED     1   1   4   1
  11P LOSS WILD-TYPE 141 164 163  22
D47V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                1                141
  T2                1                164
  T3                4                163
  T4                1                 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"
D47V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     5   2
  11P LOSS WILD-TYPE 220 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5    2
  11P LOSS WILD-TYPE  220  222
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                5                220
  1                2                222
[1] 2 2
[1] FALSE
D47V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     1   0
  11P LOSS WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1    0
  11P LOSS WILD-TYPE  277    9
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                1                277
  1                0                  9
[1] 2 2
[1] FALSE
D47V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2   5
  11P LOSS WILD-TYPE 363 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2    5
  11P LOSS WILD-TYPE  363  129
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                2                363
  MALE                  5                129
[1] 2 2
[1] FALSE
D47V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     1   5
  11P LOSS WILD-TYPE 179 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1    5
  11P LOSS WILD-TYPE  179  298
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 1                179
  YES                5                298
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  11P LOSS MUTATED                0
  11P LOSS WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  11P LOSS MUTATED                                               5
  11P LOSS WILD-TYPE                                           351
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  11P LOSS MUTATED                                                                        2
  11P LOSS WILD-TYPE                                                                     98
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  11P LOSS MUTATED                                                                     0
  11P LOSS WILD-TYPE                                                                  36
D47V9, multiclass
                                                                        clus
vv                                                                       11P LOSS MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       11P LOSS WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     6   0
  11P LOSS WILD-TYPE 414  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6    0
  11P LOSS WILD-TYPE  414   17
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 6                414
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  11P LOSS MUTATED              3                       0    4
  11P LOSS WILD-TYPE          129                      18  326
                    vv
clus                 VERY ADVANCED (T4B)
  11P LOSS MUTATED                     0
  11P LOSS WILD-TYPE                   1
D47V11, multiclass
                         clus
vv                        11P LOSS MUTATED 11P LOSS WILD-TYPE
  MINIMAL (T3)                           3                129
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   4                326
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED     6   0   0   1
  11P LOSS WILD-TYPE 377  51   4  29
D47V12, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0                6                377
  R1                0                 51
  R2                0                  4
  RX                1                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, continuous
D47V14, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     4   3
  11P LOSS WILD-TYPE 221 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    3
  11P LOSS WILD-TYPE  221  261
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  MULTIFOCAL                4                221
  UNIFOCAL                  3                261
[1] 2 2
[1] FALSE
D47V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     0
  11P LOSS WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           1     5
  11P LOSS WILD-TYPE                        26   324
D47V16, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       1                 26
  WHITE                                           5                324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V17, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0   6
  11P LOSS WILD-TYPE  38 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0    6
  11P LOSS WILD-TYPE   38  354
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                354
[1] 2 2
[1] FALSE

Clustering(48) Variable = 11Q LOSS MUTATION ANALYSIS
D48V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED     8   1
  11Q LOSS WILD-TYPE 474  15
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                489 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                 15 
$`11Q LOSS MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A190 TCGA-DE-A4MD TCGA-EL-A3GP TCGA-EL-A4K6 TCGA-EL-A4KI 
       13.78        20.58        25.12        49.51        44.15        23.90 
TCGA-EM-A22N TCGA-FE-A239 TCGA-FY-A3I5 
       10.65        33.63         7.82 

$`11Q LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       21.83        23.93         4.24        24.79        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 
       25.48        15.12        42.08        51.39        41.52         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.97        11.08        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       12.82        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       21.63        50.17        37.64        27.32        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       30.12        11.57        30.02        14.70        14.27         2.76 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       52.27        43.17        52.37         8.32        48.07       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.99        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       35.41        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74        43.96 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        39.95        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       36.33        11.34        35.87        40.96        36.99        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       30.61        19.20        23.21        21.27        20.48        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        40.70        18.97         9.60        35.67        36.43 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       23.44        27.62        30.87        30.12        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       80.52        63.19        52.44        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 
       29.98        31.50        31.04        31.30        30.84        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       30.61        31.27        31.33        14.96        39.88        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       31.00        30.15        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
      158.83        60.95       157.15        37.94        57.01       106.62 
TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GR 
       79.50        98.53        69.57       108.36        64.87       115.10 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       136.01        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      108.66        57.63        52.50        29.65       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        91.17        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        72.69        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        61.02 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 
       31.04        34.39        30.51        53.36        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       43.59        24.30        27.06        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       48.49        18.05        19.79        19.46        78.61        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        44.52         8.35        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        27.02        38.66        38.86        29.95        29.85 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       58.75        37.25        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
      123.32       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       28.24        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA 
      117.40        66.77       112.80        39.95        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE 
       85.15        85.68        78.77        71.08         4.11        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       29.10        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08        23.31        21.63        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 
       23.87        22.49        19.04        13.81        14.04        21.60 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
       31.10         8.22        25.64        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.24        33.40        40.37         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              7.82               0.20 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             49.51             178.29 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             23.90              31.27 
[1] "7.8 - 49.5 (23.9)"  "0.2 - 178.3 (31.3)"
[1] "hr=" "7.4"
D48V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  11Q LOSS MUTATED         1        2         4        1         1         0
  11Q LOSS WILD-TYPE     281       48       107        1        45         6
D48V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  1                281
  STAGE II                 2                 48
  STAGE III                4                107
  STAGE IV                 1                  1
  STAGE IVA                1                 45
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  11Q LOSS MUTATED     1   2   5   1
  11Q LOSS WILD-TYPE 141 163 162  22
D48V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                1                141
  T2                2                163
  T3                5                162
  T4                1                 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"
D48V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     6   3
  11Q LOSS WILD-TYPE 219 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6    3
  11Q LOSS WILD-TYPE  219  221
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                6                219
  1                3                221
[1] 2 2
[1] FALSE
D48V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     2   0
  11Q LOSS WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    0
  11Q LOSS WILD-TYPE  276    9
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                2                276
  1                0                  9
[1] 2 2
[1] FALSE
D48V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     2   7
  11Q LOSS WILD-TYPE 363 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    7
  11Q LOSS WILD-TYPE  363  127
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                2                363
  MALE                  7                127
[1] 2 2
[1] FALSE
D48V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1   7
  11Q LOSS WILD-TYPE 179 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1    7
  11Q LOSS WILD-TYPE  179  296
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 1                179
  YES                7                296
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  11Q LOSS MUTATED                0
  11Q LOSS WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  11Q LOSS MUTATED                                               7
  11Q LOSS WILD-TYPE                                           349
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  11Q LOSS MUTATED                                                                        2
  11Q LOSS WILD-TYPE                                                                     98
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  11Q LOSS MUTATED                                                                     0
  11Q LOSS WILD-TYPE                                                                  36
D48V9, multiclass
                                                                        clus
vv                                                                       11Q LOSS MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         7
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       11Q LOSS WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     7   0
  11Q LOSS WILD-TYPE 413  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      7    0
  11Q LOSS WILD-TYPE  413   17
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 7                413
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  11Q LOSS MUTATED              3                       0    6
  11Q LOSS WILD-TYPE          129                      18  324
                    vv
clus                 VERY ADVANCED (T4B)
  11Q LOSS MUTATED                     0
  11Q LOSS WILD-TYPE                   1
D48V11, multiclass
                         clus
vv                        11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  MINIMAL (T3)                           3                129
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   6                324
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED     8   0   0   1
  11Q LOSS WILD-TYPE 375  51   4  29
D48V12, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0                8                375
  R1                0                 51
  R2                0                  4
  RX                1                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, continuous
D48V14, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     4   5
  11Q LOSS WILD-TYPE 221 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4    5
  11Q LOSS WILD-TYPE  221  259
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  MULTIFOCAL                4                221
  UNIFOCAL                  5                259
[1] 2 2
[1] FALSE
D48V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     0
  11Q LOSS WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           1     6
  11Q LOSS WILD-TYPE                        26   323
D48V16, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       1                 26
  WHITE                                           6                323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V17, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     0   8
  11Q LOSS WILD-TYPE  38 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    8
  11Q LOSS WILD-TYPE   38  352
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                8                352
[1] 2 2
[1] FALSE

Clustering(49) Variable = 13Q LOSS MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    13   1
  13Q LOSS WILD-TYPE 469  15
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                484 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                 15 
$`13Q LOSS MUTATED`
TCGA-CE-A13K TCGA-BJ-A3F0 TCGA-DJ-A13P TCGA-DJ-A1QN TCGA-DJ-A2Q2 TCGA-EM-A1YB 
       12.66        13.94       169.32        42.58        43.96        19.46 
TCGA-EM-A22M TCGA-EM-A22Q TCGA-ET-A39N TCGA-ET-A40S TCGA-FE-A239 TCGA-FY-A3I5 
       14.53        14.24       123.32        40.21        33.63         7.82 
TCGA-FY-A3W9 TCGA-FY-A4B0 
       21.63        13.81 

$`13Q LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-DE-A0XZ TCGA-DJ-A13L TCGA-DJ-A2PR 
       30.21        22.88        23.18        35.84         9.96        27.45 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK TCGA-E3-A3E5 
       23.44        59.57        42.54         3.12        24.76        39.95 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 TCGA-EL-A3GQ 
        7.66        45.53         4.18       139.86        57.11        50.24 
TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO 
       33.50       150.48        17.52       178.29        29.72        50.40 
TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET 
       75.42         1.05         1.68        17.23         2.60        21.83 
TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       23.93         4.24        24.79        13.78        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 
       25.48        15.12        42.08        51.39        41.52        20.58 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       18.97        12.82        16.01        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       21.63        50.17        37.64        27.32        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
        2.76        48.79        38.17        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       52.27        43.17        52.37         8.32        48.07       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.99        30.58        35.41 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42        34.36        37.74        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       37.48        36.46        35.11        39.09        35.90        33.53 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        39.95        36.92        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX 
       16.41        19.56        36.33        32.81        36.33        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 
       35.87        40.96        36.99        20.22        30.61        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        40.70 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         9.60        35.67        36.43        23.44        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       30.87        30.12        33.04        34.78        27.06        26.93 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       35.54         3.12        15.81        35.38        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        92.55        47.21        66.38        80.52        63.19 
TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       52.44        31.23        35.67        31.27        29.98        31.50 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 
       31.04        31.30        30.84        25.45        30.61        31.27 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       31.33        14.96        39.88        33.50        31.00        30.15 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT 
       31.66        26.73       155.54        97.74       158.83        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 
      157.15        37.94        57.01       106.62        79.50        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS 
       69.57       108.36        64.87        49.51       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW 
       49.32        43.36        49.71        83.57       139.00       108.66 
TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       57.63        52.50        29.65       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        91.17        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        72.69        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        61.02        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YC TCGA-EM-A1YD 
       20.91        48.49        18.05        19.79        78.61        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N 
       54.08        14.73        14.50        15.75        10.45        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       44.19        41.29        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       27.02        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       33.24       106.09       107.41       108.46        84.89       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP 
       95.34        94.13        55.10        98.20        28.24        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        87.62        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       39.95        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3WA 
       16.27        15.68        16.57        18.08        23.31        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16        23.87        22.49        19.04        14.04 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       21.83        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       32.45        30.21        12.89         3.02 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              7.82               0.20 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            169.32             178.29 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            20.545             31.270 
[1] "7.8 - 169.3 (20.5)" "0.2 - 178.3 (31.3)"
[1] "hr=" "2.7"
D49V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  13Q LOSS MUTATED         7        4         3        0         0         0
  13Q LOSS WILD-TYPE     275       46       108        2        46         6
D49V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  7                275
  STAGE II                 4                 46
  STAGE III                3                108
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  13Q LOSS MUTATED     4   4   6   0
  13Q LOSS WILD-TYPE 138 161 161  23
D49V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                4                138
  T2                4                161
  T3                6                161
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    10   1
  13Q LOSS WILD-TYPE 215 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     10    1
  13Q LOSS WILD-TYPE  215  223
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               10                215
  1                1                223
[1] 2 2
[1] FALSE
D49V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     5   0
  13Q LOSS WILD-TYPE 273   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      5    0
  13Q LOSS WILD-TYPE  273    9
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0                5                273
  1                0                  9
[1] 2 2
[1] FALSE
D49V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     9   5
  13Q LOSS WILD-TYPE 356 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9    5
  13Q LOSS WILD-TYPE  356  129
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                9                356
  MALE                  5                129
[1] 2 2
[1] FALSE
D49V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     4   9
  13Q LOSS WILD-TYPE 176 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    9
  13Q LOSS WILD-TYPE  176  294
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 4                176
  YES                9                294
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  13Q LOSS MUTATED                0
  13Q LOSS WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  13Q LOSS MUTATED                                               9
  13Q LOSS WILD-TYPE                                           347
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  13Q LOSS MUTATED                                                                        5
  13Q LOSS WILD-TYPE                                                                     95
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  13Q LOSS MUTATED                                                                     0
  13Q LOSS WILD-TYPE                                                                  36
D49V9, multiclass
                                                                        clus
vv                                                                       13Q LOSS MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         9
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       13Q LOSS WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     8   4
  13Q LOSS WILD-TYPE 412  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8    4
  13Q LOSS WILD-TYPE  412   13
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 8                412
  YES                4                 13
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  13Q LOSS MUTATED              2                       0   12
  13Q LOSS WILD-TYPE          130                      18  318
                    vv
clus                 VERY ADVANCED (T4B)
  13Q LOSS MUTATED                     0
  13Q LOSS WILD-TYPE                   1
D49V11, multiclass
                         clus
vv                        13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  MINIMAL (T3)                           2                130
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                  12                318
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    11   2   0   1
  13Q LOSS WILD-TYPE 372  49   4  29
D49V12, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               11                372
  R1                2                 49
  R2                0                  4
  RX                1                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, continuous
D49V14, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     7   7
  13Q LOSS WILD-TYPE 218 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      7    7
  13Q LOSS WILD-TYPE  218  257
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  MULTIFOCAL                7                218
  UNIFOCAL                  7                257
[1] 2 2
[1] FALSE
D49V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0     2
  13Q LOSS WILD-TYPE                                1    50
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           0     9
  13Q LOSS WILD-TYPE                        27   320
D49V16, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                 50
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           9                320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V17, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     0  12
  13Q LOSS WILD-TYPE  38 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0   12
  13Q LOSS WILD-TYPE   38  348
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO               12                348
[1] 2 2
[1] FALSE

Clustering(50) Variable = 15Q LOSS MUTATION ANALYSIS
D50V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED     8   0
  15Q LOSS WILD-TYPE 474  16
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                490 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 0                 16 
$`15Q LOSS MUTATED`
TCGA-BJ-A3F0 TCGA-DJ-A4UR TCGA-EL-A3GO TCGA-EM-A1YE TCGA-EM-A2OY TCGA-EM-A3O9 
       13.94        34.78        64.87        54.08        32.32         9.24 
TCGA-ET-A39N TCGA-FY-A3I5 
      123.32         7.82 

$`15Q LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3PR TCGA-BJ-A3PT 
       20.48        18.97        12.82        16.01        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       33.04        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GP 
      106.62        79.50        98.53        69.57       108.36        49.51 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      101.13       139.99        49.32        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 
      139.00       108.66        57.63        52.50        29.65       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        91.17        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        72.69        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       61.02        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        78.61        57.01        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        44.52         8.35 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        7.33        12.53        27.02        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       28.24        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82        29.10        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08        23.31        21.63        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 
       15.16        23.87        22.49        19.04        13.81        14.04 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       21.83        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       32.45        30.21        12.89         3.02 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              7.82               0.20 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            123.32             178.29 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            33.550             31.165 
[1] "7.8 - 123.3 (33.5)" "0.2 - 178.3 (31.2)"
[1] "hr="     "9200000"
D50V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  15Q LOSS MUTATED         4        3         1        0         0         0
  15Q LOSS WILD-TYPE     278       47       110        2        46         6
D50V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  4                278
  STAGE II                 3                 47
  STAGE III                1                110
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  15Q LOSS MUTATED     1   3   4   0
  15Q LOSS WILD-TYPE 141 162 163  23
D50V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                1                141
  T2                3                162
  T3                4                163
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     6   1
  15Q LOSS WILD-TYPE 219 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6    1
  15Q LOSS WILD-TYPE  219  223
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0                6                219
  1                1                223
[1] 2 2
[1] FALSE
D50V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2   1
  15Q LOSS WILD-TYPE 276   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    1
  15Q LOSS WILD-TYPE  276    8
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0                2                276
  1                1                  8
[1] 2 2
[1] FALSE
D50V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     7   1
  15Q LOSS WILD-TYPE 358 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7    1
  15Q LOSS WILD-TYPE  358  133
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                7                358
  MALE                  1                133
[1] 2 2
[1] FALSE
D50V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2   5
  15Q LOSS WILD-TYPE 178 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    5
  15Q LOSS WILD-TYPE  178  298
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 2                178
  YES                5                298
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  15Q LOSS MUTATED                0
  15Q LOSS WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  15Q LOSS MUTATED                                               3
  15Q LOSS WILD-TYPE                                           353
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  15Q LOSS MUTATED                                                                        5
  15Q LOSS WILD-TYPE                                                                     95
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  15Q LOSS MUTATED                                                                     0
  15Q LOSS WILD-TYPE                                                                  36
D50V9, multiclass
                                                                        clus
vv                                                                       15Q LOSS MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       15Q LOSS WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     7   0
  15Q LOSS WILD-TYPE 413  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7    0
  15Q LOSS WILD-TYPE  413   17
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 7                413
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  15Q LOSS MUTATED              1                       0    7
  15Q LOSS WILD-TYPE          131                      18  323
                    vv
clus                 VERY ADVANCED (T4B)
  15Q LOSS MUTATED                     0
  15Q LOSS WILD-TYPE                   1
D50V11, multiclass
                         clus
vv                        15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   7                323
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED     8   0   0   0
  15Q LOSS WILD-TYPE 375  51   4  30
D50V12, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0                8                375
  R1                0                 51
  R2                0                  4
  RX                0                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, continuous
D50V14, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     3   5
  15Q LOSS WILD-TYPE 222 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3    5
  15Q LOSS WILD-TYPE  222  259
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  MULTIFOCAL                3                222
  UNIFOCAL                  5                259
[1] 2 2
[1] FALSE
D50V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     1
  15Q LOSS WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           0     4
  15Q LOSS WILD-TYPE                        27   325
D50V16, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 51
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           4                325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V17, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1   4
  15Q LOSS WILD-TYPE  37 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    4
  15Q LOSS WILD-TYPE   37  356
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 37
  NOT HISPANIC OR LATINO                4                356
[1] 2 2
[1] FALSE

Clustering(51) Variable = 17P LOSS MUTATION ANALYSIS
D51V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED     8   0
  17P LOSS WILD-TYPE 474  16
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                490 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 0                 16 
$`17P LOSS MUTATED`
TCGA-EL-A3D5 TCGA-E8-A432 TCGA-EL-A3ZM TCGA-EM-A1YE TCGA-EM-A3O9 TCGA-EM-A3OB 
       57.11        30.61        36.03        54.08         9.24        38.66 
TCGA-FE-A22Z TCGA-FE-A238 
       73.74        39.95 

$`17P LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3GQ 
       39.95         7.66        45.53         4.18       139.86        50.24 
TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO 
       33.50       150.48        17.52       178.29        29.72        50.40 
TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET 
       75.42         1.05         1.68        17.23         2.60        21.83 
TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       23.93         4.24        24.79        13.78        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 
       25.48        15.12        42.08        51.39        41.52        20.58 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       30.84        25.45        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       51.78        62.30        53.06        72.69        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       61.02        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        78.61        57.01        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        44.52 
TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
        8.35        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3ST TCGA-EM-A3SU 
       15.06         7.33        12.53        27.02        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       31.40        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
      117.40        66.77       112.80        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE 
       85.15        85.68        78.77        71.08         4.11        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        7.82        29.10        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08        23.31        21.63        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 
       15.16        23.87        22.49        19.04        13.81        14.04 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       21.83        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       32.45        30.21        12.89         3.02 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              9.24               0.20 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             73.74             178.29 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            39.305             31.070 
[1] "9.2 - 73.7 (39.3)"  "0.2 - 178.3 (31.1)"
[1] "hr="     "9200000"
D51V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  17P LOSS MUTATED         4        2         0        0         2         0
  17P LOSS WILD-TYPE     278       48       111        2        44         6
D51V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  4                278
  STAGE II                 2                 48
  STAGE III                0                111
  STAGE IV                 0                  2
  STAGE IVA                2                 44
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  17P LOSS MUTATED     0   3   3   2
  17P LOSS WILD-TYPE 142 162 164  21
D51V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                0                142
  T2                3                162
  T3                3                164
  T4                2                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V5, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     5   3
  17P LOSS WILD-TYPE 220 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5    3
  17P LOSS WILD-TYPE  220  221
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0                5                220
  1                3                221
[1] 2 2
[1] FALSE
D51V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     3   0
  17P LOSS WILD-TYPE 275   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3    0
  17P LOSS WILD-TYPE  275    9
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0                3                275
  1                0                  9
[1] 2 2
[1] FALSE
D51V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     6   2
  17P LOSS WILD-TYPE 359 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6    2
  17P LOSS WILD-TYPE  359  132
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                6                359
  MALE                  2                132
[1] 2 2
[1] FALSE
D51V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4   4
  17P LOSS WILD-TYPE 176 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4    4
  17P LOSS WILD-TYPE  176  299
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 4                176
  YES                4                299
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  17P LOSS MUTATED                0
  17P LOSS WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  17P LOSS MUTATED                                               4
  17P LOSS WILD-TYPE                                           352
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  17P LOSS MUTATED                                                                        4
  17P LOSS WILD-TYPE                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  17P LOSS MUTATED                                                                     0
  17P LOSS WILD-TYPE                                                                  36
D51V9, multiclass
                                                                        clus
vv                                                                       17P LOSS MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       17P LOSS WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     7   1
  17P LOSS WILD-TYPE 413  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      7    1
  17P LOSS WILD-TYPE  413   16
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 7                413
  YES                1                 16
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  17P LOSS MUTATED              2                       2    4
  17P LOSS WILD-TYPE          130                      16  326
                    vv
clus                 VERY ADVANCED (T4B)
  17P LOSS MUTATED                     0
  17P LOSS WILD-TYPE                   1
D51V11, multiclass
                         clus
vv                        17P LOSS MUTATED 17P LOSS WILD-TYPE
  MINIMAL (T3)                           2                130
  MODERATE/ADVANCED (T4A)                2                 16
  NONE                                   4                326
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED     6   2   0   0
  17P LOSS WILD-TYPE 377  49   4  30
D51V12, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0                6                377
  R1                2                 49
  R2                0                  4
  RX                0                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, continuous
D51V14, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     3   5
  17P LOSS WILD-TYPE 222 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3    5
  17P LOSS WILD-TYPE  222  259
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  MULTIFOCAL                3                222
  UNIFOCAL                  5                259
[1] 2 2
[1] FALSE
D51V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     1
  17P LOSS WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           0     3
  17P LOSS WILD-TYPE                        27   326
D51V16, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 51
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           3                326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V17, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     0   4
  17P LOSS WILD-TYPE  38 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      0    4
  17P LOSS WILD-TYPE   38  356
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                4                356
[1] 2 2
[1] FALSE

Clustering(52) Variable = 17Q LOSS MUTATION ANALYSIS
D52V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED     4   0
  17Q LOSS WILD-TYPE 478  16
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                494 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 0                 16 
$`17Q LOSS MUTATED`
TCGA-E8-A432 TCGA-EM-A3O9 TCGA-EM-A3OB TCGA-FE-A238 
       30.61         9.24        38.66        39.95 

$`17Q LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       31.30        30.84        25.45        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        78.61        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        44.52         8.35        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33        12.53 
TCGA-EM-A3OA TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       27.02        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP 
       95.34        94.13        55.10        98.20        28.24        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        87.62        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
      112.80        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              9.24               0.20 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             39.95             178.29 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            34.635             31.250 
[1] "9.2 - 40.0 (34.6)"  "0.2 - 178.3 (31.2)"
[1] "hr="     "3300000"
D52V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  17Q LOSS MUTATED         3        1         0        0         0         0
  17Q LOSS WILD-TYPE     279       49       111        2        46         6
D52V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  3                279
  STAGE II                 1                 49
  STAGE III                0                111
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  17Q LOSS MUTATED     0   2   2   0
  17Q LOSS WILD-TYPE 142 163 165  23
D52V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                142
  T2                2                163
  T3                2                165
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4   0
  17Q LOSS WILD-TYPE 221 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    0
  17Q LOSS WILD-TYPE  221  224
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0                4                221
  1                0                224
[1] 2 2
[1] FALSE
D52V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1   0
  17Q LOSS WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    0
  17Q LOSS WILD-TYPE  277    9
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0                1                277
  1                0                  9
[1] 2 2
[1] FALSE
D52V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3   1
  17Q LOSS WILD-TYPE 362 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3    1
  17Q LOSS WILD-TYPE  362  133
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                3                362
  MALE                  1                133
[1] 2 2
[1] FALSE
D52V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3   1
  17Q LOSS WILD-TYPE 177 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3    1
  17Q LOSS WILD-TYPE  177  302
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 3                177
  YES                1                302
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  17Q LOSS MUTATED                0
  17Q LOSS WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  17Q LOSS MUTATED                                               2
  17Q LOSS WILD-TYPE                                           354
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  17Q LOSS MUTATED                                                                        2
  17Q LOSS WILD-TYPE                                                                     98
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  17Q LOSS MUTATED                                                                     0
  17Q LOSS WILD-TYPE                                                                  36
D52V9, multiclass
                                                                        clus
vv                                                                       17Q LOSS MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       17Q LOSS WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4   0
  17Q LOSS WILD-TYPE 416  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    0
  17Q LOSS WILD-TYPE  416   17
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 4                416
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  17Q LOSS MUTATED              1                       0    3
  17Q LOSS WILD-TYPE          131                      18  327
                    vv
clus                 VERY ADVANCED (T4B)
  17Q LOSS MUTATED                     0
  17Q LOSS WILD-TYPE                   1
D52V11, multiclass
                         clus
vv                        17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   3                327
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED     4   0   0   0
  17Q LOSS WILD-TYPE 379  51   4  30
D52V12, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                4                379
  R1                0                 51
  R2                0                  4
  RX                0                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, continuous
D52V14, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     2   2
  17Q LOSS WILD-TYPE 223 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    2
  17Q LOSS WILD-TYPE  223  262
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  MULTIFOCAL                2                223
  UNIFOCAL                  2                262
[1] 2 2
[1] FALSE
D52V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0     1
  17Q LOSS WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           0     1
  17Q LOSS WILD-TYPE                        27   328
D52V16, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                407 
        TCGA-BJ-A290         TCGA-BJ-A291         TCGA-BJ-A45K 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CE-A13K         TCGA-DE-A0XZ         TCGA-DJ-A13L 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PR         TCGA-DJ-A3UU         TCGA-DJ-A3UW 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3V4         TCGA-DJ-A3VI         TCGA-DJ-A3VK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E3-A3E5         TCGA-EL-A3CR         TCGA-EL-A3CS 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3CY         TCGA-EL-A3D0         TCGA-EL-A3D5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3GQ         TCGA-EL-A3H2         TCGA-EL-A3H8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3MY         TCGA-EL-A3N3         TCGA-ET-A3BO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-FK-A3SD         TCGA-FY-A76V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A4HW         TCGA-L6-A4ET 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MK-A84Z         TCGA-4C-A93U         TCGA-BJ-A0YZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A0Z2         TCGA-BJ-A0Z3         TCGA-BJ-A0Z5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A0Z9         TCGA-BJ-A0ZA         TCGA-BJ-A0ZB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZC         TCGA-BJ-A0ZE         TCGA-BJ-A0ZG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZH         TCGA-BJ-A0ZJ         TCGA-BJ-A18Y 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A18Z         TCGA-BJ-A190         TCGA-BJ-A191 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A192         TCGA-BJ-A28R         TCGA-BJ-A28S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A28T         TCGA-BJ-A28V         TCGA-BJ-A28W 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A28X         TCGA-BJ-A28Z         TCGA-BJ-A2N7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A2N8         TCGA-BJ-A2N9         TCGA-BJ-A2NA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A2P4         TCGA-BJ-A3EZ         TCGA-BJ-A3F0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A3PR         TCGA-BJ-A3PT         TCGA-BJ-A3PU 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A45C         TCGA-BJ-A45D         TCGA-BJ-A45E 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A45F         TCGA-BJ-A45G         TCGA-BJ-A45H 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A45I         TCGA-BJ-A45J         TCGA-BJ-A4O8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A4O9         TCGA-CE-A27D         TCGA-CE-A3MD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CE-A3ME         TCGA-CE-A481         TCGA-CE-A482 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CE-A483         TCGA-CE-A484         TCGA-CE-A485 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DE-A0Y2         TCGA-DE-A0Y3         TCGA-DE-A2OL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DE-A3KN         TCGA-DE-A4M8         TCGA-DE-A4M9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DE-A4MA         TCGA-DE-A4MB         TCGA-DE-A4MC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DE-A4MD         TCGA-DE-A69J         TCGA-DE-A69K 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DE-A7U5         TCGA-DJ-A13M         TCGA-DJ-A13O 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A13P         TCGA-DJ-A13R         TCGA-DJ-A13S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A13T         TCGA-DJ-A13U         TCGA-DJ-A13W 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QD         TCGA-DJ-A1QE         TCGA-DJ-A1QF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QH         TCGA-DJ-A1QI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A1QO         TCGA-DJ-A1QQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PN         TCGA-DJ-A2PO         TCGA-DJ-A2PQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PS         TCGA-DJ-A2PT         TCGA-DJ-A2PU 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PV         TCGA-DJ-A2PW         TCGA-DJ-A2PX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q1         TCGA-DJ-A2Q2         TCGA-DJ-A2Q3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q4         TCGA-DJ-A2Q5         TCGA-DJ-A2Q6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q7         TCGA-DJ-A2Q9         TCGA-DJ-A2QA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2QB         TCGA-DJ-A3UK         TCGA-DJ-A3UM 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UN         TCGA-DJ-A3UO         TCGA-DJ-A3UQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UR         TCGA-DJ-A3US         TCGA-DJ-A3UT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UX         TCGA-DJ-A3UY         TCGA-DJ-A3UZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3V2         TCGA-DJ-A3V3         TCGA-DJ-A3V5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3V7         TCGA-DJ-A3V8         TCGA-DJ-A3V9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3VD         TCGA-DJ-A3VE         TCGA-DJ-A3VF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3VG         TCGA-DJ-A3VJ         TCGA-DJ-A3VL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3VM         TCGA-DJ-A4UL         TCGA-DJ-A4UP 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A4UQ         TCGA-DJ-A4UR         TCGA-DJ-A4UT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A4UW         TCGA-DJ-A4V0         TCGA-DJ-A4V4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A4V5         TCGA-DO-A1JZ         TCGA-DO-A1K0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DO-A2HM         TCGA-E3-A3DY         TCGA-E3-A3DZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E3-A3E0         TCGA-E3-A3E1         TCGA-E3-A3E2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E3-A3E3         TCGA-E8-A242         TCGA-E8-A2EA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E8-A3X7         TCGA-E8-A413         TCGA-E8-A414 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E8-A415         TCGA-E8-A416         TCGA-E8-A417 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E8-A419         TCGA-E8-A433         TCGA-E8-A434 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E8-A436         TCGA-E8-A437         TCGA-E8-A438 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E8-A44K         TCGA-E8-A44M         TCGA-EL-A3CL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3CP         TCGA-EL-A3CT         TCGA-EL-A3CU 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D1         TCGA-EL-A3D4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3D6         TCGA-EL-A3GO         TCGA-EL-A3GP 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3GR         TCGA-EL-A3GS         TCGA-EL-A3GU 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GW         TCGA-EL-A3GX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3GY         TCGA-EL-A3GZ         TCGA-EL-A3H1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3H3         TCGA-EL-A3H4         TCGA-EL-A3H5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3H7         TCGA-EL-A3MW         TCGA-EL-A3MX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3T0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3T1         TCGA-EL-A3T2         TCGA-EL-A3T3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3T6         TCGA-EL-A3T7         TCGA-EL-A3T8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3T9         TCGA-EL-A3TA         TCGA-EL-A3TB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZG         TCGA-EL-A3ZH         TCGA-EL-A3ZK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZL         TCGA-EL-A3ZN         TCGA-EL-A3ZO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZP         TCGA-EL-A3ZQ         TCGA-EL-A3ZR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZS         TCGA-EL-A3ZT         TCGA-EL-A4JV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4JW         TCGA-EL-A4JX         TCGA-EL-A4JZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4K0         TCGA-EL-A4K1         TCGA-EL-A4K2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4K4         TCGA-EL-A4K6         TCGA-EL-A4K7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4K9         TCGA-EL-A4KD         TCGA-EL-A4KG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4KH         TCGA-EL-A4KI         TCGA-EM-A22M 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EM-A22O         TCGA-EM-A2OV         TCGA-EM-A3AI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25I         TCGA-ET-A25J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A25K         TCGA-ET-A25L         TCGA-ET-A25M 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A25N         TCGA-ET-A25O         TCGA-ET-A25P 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A25R         TCGA-ET-A2MX         TCGA-ET-A2MY 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A2MZ         TCGA-ET-A2N0         TCGA-ET-A2N1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A2N3         TCGA-ET-A2N4         TCGA-ET-A2N5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A39I         TCGA-ET-A39J         TCGA-ET-A39K 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A39M         TCGA-ET-A39N         TCGA-ET-A39O 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A39P         TCGA-ET-A39R         TCGA-ET-A39S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BN         TCGA-ET-A3BP 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3BQ         TCGA-ET-A3BS         TCGA-ET-A3BT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3BU         TCGA-ET-A3BW         TCGA-ET-A3BX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3DO         TCGA-ET-A3DP         TCGA-ET-A3DQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3DR         TCGA-ET-A3DS         TCGA-ET-A3DT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3DU         TCGA-ET-A3DV         TCGA-ET-A3DW 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A40P         TCGA-ET-A40Q         TCGA-ET-A40R 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A40S         TCGA-ET-A40T         TCGA-ET-A4KN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A4KQ         TCGA-FE-A22Z         TCGA-FE-A230 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A231         TCGA-FE-A232         TCGA-FE-A233 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A234         TCGA-FE-A235         TCGA-FE-A236 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A237         TCGA-FE-A239         TCGA-FE-A23A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A3PA         TCGA-FE-A3PB         TCGA-FE-A3PC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A3PD         TCGA-FK-A3S3         TCGA-FK-A3SB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FK-A3SE         TCGA-FK-A3SG         TCGA-FK-A3SH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FK-A4UB         TCGA-FY-A2QD         TCGA-FY-A3BL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A3I4         TCGA-FY-A3I5         TCGA-FY-A3NM 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A3ON         TCGA-FY-A3R6         TCGA-FY-A3R7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A3R8         TCGA-FY-A3R9         TCGA-FY-A3RA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A3TY         TCGA-FY-A3W9         TCGA-FY-A3WA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A3YR         TCGA-FY-A40K         TCGA-FY-A40L 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A40M         TCGA-FY-A40N         TCGA-FY-A4B0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A4B3         TCGA-FY-A4B4         TCGA-GE-A2C6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-H2-A26U         TCGA-H2-A2K9         TCGA-H2-A3RH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-H2-A3RI         TCGA-H2-A421         TCGA-H2-A422 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IM-A3EB         TCGA-IM-A3ED         TCGA-IM-A3U2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IM-A3U3         TCGA-IM-A41Y         TCGA-IM-A41Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IM-A420         TCGA-IM-A4EB         TCGA-J8-A3O0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-J8-A3O1         TCGA-J8-A3O2         TCGA-J8-A3YD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-J8-A3YE         TCGA-J8-A3YF         TCGA-J8-A3YG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-J8-A3YH         TCGA-J8-A42S         TCGA-J8-A4HY 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-KS-A41F         TCGA-KS-A41I         TCGA-KS-A41J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-KS-A41L         TCGA-KS-A4I1         TCGA-KS-A4I3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-KS-A4I5         TCGA-KS-A4I7         TCGA-KS-A4I9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-KS-A4IB         TCGA-KS-A4IC         TCGA-KS-A4ID 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-L6-A4EP         TCGA-L6-A4EQ         TCGA-L6-A4EU 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MK-A4N6         TCGA-MK-A4N7         TCGA-MK-A4N9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-QD-A8IV         TCGA-E8-A418 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
D52V17, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0   2
  17Q LOSS WILD-TYPE  38 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0    2
  17Q LOSS WILD-TYPE   38  358
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                2                358
[1] 2 2
[1] FALSE

Clustering(53) Variable = 18P LOSS MUTATION ANALYSIS
D53V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED     4   0
  18P LOSS WILD-TYPE 478  16
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                494 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 0                 16 
$`18P LOSS MUTATED`
TCGA-DJ-A2Q0 TCGA-EM-A1YE TCGA-EM-A3SY TCGA-ET-A3BP 
       34.36        54.08        13.51        79.10 

$`18P LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I 
       18.05        19.79        19.46        78.61        57.01        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       27.02        38.66        38.86        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BQ 
       95.34        94.13        55.10        98.20        28.24        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             13.51               0.20 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             79.10             178.29 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            44.220             31.165 
[1] "13.5 - 79.1 (44.2)" "0.2 - 178.3 (31.2)"
[1] "hr="     "9100000"
D53V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  18P LOSS MUTATED         2        2         0        0         0         0
  18P LOSS WILD-TYPE     280       48       111        2        46         6
D53V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  2                280
  STAGE II                 2                 48
  STAGE III                0                111
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  18P LOSS MUTATED     1   3   0   0
  18P LOSS WILD-TYPE 141 162 167  23
D53V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                1                141
  T2                3                162
  T3                0                167
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     2   1
  18P LOSS WILD-TYPE 223 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    1
  18P LOSS WILD-TYPE  223  223
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0                2                223
  1                1                223
[1] 2 2
[1] FALSE
D53V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1   0
  18P LOSS WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    0
  18P LOSS WILD-TYPE  277    9
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0                1                277
  1                0                  9
[1] 2 2
[1] FALSE
D53V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3   1
  18P LOSS WILD-TYPE 362 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3    1
  18P LOSS WILD-TYPE  362  133
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                3                362
  MALE                  1                133
[1] 2 2
[1] FALSE
D53V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     2   2
  18P LOSS WILD-TYPE 178 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    2
  18P LOSS WILD-TYPE  178  301
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 2                178
  YES                2                301
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  18P LOSS MUTATED                0
  18P LOSS WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  18P LOSS MUTATED                                               2
  18P LOSS WILD-TYPE                                           354
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  18P LOSS MUTATED                                                                        2
  18P LOSS WILD-TYPE                                                                     98
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  18P LOSS MUTATED                                                                     0
  18P LOSS WILD-TYPE                                                                  36
D53V9, multiclass
                                                                        clus
vv                                                                       18P LOSS MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       18P LOSS WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     4   0
  18P LOSS WILD-TYPE 416  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    0
  18P LOSS WILD-TYPE  416   17
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 4                416
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  18P LOSS MUTATED              0                       0    4
  18P LOSS WILD-TYPE          132                      18  326
                    vv
clus                 VERY ADVANCED (T4B)
  18P LOSS MUTATED                     0
  18P LOSS WILD-TYPE                   1
D53V11, multiclass
                         clus
vv                        18P LOSS MUTATED 18P LOSS WILD-TYPE
  MINIMAL (T3)                           0                132
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   4                326
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED     4   0   0   0
  18P LOSS WILD-TYPE 379  51   4  30
D53V12, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0                4                379
  R1                0                 51
  R2                0                  4
  RX                0                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, continuous
D53V14, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1   3
  18P LOSS WILD-TYPE 224 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    3
  18P LOSS WILD-TYPE  224  261
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  MULTIFOCAL                1                224
  UNIFOCAL                  3                261
[1] 2 2
[1] FALSE
D53V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     0
  18P LOSS WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           0     2
  18P LOSS WILD-TYPE                        27   327
D53V16, multiclass
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                407 
        TCGA-BJ-A290         TCGA-BJ-A291         TCGA-BJ-A45K 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CE-A13K         TCGA-DE-A0XZ         TCGA-DJ-A13L 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2PR         TCGA-DJ-A3UU         TCGA-DJ-A3UW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3V4         TCGA-DJ-A3VI         TCGA-DJ-A3VK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E3-A3E5         TCGA-EL-A3CR         TCGA-EL-A3CS 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3CY         TCGA-EL-A3D0         TCGA-EL-A3D5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3GQ         TCGA-EL-A3H2         TCGA-EL-A3H8 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3MY         TCGA-EL-A3N3         TCGA-ET-A3BO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-FK-A3SD         TCGA-FY-A76V 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A4HW         TCGA-L6-A4ET 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-MK-A84Z         TCGA-4C-A93U         TCGA-BJ-A0YZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A0Z2         TCGA-BJ-A0Z3         TCGA-BJ-A0Z5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A0Z9         TCGA-BJ-A0ZA         TCGA-BJ-A0ZB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A0ZC         TCGA-BJ-A0ZE         TCGA-BJ-A0ZG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A0ZH         TCGA-BJ-A0ZJ         TCGA-BJ-A18Y 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A18Z         TCGA-BJ-A190         TCGA-BJ-A191 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A192         TCGA-BJ-A28R         TCGA-BJ-A28S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A28T         TCGA-BJ-A28V         TCGA-BJ-A28W 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A28X         TCGA-BJ-A28Z         TCGA-BJ-A2N7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A2N8         TCGA-BJ-A2N9         TCGA-BJ-A2NA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A2P4         TCGA-BJ-A3EZ         TCGA-BJ-A3F0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A3PR         TCGA-BJ-A3PT         TCGA-BJ-A3PU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A45C         TCGA-BJ-A45D         TCGA-BJ-A45E 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A45F         TCGA-BJ-A45G         TCGA-BJ-A45H 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A45I         TCGA-BJ-A45J         TCGA-BJ-A4O8 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A4O9         TCGA-CE-A27D         TCGA-CE-A3MD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CE-A3ME         TCGA-CE-A481         TCGA-CE-A482 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CE-A483         TCGA-CE-A484         TCGA-CE-A485 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DE-A0Y2         TCGA-DE-A0Y3         TCGA-DE-A2OL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DE-A3KN         TCGA-DE-A4M8         TCGA-DE-A4M9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DE-A4MA         TCGA-DE-A4MB         TCGA-DE-A4MC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DE-A4MD         TCGA-DE-A69J         TCGA-DE-A69K 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DE-A7U5         TCGA-DJ-A13M         TCGA-DJ-A13O 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A13P         TCGA-DJ-A13R         TCGA-DJ-A13S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A13T         TCGA-DJ-A13U         TCGA-DJ-A13W 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A1QD         TCGA-DJ-A1QE         TCGA-DJ-A1QF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QH         TCGA-DJ-A1QI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A1QO         TCGA-DJ-A1QQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2PN         TCGA-DJ-A2PO         TCGA-DJ-A2PQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2PS         TCGA-DJ-A2PT         TCGA-DJ-A2PU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2PV         TCGA-DJ-A2PW         TCGA-DJ-A2PX 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2Q2         TCGA-DJ-A2Q3         TCGA-DJ-A2Q4 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2Q9         TCGA-DJ-A2QA         TCGA-DJ-A2QB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3UK         TCGA-DJ-A3UM         TCGA-DJ-A3UN 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3UO         TCGA-DJ-A3UQ         TCGA-DJ-A3UR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3US         TCGA-DJ-A3UT         TCGA-DJ-A3UX 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3UY         TCGA-DJ-A3UZ         TCGA-DJ-A3V2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3V3         TCGA-DJ-A3V5         TCGA-DJ-A3V7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3V8         TCGA-DJ-A3V9         TCGA-DJ-A3VD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3VE         TCGA-DJ-A3VF         TCGA-DJ-A3VG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3VJ         TCGA-DJ-A3VL         TCGA-DJ-A3VM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A4UL         TCGA-DJ-A4UP         TCGA-DJ-A4UQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A4UR         TCGA-DJ-A4UT         TCGA-DJ-A4UW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A4V0         TCGA-DJ-A4V4         TCGA-DJ-A4V5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DO-A1JZ         TCGA-DO-A1K0         TCGA-DO-A2HM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E3-A3DY         TCGA-E3-A3DZ         TCGA-E3-A3E0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E3-A3E1         TCGA-E3-A3E2         TCGA-E3-A3E3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A242         TCGA-E8-A2EA         TCGA-E8-A3X7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A413         TCGA-E8-A414         TCGA-E8-A415 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A416         TCGA-E8-A417         TCGA-E8-A419 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A432         TCGA-E8-A433         TCGA-E8-A434 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A436         TCGA-E8-A437         TCGA-E8-A438 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A44K         TCGA-E8-A44M         TCGA-EL-A3CL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3CP         TCGA-EL-A3CT         TCGA-EL-A3CU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D1         TCGA-EL-A3D4 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3D6         TCGA-EL-A3GO         TCGA-EL-A3GP 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3GR         TCGA-EL-A3GS         TCGA-EL-A3GU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GW         TCGA-EL-A3GX 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3GY         TCGA-EL-A3GZ         TCGA-EL-A3H1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3H3         TCGA-EL-A3H4         TCGA-EL-A3H5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3H7         TCGA-EL-A3MW         TCGA-EL-A3MX 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3T0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3T1         TCGA-EL-A3T2         TCGA-EL-A3T3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3T6         TCGA-EL-A3T7         TCGA-EL-A3T8 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3T9         TCGA-EL-A3TA         TCGA-EL-A3TB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3ZG         TCGA-EL-A3ZH         TCGA-EL-A3ZK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3ZL         TCGA-EL-A3ZN         TCGA-EL-A3ZO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3ZP         TCGA-EL-A3ZQ         TCGA-EL-A3ZR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3ZS         TCGA-EL-A3ZT         TCGA-EL-A4JV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4JW         TCGA-EL-A4JX         TCGA-EL-A4JZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4K0         TCGA-EL-A4K1         TCGA-EL-A4K2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4K4         TCGA-EL-A4K6         TCGA-EL-A4K7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4K9         TCGA-EL-A4KD         TCGA-EL-A4KG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4KH         TCGA-EL-A4KI         TCGA-EM-A22M 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EM-A22O         TCGA-EM-A2OV         TCGA-EM-A3AI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25I         TCGA-ET-A25J 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A25K         TCGA-ET-A25L         TCGA-ET-A25M 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A25N         TCGA-ET-A25O         TCGA-ET-A25P 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A25R         TCGA-ET-A2MX         TCGA-ET-A2MY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A2MZ         TCGA-ET-A2N0         TCGA-ET-A2N1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A2N3         TCGA-ET-A2N4         TCGA-ET-A2N5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A39I         TCGA-ET-A39J         TCGA-ET-A39K 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A39M         TCGA-ET-A39N         TCGA-ET-A39O 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A39P         TCGA-ET-A39R         TCGA-ET-A39S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BN         TCGA-ET-A3BQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3BW         TCGA-ET-A3BX         TCGA-ET-A3DO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3DP         TCGA-ET-A3DQ         TCGA-ET-A3DR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3DV         TCGA-ET-A3DW         TCGA-ET-A40P 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A40Q         TCGA-ET-A40R         TCGA-ET-A40S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A40T         TCGA-ET-A4KN         TCGA-ET-A4KQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A238         TCGA-FE-A239         TCGA-FE-A23A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A3PA         TCGA-FE-A3PB         TCGA-FE-A3PC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A3PD         TCGA-FK-A3S3         TCGA-FK-A3SB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FK-A3SE         TCGA-FK-A3SG         TCGA-FK-A3SH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FK-A4UB         TCGA-FY-A2QD         TCGA-FY-A3BL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A3I4         TCGA-FY-A3I5         TCGA-FY-A3NM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A3ON         TCGA-FY-A3R6         TCGA-FY-A3R7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A3R8         TCGA-FY-A3R9         TCGA-FY-A3RA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A3TY         TCGA-FY-A3W9         TCGA-FY-A3WA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A3YR         TCGA-FY-A40K         TCGA-FY-A40L 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A40M         TCGA-FY-A40N         TCGA-FY-A4B0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A4B3         TCGA-FY-A4B4         TCGA-GE-A2C6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-H2-A26U         TCGA-H2-A2K9         TCGA-H2-A3RH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-H2-A3RI         TCGA-H2-A421         TCGA-H2-A422 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IM-A3EB         TCGA-IM-A3ED         TCGA-IM-A3U2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IM-A3U3         TCGA-IM-A41Y         TCGA-IM-A41Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IM-A420         TCGA-IM-A4EB         TCGA-J8-A3O0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-J8-A3O1         TCGA-J8-A3O2         TCGA-J8-A3YD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-J8-A3YE         TCGA-J8-A3YF         TCGA-J8-A3YG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-J8-A3YH         TCGA-J8-A42S         TCGA-J8-A4HY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KS-A41F         TCGA-KS-A41I         TCGA-KS-A41J 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KS-A41L         TCGA-KS-A4I1         TCGA-KS-A4I3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KS-A4I5         TCGA-KS-A4I7         TCGA-KS-A4I9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KS-A4IB         TCGA-KS-A4IC         TCGA-KS-A4ID 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L6-A4EP         TCGA-L6-A4EQ         TCGA-L6-A4EU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-MK-A4N6         TCGA-MK-A4N7         TCGA-MK-A4N9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-QD-A8IV         TCGA-E8-A418 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
D53V17, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1   1
  18P LOSS WILD-TYPE  37 359
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    1
  18P LOSS WILD-TYPE   37  359
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 37
  NOT HISPANIC OR LATINO                1                359
[1] 2 2
[1] FALSE

Clustering(54) Variable = 18Q LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED     4   0
  18Q LOSS WILD-TYPE 478  16
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                494 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 0                 16 
$`18Q LOSS MUTATED`
TCGA-DJ-A2Q0 TCGA-EM-A1YE TCGA-EM-A3SY TCGA-ET-A3BP 
       34.36        54.08        13.51        79.10 

$`18Q LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I 
       18.05        19.79        19.46        78.61        57.01        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       27.02        38.66        38.86        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BQ 
       95.34        94.13        55.10        98.20        28.24        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             13.51               0.20 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             79.10             178.29 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            44.220             31.165 
[1] "13.5 - 79.1 (44.2)" "0.2 - 178.3 (31.2)"
[1] "hr="     "9100000"
D54V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  18Q LOSS MUTATED         2        2         0        0         0         0
  18Q LOSS WILD-TYPE     280       48       111        2        46         6
D54V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  2                280
  STAGE II                 2                 48
  STAGE III                0                111
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  18Q LOSS MUTATED     1   3   0   0
  18Q LOSS WILD-TYPE 141 162 167  23
D54V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                1                141
  T2                3                162
  T3                0                167
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     2   1
  18Q LOSS WILD-TYPE 223 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2    1
  18Q LOSS WILD-TYPE  223  223
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0                2                223
  1                1                223
[1] 2 2
[1] FALSE
D54V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     1   0
  18Q LOSS WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    0
  18Q LOSS WILD-TYPE  277    9
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0                1                277
  1                0                  9
[1] 2 2
[1] FALSE
D54V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3   1
  18Q LOSS WILD-TYPE 362 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    1
  18Q LOSS WILD-TYPE  362  133
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                3                362
  MALE                  1                133
[1] 2 2
[1] FALSE
D54V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     2   2
  18Q LOSS WILD-TYPE 178 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2    2
  18Q LOSS WILD-TYPE  178  301
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 2                178
  YES                2                301
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  18Q LOSS MUTATED                0
  18Q LOSS WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  18Q LOSS MUTATED                                               2
  18Q LOSS WILD-TYPE                                           354
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  18Q LOSS MUTATED                                                                        2
  18Q LOSS WILD-TYPE                                                                     98
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  18Q LOSS MUTATED                                                                     0
  18Q LOSS WILD-TYPE                                                                  36
D54V9, multiclass
                                                                        clus
vv                                                                       18Q LOSS MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       18Q LOSS WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     4   0
  18Q LOSS WILD-TYPE 416  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4    0
  18Q LOSS WILD-TYPE  416   17
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 4                416
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  18Q LOSS MUTATED              0                       0    4
  18Q LOSS WILD-TYPE          132                      18  326
                    vv
clus                 VERY ADVANCED (T4B)
  18Q LOSS MUTATED                     0
  18Q LOSS WILD-TYPE                   1
D54V11, multiclass
                         clus
vv                        18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  MINIMAL (T3)                           0                132
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   4                326
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED     4   0   0   0
  18Q LOSS WILD-TYPE 379  51   4  30
D54V12, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0                4                379
  R1                0                 51
  R2                0                  4
  RX                0                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, continuous
D54V14, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     1   3
  18Q LOSS WILD-TYPE 224 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    3
  18Q LOSS WILD-TYPE  224  261
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  MULTIFOCAL                1                224
  UNIFOCAL                  3                261
[1] 2 2
[1] FALSE
D54V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     0
  18Q LOSS WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           0     2
  18Q LOSS WILD-TYPE                        27   327
D54V16, multiclass
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                407 
        TCGA-BJ-A290         TCGA-BJ-A291         TCGA-BJ-A45K 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CE-A13K         TCGA-DE-A0XZ         TCGA-DJ-A13L 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PR         TCGA-DJ-A3UU         TCGA-DJ-A3UW 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3V4         TCGA-DJ-A3VI         TCGA-DJ-A3VK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E3-A3E5         TCGA-EL-A3CR         TCGA-EL-A3CS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3CY         TCGA-EL-A3D0         TCGA-EL-A3D5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3GQ         TCGA-EL-A3H2         TCGA-EL-A3H8 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3MY         TCGA-EL-A3N3         TCGA-ET-A3BO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-FK-A3SD         TCGA-FY-A76V 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A4HW         TCGA-L6-A4ET 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-MK-A84Z         TCGA-4C-A93U         TCGA-BJ-A0YZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A0Z2         TCGA-BJ-A0Z3         TCGA-BJ-A0Z5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A0Z9         TCGA-BJ-A0ZA         TCGA-BJ-A0ZB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZC         TCGA-BJ-A0ZE         TCGA-BJ-A0ZG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZH         TCGA-BJ-A0ZJ         TCGA-BJ-A18Y 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A18Z         TCGA-BJ-A190         TCGA-BJ-A191 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A192         TCGA-BJ-A28R         TCGA-BJ-A28S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A28T         TCGA-BJ-A28V         TCGA-BJ-A28W 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A28X         TCGA-BJ-A28Z         TCGA-BJ-A2N7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A2N8         TCGA-BJ-A2N9         TCGA-BJ-A2NA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A2P4         TCGA-BJ-A3EZ         TCGA-BJ-A3F0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A3PR         TCGA-BJ-A3PT         TCGA-BJ-A3PU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A45C         TCGA-BJ-A45D         TCGA-BJ-A45E 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A45F         TCGA-BJ-A45G         TCGA-BJ-A45H 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A45I         TCGA-BJ-A45J         TCGA-BJ-A4O8 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A4O9         TCGA-CE-A27D         TCGA-CE-A3MD 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CE-A3ME         TCGA-CE-A481         TCGA-CE-A482 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CE-A483         TCGA-CE-A484         TCGA-CE-A485 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DE-A0Y2         TCGA-DE-A0Y3         TCGA-DE-A2OL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DE-A3KN         TCGA-DE-A4M8         TCGA-DE-A4M9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DE-A4MA         TCGA-DE-A4MB         TCGA-DE-A4MC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DE-A4MD         TCGA-DE-A69J         TCGA-DE-A69K 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DE-A7U5         TCGA-DJ-A13M         TCGA-DJ-A13O 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A13P         TCGA-DJ-A13R         TCGA-DJ-A13S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A13T         TCGA-DJ-A13U         TCGA-DJ-A13W 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QD         TCGA-DJ-A1QE         TCGA-DJ-A1QF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QH         TCGA-DJ-A1QI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A1QO         TCGA-DJ-A1QQ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PN         TCGA-DJ-A2PO         TCGA-DJ-A2PQ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PS         TCGA-DJ-A2PT         TCGA-DJ-A2PU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PV         TCGA-DJ-A2PW         TCGA-DJ-A2PX 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q2         TCGA-DJ-A2Q3         TCGA-DJ-A2Q4 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q9         TCGA-DJ-A2QA         TCGA-DJ-A2QB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UK         TCGA-DJ-A3UM         TCGA-DJ-A3UN 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UO         TCGA-DJ-A3UQ         TCGA-DJ-A3UR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3US         TCGA-DJ-A3UT         TCGA-DJ-A3UX 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UY         TCGA-DJ-A3UZ         TCGA-DJ-A3V2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3V3         TCGA-DJ-A3V5         TCGA-DJ-A3V7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3V8         TCGA-DJ-A3V9         TCGA-DJ-A3VD 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3VE         TCGA-DJ-A3VF         TCGA-DJ-A3VG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3VJ         TCGA-DJ-A3VL         TCGA-DJ-A3VM 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A4UL         TCGA-DJ-A4UP         TCGA-DJ-A4UQ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A4UR         TCGA-DJ-A4UT         TCGA-DJ-A4UW 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A4V0         TCGA-DJ-A4V4         TCGA-DJ-A4V5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DO-A1JZ         TCGA-DO-A1K0         TCGA-DO-A2HM 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E3-A3DY         TCGA-E3-A3DZ         TCGA-E3-A3E0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E3-A3E1         TCGA-E3-A3E2         TCGA-E3-A3E3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A242         TCGA-E8-A2EA         TCGA-E8-A3X7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A413         TCGA-E8-A414         TCGA-E8-A415 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A416         TCGA-E8-A417         TCGA-E8-A419 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A432         TCGA-E8-A433         TCGA-E8-A434 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A436         TCGA-E8-A437         TCGA-E8-A438 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A44K         TCGA-E8-A44M         TCGA-EL-A3CL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3CP         TCGA-EL-A3CT         TCGA-EL-A3CU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D1         TCGA-EL-A3D4 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3D6         TCGA-EL-A3GO         TCGA-EL-A3GP 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3GR         TCGA-EL-A3GS         TCGA-EL-A3GU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GW         TCGA-EL-A3GX 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3GY         TCGA-EL-A3GZ         TCGA-EL-A3H1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3H3         TCGA-EL-A3H4         TCGA-EL-A3H5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3H7         TCGA-EL-A3MW         TCGA-EL-A3MX 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3T0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3T1         TCGA-EL-A3T2         TCGA-EL-A3T3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3T6         TCGA-EL-A3T7         TCGA-EL-A3T8 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3T9         TCGA-EL-A3TA         TCGA-EL-A3TB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZG         TCGA-EL-A3ZH         TCGA-EL-A3ZK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZL         TCGA-EL-A3ZN         TCGA-EL-A3ZO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZP         TCGA-EL-A3ZQ         TCGA-EL-A3ZR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZS         TCGA-EL-A3ZT         TCGA-EL-A4JV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4JW         TCGA-EL-A4JX         TCGA-EL-A4JZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4K0         TCGA-EL-A4K1         TCGA-EL-A4K2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4K4         TCGA-EL-A4K6         TCGA-EL-A4K7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4K9         TCGA-EL-A4KD         TCGA-EL-A4KG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4KH         TCGA-EL-A4KI         TCGA-EM-A22M 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EM-A22O         TCGA-EM-A2OV         TCGA-EM-A3AI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25I         TCGA-ET-A25J 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A25K         TCGA-ET-A25L         TCGA-ET-A25M 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A25N         TCGA-ET-A25O         TCGA-ET-A25P 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A25R         TCGA-ET-A2MX         TCGA-ET-A2MY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A2MZ         TCGA-ET-A2N0         TCGA-ET-A2N1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A2N3         TCGA-ET-A2N4         TCGA-ET-A2N5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A39I         TCGA-ET-A39J         TCGA-ET-A39K 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A39M         TCGA-ET-A39N         TCGA-ET-A39O 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A39P         TCGA-ET-A39R         TCGA-ET-A39S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BN         TCGA-ET-A3BQ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3BW         TCGA-ET-A3BX         TCGA-ET-A3DO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3DP         TCGA-ET-A3DQ         TCGA-ET-A3DR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3DV         TCGA-ET-A3DW         TCGA-ET-A40P 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A40Q         TCGA-ET-A40R         TCGA-ET-A40S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A40T         TCGA-ET-A4KN         TCGA-ET-A4KQ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A238         TCGA-FE-A239         TCGA-FE-A23A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A3PA         TCGA-FE-A3PB         TCGA-FE-A3PC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A3PD         TCGA-FK-A3S3         TCGA-FK-A3SB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FK-A3SE         TCGA-FK-A3SG         TCGA-FK-A3SH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FK-A4UB         TCGA-FY-A2QD         TCGA-FY-A3BL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A3I4         TCGA-FY-A3I5         TCGA-FY-A3NM 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A3ON         TCGA-FY-A3R6         TCGA-FY-A3R7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A3R8         TCGA-FY-A3R9         TCGA-FY-A3RA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A3TY         TCGA-FY-A3W9         TCGA-FY-A3WA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A3YR         TCGA-FY-A40K         TCGA-FY-A40L 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A40M         TCGA-FY-A40N         TCGA-FY-A4B0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A4B3         TCGA-FY-A4B4         TCGA-GE-A2C6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-H2-A26U         TCGA-H2-A2K9         TCGA-H2-A3RH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-H2-A3RI         TCGA-H2-A421         TCGA-H2-A422 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IM-A3EB         TCGA-IM-A3ED         TCGA-IM-A3U2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IM-A3U3         TCGA-IM-A41Y         TCGA-IM-A41Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IM-A420         TCGA-IM-A4EB         TCGA-J8-A3O0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-J8-A3O1         TCGA-J8-A3O2         TCGA-J8-A3YD 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-J8-A3YE         TCGA-J8-A3YF         TCGA-J8-A3YG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-J8-A3YH         TCGA-J8-A42S         TCGA-J8-A4HY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KS-A41F         TCGA-KS-A41I         TCGA-KS-A41J 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KS-A41L         TCGA-KS-A4I1         TCGA-KS-A4I3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KS-A4I5         TCGA-KS-A4I7         TCGA-KS-A4I9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KS-A4IB         TCGA-KS-A4IC         TCGA-KS-A4ID 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-L6-A4EP         TCGA-L6-A4EQ         TCGA-L6-A4EU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-MK-A4N6         TCGA-MK-A4N7         TCGA-MK-A4N9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-QD-A8IV         TCGA-E8-A418 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D54V17, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     1   1
  18Q LOSS WILD-TYPE  37 359
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    1
  18Q LOSS WILD-TYPE   37  359
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 37
  NOT HISPANIC OR LATINO                1                359
[1] 2 2
[1] FALSE

Clustering(55) Variable = 19P LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED     4   1
  19P LOSS WILD-TYPE 478  15
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                493 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 15 
$`19P LOSS MUTATED`
TCGA-EL-A3D5 TCGA-EL-A3H2 TCGA-BJ-A0YZ TCGA-ET-A39N TCGA-FY-A3WA 
       57.11        33.50        24.79       123.32        17.06 

$`19P LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3GQ 
       39.95         7.66        45.53         4.18       139.86        50.24 
TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO TCGA-ET-A3BV 
      150.48        17.52       178.29        29.72        50.40        75.42 
TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET TCGA-MK-A84Z 
        1.05         1.68        17.23         2.60        21.83        23.93 
TCGA-4C-A93U TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        13.78        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       42.08        51.39        41.52        20.58         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       11.08        18.38        16.57        20.48        18.97        12.82 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 
       11.38        10.68        15.02        12.43        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        27.32        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       52.27        43.17        52.37         8.32        48.07       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.99        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       35.41        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74        43.96 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        39.95        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       36.33        11.34        35.87        40.96        36.99        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       30.61        19.20        23.21        21.27        20.48        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        40.70        18.97         9.60        35.67        36.43 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       23.44        27.62        30.87        30.12        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       80.52        63.19        52.44        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 
       29.98        31.50        31.04        31.30        30.84        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       30.61        31.27        31.33        14.96        39.88        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       31.00        30.15        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
      158.83        60.95       157.15        37.94        57.01       106.62 
TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       79.50        98.53        69.57       108.36        64.87        49.51 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      101.13       139.99        49.32        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 
      139.00       108.66        57.63        52.50        29.65       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        91.17        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        72.69        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       61.02        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.46        78.61        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
       23.31        21.63        17.36        15.16        23.87        22.49 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04        13.81        14.04        21.60        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46        11.01        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       24.69        22.29         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV 
       40.37         9.50        36.10        32.45        30.21        12.89 
TCGA-E8-A418 
        3.02 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             17.06               0.20 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            123.32             178.29 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             33.50              31.23 
[1] "17.1 - 123.3 (33.5)" "0.2 - 178.3 (31.2)" 
[1] "hr=" "5"  
D55V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  19P LOSS MUTATED         3        2         0        0         0         0
  19P LOSS WILD-TYPE     279       48       111        2        46         6
D55V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  3                279
  STAGE II                 2                 48
  STAGE III                0                111
  STAGE IV                 0                  2
  STAGE IVA                0                 46
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  19P LOSS MUTATED     1   2   2   0
  19P LOSS WILD-TYPE 141 163 165  23
D55V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                1                141
  T2                2                163
  T3                2                165
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2   1
  19P LOSS WILD-TYPE 223 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    1
  19P LOSS WILD-TYPE  223  223
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                2                223
  1                1                223
[1] 2 2
[1] FALSE
D55V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2   0
  19P LOSS WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    0
  19P LOSS WILD-TYPE  276    9
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                2                276
  1                0                  9
[1] 2 2
[1] FALSE
D55V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3   2
  19P LOSS WILD-TYPE 362 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    2
  19P LOSS WILD-TYPE  362  132
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                3                362
  MALE                  2                132
[1] 2 2
[1] FALSE
D55V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2   3
  19P LOSS WILD-TYPE 178 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    3
  19P LOSS WILD-TYPE  178  300
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 2                178
  YES                3                300
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  19P LOSS MUTATED                0
  19P LOSS WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  19P LOSS MUTATED                                               4
  19P LOSS WILD-TYPE                                           352
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  19P LOSS MUTATED                                                                        1
  19P LOSS WILD-TYPE                                                                     99
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  19P LOSS MUTATED                                                                     0
  19P LOSS WILD-TYPE                                                                  36
D55V9, multiclass
                                                                        clus
vv                                                                       19P LOSS MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       19P LOSS WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3   2
  19P LOSS WILD-TYPE 417  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    2
  19P LOSS WILD-TYPE  417   15
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 3                417
  YES                2                 15
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  19P LOSS MUTATED              1                       0    4
  19P LOSS WILD-TYPE          131                      18  326
                    vv
clus                 VERY ADVANCED (T4B)
  19P LOSS MUTATED                     0
  19P LOSS WILD-TYPE                   1
D55V11, multiclass
                         clus
vv                        19P LOSS MUTATED 19P LOSS WILD-TYPE
  MINIMAL (T3)                           1                131
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   4                326
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED     4   1   0   0
  19P LOSS WILD-TYPE 379  50   4  30
D55V12, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0                4                379
  R1                1                 50
  R2                0                  4
  RX                0                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V13, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                385 
        TCGA-BJ-A290         TCGA-BJ-A291         TCGA-BJ-A45K 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CE-A13K         TCGA-DE-A0XZ         TCGA-DJ-A2PR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3UU         TCGA-DJ-A3UW         TCGA-DJ-A3V4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3VI         TCGA-DJ-A3VK         TCGA-E3-A3E5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3CR         TCGA-EL-A3CS         TCGA-EL-A3CY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3D0         TCGA-EL-A3GQ         TCGA-EL-A3H8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3AQ         TCGA-ET-A3BO         TCGA-ET-A3BV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A4HW         TCGA-4C-A93U 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A0Z0         TCGA-BJ-A0Z3         TCGA-BJ-A0Z5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A0Z9         TCGA-BJ-A0ZA         TCGA-BJ-A0ZB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A0ZH         TCGA-BJ-A0ZJ         TCGA-BJ-A18Y 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A18Z         TCGA-BJ-A190         TCGA-BJ-A191 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A28R         TCGA-BJ-A28T         TCGA-BJ-A28W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A28X         TCGA-BJ-A28Z         TCGA-BJ-A2N8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A2N9         TCGA-BJ-A2NA         TCGA-BJ-A3EZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A3PR         TCGA-BJ-A3PU         TCGA-BJ-A45C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A45D         TCGA-BJ-A45E         TCGA-BJ-A45G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A45I         TCGA-BJ-A45J         TCGA-BJ-A4O8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A4O9         TCGA-CE-A3MD         TCGA-CE-A483 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CE-A484         TCGA-CE-A485         TCGA-DE-A0Y2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DE-A0Y3         TCGA-DE-A3KN         TCGA-DE-A4M8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DE-A4MA         TCGA-DE-A4MB         TCGA-DE-A4MC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DE-A4MD         TCGA-DE-A69K         TCGA-DE-A7U5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A13M         TCGA-DJ-A13O         TCGA-DJ-A13R 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A13T         TCGA-DJ-A13V         TCGA-DJ-A13W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A13X         TCGA-DJ-A1QG         TCGA-DJ-A1QH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A2PO         TCGA-DJ-A2PP 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2PQ         TCGA-DJ-A2PS         TCGA-DJ-A2PT 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2PU         TCGA-DJ-A2PV         TCGA-DJ-A2PW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2PX         TCGA-DJ-A2PY         TCGA-DJ-A2PZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2Q0         TCGA-DJ-A2Q1         TCGA-DJ-A2Q2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2Q3         TCGA-DJ-A2Q4         TCGA-DJ-A2Q5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2Q6         TCGA-DJ-A2Q7         TCGA-DJ-A2Q8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2Q9         TCGA-DJ-A2QA         TCGA-DJ-A2QB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3UK         TCGA-DJ-A3UM         TCGA-DJ-A3UN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3UO         TCGA-DJ-A3UP         TCGA-DJ-A3UQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3UR         TCGA-DJ-A3UX         TCGA-DJ-A3UZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3V0         TCGA-DJ-A3V2         TCGA-DJ-A3V3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3V5         TCGA-DJ-A3V7         TCGA-DJ-A3V8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3V9         TCGA-DJ-A3VA         TCGA-DJ-A3VB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3VD         TCGA-DJ-A3VF         TCGA-DJ-A3VG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3VJ         TCGA-DJ-A3VL         TCGA-DJ-A4UL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A4UP         TCGA-DJ-A4UQ         TCGA-DJ-A4UR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A4UW         TCGA-DJ-A4V2         TCGA-DJ-A4V5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-DO-A2HM         TCGA-E3-A3DY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E3-A3DZ         TCGA-E3-A3E0         TCGA-E3-A3E1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E3-A3E2         TCGA-E3-A3E3         TCGA-E8-A242 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E8-A2EA         TCGA-E8-A414         TCGA-E8-A415 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E8-A417         TCGA-E8-A419         TCGA-E8-A433 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E8-A436         TCGA-E8-A438         TCGA-E8-A44K 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3CM         TCGA-EL-A3CN         TCGA-EL-A3CO 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3D1         TCGA-EL-A3D4         TCGA-EL-A3D6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3GU         TCGA-EL-A3GV         TCGA-EL-A3GX 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3H3         TCGA-EL-A3H4         TCGA-EL-A3H5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3H7         TCGA-EL-A3MW         TCGA-EL-A3MX 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3T0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3T1         TCGA-EL-A3T2         TCGA-EL-A3TB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3ZH         TCGA-EL-A3ZK         TCGA-EL-A3ZL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3ZM         TCGA-EL-A3ZN         TCGA-EL-A3ZO 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3ZP         TCGA-EL-A3ZS         TCGA-EL-A4JV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A4JW         TCGA-EL-A4JX         TCGA-EL-A4JZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A4K0         TCGA-EL-A4K1         TCGA-EL-A4K2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A4K4         TCGA-EL-A4K6         TCGA-EL-A4K7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A4KD         TCGA-EL-A4KG         TCGA-EL-A4KI 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A1CS         TCGA-EM-A1CT         TCGA-EM-A1CU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A1CV         TCGA-EM-A1CW         TCGA-EM-A1YC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A1YD         TCGA-EM-A1YE         TCGA-EM-A22I 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A22J         TCGA-EM-A22K         TCGA-EM-A22L 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22N         TCGA-EM-A22O 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A22P         TCGA-EM-A22Q         TCGA-EM-A2CK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A2CN         TCGA-EM-A2CP         TCGA-EM-A2CQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A2CT         TCGA-EM-A2CU         TCGA-EM-A2OV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A2OX         TCGA-EM-A2OY         TCGA-EM-A2OZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A2P0         TCGA-EM-A2P1         TCGA-EM-A2P2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3AJ         TCGA-EM-A3AK         TCGA-EM-A3AL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3AN         TCGA-EM-A3AO         TCGA-EM-A3AR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3FJ         TCGA-EM-A3FK         TCGA-EM-A3FM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3FN         TCGA-EM-A3FO         TCGA-EM-A3FP 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3FQ         TCGA-EM-A3FR         TCGA-EM-A3O3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3O8         TCGA-EM-A3O9         TCGA-EM-A3OA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3OB         TCGA-EM-A3ST         TCGA-EM-A3SU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3SX         TCGA-EM-A3SZ         TCGA-EM-A4FF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A4FM         TCGA-EM-A4FN         TCGA-EM-A4FO 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A4FQ         TCGA-EM-A4FR         TCGA-EM-A4FV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A4G1         TCGA-ET-A25G         TCGA-ET-A25I 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A25J         TCGA-ET-A25K         TCGA-ET-A25L 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25N         TCGA-ET-A25O 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A25P         TCGA-ET-A2MX         TCGA-ET-A2MZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A2N0         TCGA-ET-A2N1         TCGA-ET-A2N4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A39K         TCGA-ET-A39L         TCGA-ET-A39O 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A39P         TCGA-ET-A39R         TCGA-ET-A39S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BP         TCGA-ET-A3BQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A3BX         TCGA-ET-A3DQ         TCGA-ET-A3DR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A3DV         TCGA-ET-A3DW         TCGA-ET-A40P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A40Q         TCGA-ET-A40R         TCGA-ET-A40S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A40T         TCGA-ET-A4KN         TCGA-FE-A22Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A230         TCGA-FE-A231         TCGA-FE-A232 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A233         TCGA-FE-A234         TCGA-FE-A235 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A236         TCGA-FE-A237         TCGA-FE-A238 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FE-A3PB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A3PC         TCGA-FE-A3PD         TCGA-FK-A3S3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FK-A3SB         TCGA-FK-A3SE         TCGA-FK-A3SG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FK-A3SH         TCGA-FK-A4UB         TCGA-FY-A2QD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A3I4         TCGA-FY-A3I5         TCGA-FY-A3NM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A3NN         TCGA-FY-A3ON         TCGA-FY-A3R6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A3R7         TCGA-FY-A3R9         TCGA-FY-A3TY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A3W9         TCGA-FY-A3YR         TCGA-FY-A40K 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A40L         TCGA-FY-A40M         TCGA-FY-A40N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A4B3         TCGA-FY-A4B4         TCGA-GE-A2C6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-H2-A26U         TCGA-H2-A2K9         TCGA-H2-A3RH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-H2-A3RI         TCGA-H2-A421         TCGA-H2-A422 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IM-A3EB         TCGA-IM-A3ED         TCGA-IM-A3U2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IM-A3U3         TCGA-IM-A41Y         TCGA-IM-A41Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IM-A420         TCGA-IM-A4EB         TCGA-J8-A3O0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-J8-A3O1         TCGA-J8-A3O2         TCGA-J8-A3YD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-J8-A3YE         TCGA-J8-A3YF         TCGA-J8-A3YG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-J8-A3YH         TCGA-J8-A42S         TCGA-J8-A4HY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-KS-A41F         TCGA-KS-A41I         TCGA-KS-A41J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-KS-A41L         TCGA-KS-A4I1         TCGA-KS-A4I3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-KS-A4I5         TCGA-KS-A4I7         TCGA-KS-A4I9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-KS-A4IB         TCGA-KS-A4IC         TCGA-KS-A4ID 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-L6-A4EP         TCGA-L6-A4EQ         TCGA-L6-A4EU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MK-A4N6         TCGA-MK-A4N7         TCGA-MK-A4N9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-QD-A8IV 
"19P LOSS WILD-TYPE" 
D55V14, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1   4
  19P LOSS WILD-TYPE 224 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1    4
  19P LOSS WILD-TYPE  224  260
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  MULTIFOCAL                1                224
  UNIFOCAL                  4                260
[1] 2 2
[1] FALSE
D55V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     0
  19P LOSS WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           0     5
  19P LOSS WILD-TYPE                        27   324
D55V16, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           5                324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V17, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0   5
  19P LOSS WILD-TYPE  38 355
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    5
  19P LOSS WILD-TYPE   38  355
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                355
[1] 2 2
[1] FALSE

Clustering(56) Variable = 21Q LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED     8   0
  21Q LOSS WILD-TYPE 474  16
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                490 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 0                 16 
$`21Q LOSS MUTATED`
TCGA-J8-A4HW TCGA-BJ-A190 TCGA-CE-A485 TCGA-DJ-A2Q0 TCGA-E8-A432 TCGA-EM-A22P 
        2.60        20.58        12.66        34.36        30.61        41.29 
TCGA-EM-A2OY TCGA-FY-A3I5 
       32.32         7.82 

$`21Q LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-L6-A4ET 
       50.40        75.42         1.05         1.68        17.23        21.83 
TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       23.93         4.24        24.79        13.78        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 
       25.48        15.12        42.08        51.39        41.52         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.97        11.08        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       12.82        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-DE-A0Y2 
       12.46        11.38        10.68        15.02        12.43        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        27.32        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       52.27        43.17        52.37         8.32        48.07       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.99        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       35.41        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
       28.96         8.78         8.42        37.74        43.96        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       33.53        35.18        39.95        36.92        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        36.33 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        35.87        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       40.70        18.97         9.60        35.67        36.43        23.44 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        30.12        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       63.19        52.44        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A433 
       31.50        31.04        31.30        30.84        25.45        31.27 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       31.33        14.96        39.88        33.50        31.00        30.15 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT 
       31.66        26.73       155.54        97.74       158.83        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 
      157.15        37.94        57.01       106.62        79.50        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS 
       69.57       108.36        64.87        49.51       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW 
       49.32        43.36        49.71        83.57       139.00       108.66 
TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       57.63        52.50        29.65       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        91.17        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        72.69        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        61.02        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        10.65        44.19        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        40.34        19.73        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        44.52         8.35        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        27.02        38.66        38.86        29.95        29.85 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       58.75        37.25        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
      123.32       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       28.24        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82        29.10        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08        23.31        21.63        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 
       15.16        23.87        22.49        19.04        13.81        14.04 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       21.83        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       32.45        30.21        12.89         3.02 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               2.6                0.2 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             41.29             178.29 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            25.595             31.270 
[1] "2.6 - 41.3 (25.6)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "3300000"
D56V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  21Q LOSS MUTATED         1        4         2        0         1         0
  21Q LOSS WILD-TYPE     281       46       109        2        45         6
D56V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  1                281
  STAGE II                 4                 46
  STAGE III                2                109
  STAGE IV                 0                  2
  STAGE IVA                1                 45
  STAGE IVC                0                  6
[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                  T1  T2  T3  T4
  21Q LOSS MUTATED     1   6   1   0
  21Q LOSS WILD-TYPE 141 159 166  23
D56V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                1                141
  T2                6                159
  T3                1                166
  T4                0                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V5, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     5   3
  21Q LOSS WILD-TYPE 220 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5    3
  21Q LOSS WILD-TYPE  220  221
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0                5                220
  1                3                221
[1] 2 2
[1] FALSE
D56V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4   0
  21Q LOSS WILD-TYPE 274   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4    0
  21Q LOSS WILD-TYPE  274    9
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0                4                274
  1                0                  9
[1] 2 2
[1] FALSE
D56V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     5   3
  21Q LOSS WILD-TYPE 360 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5    3
  21Q LOSS WILD-TYPE  360  131
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                5                360
  MALE                  3                131
[1] 2 2
[1] FALSE
D56V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     3   4
  21Q LOSS WILD-TYPE 177 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    4
  21Q LOSS WILD-TYPE  177  299
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 3                177
  YES                4                299
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  21Q LOSS MUTATED                0
  21Q LOSS WILD-TYPE              7
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  21Q LOSS MUTATED                                               6
  21Q LOSS WILD-TYPE                                           350
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  21Q LOSS MUTATED                                                                        2
  21Q LOSS WILD-TYPE                                                                     98
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  21Q LOSS MUTATED                                                                     0
  21Q LOSS WILD-TYPE                                                                  36
D56V9, multiclass
                                                                        clus
vv                                                                       21Q LOSS MUTATED
  OTHER, SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       21Q LOSS WILD-TYPE
  OTHER, SPECIFY                                                                          7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     7   0
  21Q LOSS WILD-TYPE 413  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      7    0
  21Q LOSS WILD-TYPE  413   17
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 7                413
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  21Q LOSS MUTATED              0                       0    8
  21Q LOSS WILD-TYPE          132                      18  322
                    vv
clus                 VERY ADVANCED (T4B)
  21Q LOSS MUTATED                     0
  21Q LOSS WILD-TYPE                   1
D56V11, multiclass
                         clus
vv                        21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  MINIMAL (T3)                           0                132
  MODERATE/ADVANCED (T4A)                0                 18
  NONE                                   8                322
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED     7   1   0   0
  21Q LOSS WILD-TYPE 376  50   4  30
D56V12, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0                7                376
  R1                1                 50
  R2                0                  4
  RX                0                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, continuous
D56V14, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     6   2
  21Q LOSS WILD-TYPE 219 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      6    2
  21Q LOSS WILD-TYPE  219  262
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  MULTIFOCAL                6                219
  UNIFOCAL                  2                262
[1] 2 2
[1] FALSE
D56V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0     2
  21Q LOSS WILD-TYPE                                1    50
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           0     4
  21Q LOSS WILD-TYPE                        27   325
D56V16, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                 50
  BLACK OR AFRICAN AMERICAN                       0                 27
  WHITE                                           4                325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V17, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     0   5
  21Q LOSS WILD-TYPE  38 355
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      0    5
  21Q LOSS WILD-TYPE   38  355
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                355
[1] 2 2
[1] FALSE

Clustering(57) Variable = 22Q LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    88   1
  22Q LOSS WILD-TYPE 394  15
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                89                409 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 15 
$`22Q LOSS MUTATED`
TCGA-DE-A0XZ TCGA-DJ-A3VK TCGA-E3-A3E5 TCGA-EL-A3D0 TCGA-MK-A84Z TCGA-4C-A93U 
       35.84        24.76        39.95       139.86        23.93         4.24 
TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A2P4 
       49.78        14.73        15.12        51.39        20.58        12.82 
TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A4M8 TCGA-DJ-A13M 
       23.31        10.88         3.45        12.43        18.54        48.79 
TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS TCGA-DJ-A2Q0 TCGA-DJ-A2Q7 
       56.19        44.98        42.58        26.20        34.36        35.11 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       33.53        35.18        36.92        32.42        31.46        16.41 
TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E8-A432 TCGA-E8-A434 TCGA-EL-A3CL 
       27.62        34.78        47.21        30.61        31.33        31.66 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3GP TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL 
       98.53        69.57        49.51        50.20        32.48        62.30 
TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4JZ TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EL-A4KI 
       60.16        57.47        61.02        44.15        47.84        23.90 
TCGA-EM-A1CS TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ 
       26.86        15.75        10.45        14.53        41.29        47.57 
TCGA-EM-A2OY TCGA-EM-A3AP TCGA-EM-A3FO TCGA-EM-A3O9 TCGA-EM-A3SX TCGA-EM-A3SZ 
       32.32         8.35        17.49         9.24        29.85        12.79 
TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FU TCGA-ET-A25L TCGA-ET-A25O TCGA-ET-A2N4 
       26.37        21.53        60.49        56.58        65.29         2.66 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P 
      108.46        84.89       123.32        79.10        66.84        43.99 
TCGA-ET-A40T TCGA-FE-A237 TCGA-FE-A3PB TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA 
       37.48       112.80        85.15        16.27        21.63        17.06 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD 
       21.60        12.53        16.90        31.10        43.17        31.82 
TCGA-J8-A3YH TCGA-KS-A41I TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-QD-A8IV 
        5.75        15.98        32.45        84.72        12.89 

$`22Q LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DJ-A13L TCGA-DJ-A2PR 
       30.21        22.88        23.18        12.66         9.96        27.45 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-EL-A3CR TCGA-EL-A3CS 
       23.44        59.57        42.54         3.12         7.66        45.53 
TCGA-EL-A3CY TCGA-EL-A3D5 TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY 
        4.18        57.11        50.24        33.50       150.48        17.52 
TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V 
      178.29        29.72        50.40        75.42         1.05         1.68 
TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 
       17.23         2.60        21.83        24.79        13.78        16.34 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZJ TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       42.08        41.52         4.83        44.35        42.15        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 
       35.54        32.45        11.31        30.97        11.08        18.38 
TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       16.57        20.48        18.97        16.01        13.94        36.39 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45E TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       18.64         7.99        21.01        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       11.38        10.68        15.02        12.66        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       37.64        27.32        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13O TCGA-DJ-A13P 
       25.12        14.70        14.27         2.76        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
       18.58         8.71        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
       48.07       135.91        30.61        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
        6.02        47.41        17.56        10.09         7.99        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       35.41        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42        37.74        43.96        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QC TCGA-DJ-A3UM 
       37.48        36.46        39.09        35.90        39.95        31.04 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UP 
        9.60        35.67        36.43        23.44        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       33.04        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3E0 
       35.38        54.90        21.53         2.33        92.55        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       80.52        63.19        52.44        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 
       29.98        31.50        31.04        31.30        30.84        25.45 
TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       31.27        14.96        39.88        33.50        31.00        30.15 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D6 TCGA-EL-A3GO 
       37.94        57.01       106.62        79.50       108.36        64.87 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY 
      115.10        65.39       136.01        50.37       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      108.66        57.63        52.50        29.65       142.52       129.57 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZM TCGA-EL-A3ZN 
       82.82        89.56        91.17        51.78        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW 
       72.69        65.49        61.22         7.07        59.44        34.72 
TCGA-EL-A4JX TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 
       45.96        31.04        34.39        30.51        53.36        41.13 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       43.59        24.30        27.06        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        78.61        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK 
       14.73        14.50        10.65        44.19        14.24        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        40.34        19.73        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       14.14        33.07        44.52        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       47.38        21.01        12.07        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33        12.53        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SY TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       38.86        29.95        13.51        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        5.33        26.37        22.45        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25P 
       81.70        77.56        70.42        60.20        63.39        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O 
       83.34        80.88        33.24       106.09       107.41       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BQ 
       95.34        94.13        55.10        98.20        28.24        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       94.59        84.85        80.58        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A4KN TCGA-ET-A4KQ 
       24.72        46.26        44.38        40.21        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
      117.40        66.77        39.95        33.63        81.83       106.36 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10       116.09         1.25        20.42        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       29.10        19.56        13.91        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       23.31        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       13.81        14.04        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A41Y 
       20.05        18.61        48.92        47.41        18.51        21.83 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF 
        8.22        25.64        27.19        11.24        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A41L 
       22.29         2.47         0.20       143.57        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID 
       26.70        43.69        18.64        87.39        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-E8-A418 
        3.02 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              2.66               0.20 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            139.86             178.29 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             32.42              30.97 
[1] "2.7 - 139.9 (32.4)" "0.2 - 178.3 (31.0)"
[1] "hr=" "3.2"
D57V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  22Q LOSS MUTATED        49       10        18        1        10         1
  22Q LOSS WILD-TYPE     233       40        93        1        36         5
D57V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                 49                233
  STAGE II                10                 40
  STAGE III               18                 93
  STAGE IV                 1                  1
  STAGE IVA               10                 36
  STAGE IVC                1                  5
[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                  T1  T2  T3  T4
  22Q LOSS MUTATED    24  33  28   4
  22Q LOSS WILD-TYPE 118 132 139  19
D57V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               24                118
  T2               33                132
  T3               28                139
  T4                4                 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"
D57V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    45  36
  22Q LOSS WILD-TYPE 180 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     45   36
  22Q LOSS WILD-TYPE  180  188
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               45                180
  1               36                188
[1] 2 2
[1] FALSE
D57V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    45   2
  22Q LOSS WILD-TYPE 233   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     45    2
  22Q LOSS WILD-TYPE  233    7
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               45                233
  1                2                  7
[1] 2 2
[1] FALSE
D57V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    62  27
  22Q LOSS WILD-TYPE 303 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     62   27
  22Q LOSS WILD-TYPE  303  107
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               62                303
  MALE                 27                107
[1] 2 2
[1] FALSE
D57V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    25  63
  22Q LOSS WILD-TYPE 155 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     25   63
  22Q LOSS WILD-TYPE  155  240
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                25                155
  YES               63                240
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER, SPECIFY
  22Q LOSS MUTATED                1
  22Q LOSS WILD-TYPE              6
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  22Q LOSS MUTATED                                              61
  22Q LOSS WILD-TYPE                                           295
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  22Q LOSS MUTATED                                                                       24
  22Q LOSS WILD-TYPE                                                                     76
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  22Q LOSS MUTATED                                                                     3
  22Q LOSS WILD-TYPE                                                                  33
D57V9, multiclass
                                                                        clus
vv                                                                       22Q LOSS MUTATED
  OTHER, SPECIFY                                                                        1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        61
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               24
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   3
                                                                        clus
vv                                                                       22Q LOSS WILD-TYPE
  OTHER, SPECIFY                                                                          6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         295
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 76
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    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"
D57V10, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    79   1
  22Q LOSS WILD-TYPE 341  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     79    1
  22Q LOSS WILD-TYPE  341   16
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                79                341
  YES                1                 16
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  22Q LOSS MUTATED             19                       2   63
  22Q LOSS WILD-TYPE          113                      16  267
                    vv
clus                 VERY ADVANCED (T4B)
  22Q LOSS MUTATED                     0
  22Q LOSS WILD-TYPE                   1
D57V11, multiclass
                         clus
vv                        22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  MINIMAL (T3)                          19                113
  MODERATE/ADVANCED (T4A)                2                 16
  NONE                                  63                267
  VERY ADVANCED (T4B)                    0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    68   6   1   8
  22Q LOSS WILD-TYPE 315  45   3  22
D57V12, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               68                315
  R1                6                 45
  R2                1                  3
  RX                8                 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"
D57V13, continuous
D57V14, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    45  42
  22Q LOSS WILD-TYPE 180 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     45   42
  22Q LOSS WILD-TYPE  180  222
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  MULTIFOCAL               45                180
  UNIFOCAL                 42                222
[1] 2 2
[1] FALSE
D57V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  0    11
  22Q LOSS WILD-TYPE                                1    41
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           7    54
  22Q LOSS WILD-TYPE                        20   275
D57V16, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          11                 41
  BLACK OR AFRICAN AMERICAN                       7                 20
  WHITE                                          54                275
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V17, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     6  63
  22Q LOSS WILD-TYPE  32 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6   63
  22Q LOSS WILD-TYPE   32  297
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 32
  NOT HISPANIC OR LATINO               63                297
[1] 2 2
[1] FALSE

Clustering(58) Variable = XP LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED     4   0
  XP LOSS WILD-TYPE 478  16
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                4               494 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                0                16 
$`XP LOSS MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A190 TCGA-EM-A1YE TCGA-EM-A3FK 
       13.78        20.58        54.08        23.77 

$`XP LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       21.83        23.93         4.24        24.79        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 
       25.48        15.12        42.08        51.39        41.52         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.97        11.08        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       12.82        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       21.63        50.17        37.64        27.32        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        52.27        43.17        52.37         8.32        48.07 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       30.58        35.41        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        57.01        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FL TCGA-EM-A3FM 
       44.52         8.35        37.25        27.95        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33        12.53         9.24        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
            13.78              0.20 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            54.08            178.29 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           22.175            31.270 
[1] "13.8 - 54.1 (22.2)" "0.2 - 178.3 (31.3)"
[1] "hr="     "3300000"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  XP LOSS MUTATED         1        3         0        0         0         0
  XP LOSS WILD-TYPE     281       47       111        2        46         6
D58V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 1               281
  STAGE II                3                47
  STAGE III               0               111
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  XP LOSS MUTATED     1   3   0   0
  XP LOSS WILD-TYPE 141 162 167  23
D58V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               1               141
  T2               3               162
  T3               0               167
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V5, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     3   1
  XP LOSS WILD-TYPE 222 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      3    1
  XP LOSS WILD-TYPE  222  223
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0               3               222
  1               1               223
[1] 2 2
[1] FALSE
D58V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     0   0
  XP LOSS WILD-TYPE 278   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0    0
  XP LOSS WILD-TYPE  278    9
D58V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     2   2
  XP LOSS WILD-TYPE 363 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2    2
  XP LOSS WILD-TYPE  363  132
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE               2               363
  MALE                 2               132
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     0   4
  XP LOSS WILD-TYPE 180 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0    4
  XP LOSS WILD-TYPE  180  299
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                0               180
  YES               4               299
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  XP LOSS MUTATED                0
  XP LOSS WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  XP LOSS MUTATED                                               3
  XP LOSS WILD-TYPE                                           353
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  XP LOSS MUTATED                                                                        1
  XP LOSS WILD-TYPE                                                                     99
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  XP LOSS MUTATED                                                                     0
  XP LOSS WILD-TYPE                                                                  36
D58V9, multiclass
                                                                        clus
vv                                                                       XP LOSS MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       XP LOSS WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     3   0
  XP LOSS WILD-TYPE 417  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      3    0
  XP LOSS WILD-TYPE  417   17
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                3               417
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  XP LOSS MUTATED              0                       0    4
  XP LOSS WILD-TYPE          132                      18  326
                   vv
clus                VERY ADVANCED (T4B)
  XP LOSS MUTATED                     0
  XP LOSS WILD-TYPE                   1
D58V11, multiclass
                         clus
vv                        XP LOSS MUTATED XP LOSS WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  4               326
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED     4   0   0   0
  XP LOSS WILD-TYPE 379  51   4  30
D58V12, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0               4               379
  R1               0                51
  R2               0                 4
  RX               0                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, continuous
D58V14, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     2   2
  XP LOSS WILD-TYPE 223 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2    2
  XP LOSS WILD-TYPE  223  262
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  MULTIFOCAL               2               223
  UNIFOCAL                 2               262
[1] 2 2
[1] FALSE
D58V15, continuous
[1] "Remove cluster labels:" "XP LOSS MUTATED"       
clus
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                2               399 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A45K        TCGA-CE-A13K 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DJ-A13L        TCGA-DJ-A2PR        TCGA-DJ-A3UU 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3UW        TCGA-DJ-A3V4        TCGA-DJ-A3VK        TCGA-EL-A3CR 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CY        TCGA-EL-A3D0        TCGA-EL-A3D5 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3H2        TCGA-EL-A3H8        TCGA-EL-A3MY 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3N3        TCGA-EM-A3AQ        TCGA-ET-A3BO        TCGA-ET-A3BV 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FY-A76V        TCGA-L6-A4ET        TCGA-MK-A84Z        TCGA-4C-A93U 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A0ZB        TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ        TCGA-BJ-A18Y        TCGA-BJ-A18Z 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A191        TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A28T        TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A2N8        TCGA-BJ-A2N9        TCGA-BJ-A2P4        TCGA-BJ-A3PU 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45F 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A45G        TCGA-BJ-A45H        TCGA-BJ-A45I        TCGA-BJ-A45J 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A27D        TCGA-CE-A3MD 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-CE-A3ME        TCGA-CE-A481        TCGA-CE-A482        TCGA-CE-A483 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-CE-A484        TCGA-CE-A485        TCGA-DE-A0Y2        TCGA-DE-A0Y3 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DE-A4M8        TCGA-DE-A4M9 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A69J        TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A13O        TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13U 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X        TCGA-DJ-A1QD 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG        TCGA-DJ-A1QH 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM        TCGA-DJ-A1QN 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A1QO        TCGA-DJ-A1QQ        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PS        TCGA-DJ-A2PT 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ        TCGA-DJ-A3UR 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3US        TCGA-DJ-A3UT        TCGA-DJ-A3UX        TCGA-DJ-A3UY 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3V0        TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V5 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3VA        TCGA-DJ-A3VB 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3VD        TCGA-DJ-A3VE        TCGA-DJ-A3VF        TCGA-DJ-A3VG 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A3VM        TCGA-DJ-A4UL 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A4UP        TCGA-DJ-A4UQ        TCGA-DJ-A4UT        TCGA-DJ-A4V0 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A4V2        TCGA-DJ-A4V4        TCGA-DJ-A4V5        TCGA-DO-A1JZ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY        TCGA-E3-A3DZ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2        TCGA-E3-A3E3 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-E8-A419        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CT 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D6 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GR        TCGA-EL-A3GS 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H3        TCGA-EL-A3H4 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3MW        TCGA-EL-A3MX 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T1        TCGA-EL-A3T2 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3T3        TCGA-EL-A3T6        TCGA-EL-A3T7        TCGA-EL-A3T8 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3T9        TCGA-EL-A3TA        TCGA-EL-A3TB        TCGA-EL-A3ZG 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3ZH        TCGA-EL-A3ZK        TCGA-EL-A3ZL        TCGA-EL-A3ZM 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP        TCGA-EL-A3ZQ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3ZR        TCGA-EL-A3ZS        TCGA-EL-A3ZT        TCGA-EL-A4JV 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A4K7        TCGA-EL-A4K9        TCGA-EL-A4KD        TCGA-EL-A4KG 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A4KH        TCGA-EL-A4KI        TCGA-EM-A1CS        TCGA-EM-A1CT 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A22I 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L        TCGA-EM-A22N 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A22O        TCGA-EM-A22P        TCGA-EM-A22Q        TCGA-EM-A2CJ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN        TCGA-EM-A2CO 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CT        TCGA-EM-A2CU 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A2OW        TCGA-EM-A2OX        TCGA-EM-A2OY        TCGA-EM-A2P0 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A2P2        TCGA-EM-A2P3        TCGA-EM-A3AI 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A3AJ        TCGA-EM-A3AK        TCGA-EM-A3AL        TCGA-EM-A3AN 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A3AO        TCGA-EM-A3AP        TCGA-EM-A3AR        TCGA-EM-A3FJ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A3FM        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O6        TCGA-EM-A3O7 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A3O8        TCGA-EM-A3O9        TCGA-EM-A3OA        TCGA-EM-A3OB 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A3ST        TCGA-EM-A3SU        TCGA-EM-A3SX        TCGA-EM-A3SY 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A3SZ        TCGA-EM-A4FF        TCGA-EM-A4FH        TCGA-EM-A4FK 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A4FM        TCGA-EM-A4FN        TCGA-EM-A4FQ        TCGA-EM-A4FR 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A4FU        TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A25R        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39J        TCGA-ET-A39M        TCGA-ET-A39N 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A39O        TCGA-ET-A39P        TCGA-ET-A39T        TCGA-ET-A3BN 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A40P        TCGA-ET-A40Q 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A4KN        TCGA-ET-A4KQ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A232        TCGA-FE-A233 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FY-A2QD 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3I5        TCGA-FY-A3ON        TCGA-FY-A3R8 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FY-A3TY        TCGA-FY-A3W9        TCGA-FY-A3YR        TCGA-FY-A40K 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B3 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A421        TCGA-IM-A3EB        TCGA-IM-A3ED 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3O0        TCGA-J8-A3YD 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-J8-A3YG        TCGA-KS-A41F        TCGA-KS-A41I        TCGA-KS-A41J 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-KS-A41L        TCGA-KS-A4I3        TCGA-KS-A4I5        TCGA-KS-A4I7 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-KS-A4I9        TCGA-KS-A4IB        TCGA-KS-A4IC        TCGA-KS-A4ID 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-L6-A4EP        TCGA-L6-A4EQ        TCGA-L6-A4EU        TCGA-MK-A4N6 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-MK-A4N7        TCGA-MK-A4N9        TCGA-QD-A8IV 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  0     0
  XP LOSS WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                           0     1
  XP LOSS WILD-TYPE                        27   328
D58V16, multiclass
[1] "Remove cluster labels:" "XP LOSS MUTATED"       
clus
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                1               408 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A45K        TCGA-CE-A13K 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DJ-A13L        TCGA-DJ-A2PR        TCGA-DJ-A3UU 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3UW        TCGA-DJ-A3V4        TCGA-DJ-A3VI        TCGA-DJ-A3VK 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CY 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D5        TCGA-EL-A3GQ        TCGA-EL-A3H2 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MY        TCGA-EL-A3N3        TCGA-ET-A3BO 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-FK-A3SD        TCGA-FY-A76V        TCGA-J8-A3NZ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-L6-A4ET        TCGA-MK-A84Z        TCGA-4C-A93U 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z        TCGA-BJ-A2N7 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A2N8        TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-BJ-A3PR        TCGA-BJ-A3PT 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A45F        TCGA-BJ-A45G        TCGA-BJ-A45H        TCGA-BJ-A45I 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A45J        TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A27D 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481        TCGA-CE-A482 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485        TCGA-DE-A0Y2 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A0Y3        TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DE-A4M8 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A4M9        TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A4MD        TCGA-DE-A69J        TCGA-DE-A69K        TCGA-DE-A7U5 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13P        TCGA-DJ-A13R 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A13S        TCGA-DJ-A13T        TCGA-DJ-A13U        TCGA-DJ-A13W 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A1QH        TCGA-DJ-A1QI        TCGA-DJ-A1QM        TCGA-DJ-A1QO 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A1QQ        TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PQ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A2PS        TCGA-DJ-A2PT        TCGA-DJ-A2PU        TCGA-DJ-A2PV 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A2PW        TCGA-DJ-A2PX        TCGA-DJ-A2PY        TCGA-DJ-A2PZ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q3 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3UM        TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UQ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3UR        TCGA-DJ-A3US        TCGA-DJ-A3UT        TCGA-DJ-A3UX 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3UY        TCGA-DJ-A3UZ        TCGA-DJ-A3V2        TCGA-DJ-A3V3 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3VD        TCGA-DJ-A3VE        TCGA-DJ-A3VF        TCGA-DJ-A3VG 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A3VM        TCGA-DJ-A4UL 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A4UP        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UT 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A4UW        TCGA-DJ-A4V0        TCGA-DJ-A4V4        TCGA-DJ-A4V5 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-E3-A3E3        TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A3X7 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-E8-A413        TCGA-E8-A414        TCGA-E8-A415        TCGA-E8-A416 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A432        TCGA-E8-A433 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-E8-A434        TCGA-E8-A436        TCGA-E8-A437        TCGA-E8-A438 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-E8-A44K        TCGA-E8-A44M        TCGA-EL-A3CL        TCGA-EL-A3CM 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CT 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D6 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GR        TCGA-EL-A3GS 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H3 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3MW 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3T3        TCGA-EL-A3T6 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3T7        TCGA-EL-A3T8        TCGA-EL-A3T9        TCGA-EL-A3TA 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3TB        TCGA-EL-A3ZG        TCGA-EL-A3ZH        TCGA-EL-A3ZK 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3ZQ        TCGA-EL-A3ZR        TCGA-EL-A3ZS        TCGA-EL-A3ZT 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4K9        TCGA-EL-A4KD 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A4KG        TCGA-EL-A4KH        TCGA-EL-A4KI        TCGA-EM-A22M 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A22O        TCGA-EM-A2OV        TCGA-EM-A3AI        TCGA-ET-A25G 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A25R        TCGA-ET-A2MX        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N3        TCGA-ET-A2N4 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39K 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39O        TCGA-ET-A39P 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BN 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A40P        TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A40T        TCGA-ET-A4KN        TCGA-ET-A4KQ        TCGA-FE-A22Z 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG        TCGA-FK-A3SH 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3I4 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FY-A3I5        TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FY-A3TY        TCGA-FY-A3W9        TCGA-FY-A3WA        TCGA-FY-A3YR 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FY-A4B0        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3O0        TCGA-J8-A3O1 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE        TCGA-J8-A3YF 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S        TCGA-J8-A4HY 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-KS-A41F        TCGA-KS-A41I        TCGA-KS-A41J        TCGA-KS-A41L 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-KS-A4I1        TCGA-KS-A4I3        TCGA-KS-A4I5        TCGA-KS-A4I7 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-KS-A4I9        TCGA-KS-A4IB        TCGA-KS-A4IC        TCGA-KS-A4ID 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-L6-A4EP        TCGA-L6-A4EQ        TCGA-L6-A4EU        TCGA-MK-A4N6 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-MK-A4N7        TCGA-MK-A4N9        TCGA-QD-A8IV        TCGA-E8-A418 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
D58V17, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     0   2
  XP LOSS WILD-TYPE  38 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0    2
  XP LOSS WILD-TYPE   38  358
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               358
[1] 2 2
[1] FALSE

Clustering(59) Variable = XQ LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED     5   0
  XQ LOSS WILD-TYPE 477  16
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               493 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                0                16 
$`XQ LOSS MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A190 TCGA-EM-A1YE TCGA-EM-A3FK TCGA-ET-A40S 
       13.78        20.58        54.08        23.77        40.21 

$`XQ LOSS WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       21.83        23.93         4.24        24.79        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 
       25.48        15.12        42.08        51.39        41.52         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.97        11.08        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       12.82        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       21.63        50.17        37.64        27.32        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        52.27        43.17        52.37         8.32        48.07 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       30.58        35.41        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        57.01        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FL TCGA-EM-A3FM 
       44.52         8.35        37.25        27.95        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33        12.53         9.24        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T 
      166.62        24.72        43.99        46.26        44.38        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25        20.42        17.82         7.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
       21.63        17.06        17.36        15.16        23.87        22.49 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04        13.81        14.04        21.60        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46        11.01        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       24.69        22.29         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV 
       40.37         9.50        36.10        32.45        30.21        12.89 
TCGA-E8-A418 
        3.02 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            13.78              0.20 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            54.08            178.29 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            23.77             31.27 
[1] "13.8 - 54.1 (23.8)" "0.2 - 178.3 (31.3)"
[1] "hr="     "3300000"
D59V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  XQ LOSS MUTATED         1        4         0        0         0         0
  XQ LOSS WILD-TYPE     281       46       111        2        46         6
D59V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 1               281
  STAGE II                4                46
  STAGE III               0               111
  STAGE IV                0                 2
  STAGE IVA               0                46
  STAGE IVC               0                 6
[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                 T1  T2  T3  T4
  XQ LOSS MUTATED     1   4   0   0
  XQ LOSS WILD-TYPE 141 161 167  23
D59V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               1               141
  T2               4               161
  T3               0               167
  T4               0                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     4   1
  XQ LOSS WILD-TYPE 221 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4    1
  XQ LOSS WILD-TYPE  221  223
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0               4               221
  1               1               223
[1] 2 2
[1] FALSE
D59V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0   0
  XQ LOSS WILD-TYPE 278   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    0
  XQ LOSS WILD-TYPE  278    9
D59V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2   3
  XQ LOSS WILD-TYPE 363 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2    3
  XQ LOSS WILD-TYPE  363  131
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               2               363
  MALE                 3               131
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0   5
  XQ LOSS WILD-TYPE 180 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    5
  XQ LOSS WILD-TYPE  180  298
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                0               180
  YES               5               298
[1] 2 2
[1] FALSE
                   vv
clus                OTHER, SPECIFY
  XQ LOSS MUTATED                0
  XQ LOSS WILD-TYPE              7
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  XQ LOSS MUTATED                                               4
  XQ LOSS WILD-TYPE                                           352
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  XQ LOSS MUTATED                                                                        1
  XQ LOSS WILD-TYPE                                                                     99
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  XQ LOSS MUTATED                                                                     0
  XQ LOSS WILD-TYPE                                                                  36
D59V9, multiclass
                                                                        clus
vv                                                                       XQ LOSS MUTATED
  OTHER, SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       XQ LOSS WILD-TYPE
  OTHER, SPECIFY                                                                         7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     3   1
  XQ LOSS WILD-TYPE 417  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    1
  XQ LOSS WILD-TYPE  417   16
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                3               417
  YES               1                16
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  XQ LOSS MUTATED              0                       0    5
  XQ LOSS WILD-TYPE          132                      18  325
                   vv
clus                VERY ADVANCED (T4B)
  XQ LOSS MUTATED                     0
  XQ LOSS WILD-TYPE                   1
D59V11, multiclass
                         clus
vv                        XQ LOSS MUTATED XQ LOSS WILD-TYPE
  MINIMAL (T3)                          0               132
  MODERATE/ADVANCED (T4A)               0                18
  NONE                                  5               325
  VERY ADVANCED (T4B)                   0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED     4   0   0   1
  XQ LOSS WILD-TYPE 379  51   4  29
D59V12, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0               4               379
  R1               0                51
  R2               0                 4
  RX               1                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, continuous
D59V14, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     3   2
  XQ LOSS WILD-TYPE 222 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    2
  XQ LOSS WILD-TYPE  222  262
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  MULTIFOCAL               3               222
  UNIFOCAL                 2               262
[1] 2 2
[1] FALSE
D59V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     0
  XQ LOSS WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           0     2
  XQ LOSS WILD-TYPE                        27   327
D59V16, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2               407 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A45K        TCGA-CE-A13K 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DJ-A13L        TCGA-DJ-A2PR        TCGA-DJ-A3UU 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3UW        TCGA-DJ-A3V4        TCGA-DJ-A3VI        TCGA-DJ-A3VK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D5        TCGA-EL-A3GQ        TCGA-EL-A3H2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MY        TCGA-EL-A3N3        TCGA-ET-A3BO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-FK-A3SD        TCGA-FY-A76V        TCGA-J8-A3NZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-L6-A4ET        TCGA-MK-A84Z        TCGA-4C-A93U 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z        TCGA-BJ-A2N7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A2N8        TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-BJ-A3PR        TCGA-BJ-A3PT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A45F        TCGA-BJ-A45G        TCGA-BJ-A45H        TCGA-BJ-A45I 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A45J        TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A27D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481        TCGA-CE-A482 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485        TCGA-DE-A0Y2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A0Y3        TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DE-A4M8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A4M9        TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A4MD        TCGA-DE-A69J        TCGA-DE-A69K        TCGA-DE-A7U5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13P        TCGA-DJ-A13R 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A13S        TCGA-DJ-A13T        TCGA-DJ-A13U        TCGA-DJ-A13W 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A1QH        TCGA-DJ-A1QI        TCGA-DJ-A1QM        TCGA-DJ-A1QO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A1QQ        TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PQ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2PS        TCGA-DJ-A2PT        TCGA-DJ-A2PU        TCGA-DJ-A2PV 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2PW        TCGA-DJ-A2PX        TCGA-DJ-A2PY        TCGA-DJ-A2PZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3UM        TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UQ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3UR        TCGA-DJ-A3US        TCGA-DJ-A3UT        TCGA-DJ-A3UX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3UY        TCGA-DJ-A3UZ        TCGA-DJ-A3V2        TCGA-DJ-A3V3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3VD        TCGA-DJ-A3VE        TCGA-DJ-A3VF        TCGA-DJ-A3VG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A3VM        TCGA-DJ-A4UL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A4UP        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A4UW        TCGA-DJ-A4V0        TCGA-DJ-A4V4        TCGA-DJ-A4V5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E3-A3E3        TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A3X7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E8-A413        TCGA-E8-A414        TCGA-E8-A415        TCGA-E8-A416 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A432        TCGA-E8-A433 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E8-A434        TCGA-E8-A436        TCGA-E8-A437        TCGA-E8-A438 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E8-A44K        TCGA-E8-A44M        TCGA-EL-A3CL        TCGA-EL-A3CM 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GR        TCGA-EL-A3GS 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3MW 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3T3        TCGA-EL-A3T6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3T7        TCGA-EL-A3T8        TCGA-EL-A3T9        TCGA-EL-A3TA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3TB        TCGA-EL-A3ZG        TCGA-EL-A3ZH        TCGA-EL-A3ZK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3ZQ        TCGA-EL-A3ZR        TCGA-EL-A3ZS        TCGA-EL-A3ZT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4K9        TCGA-EL-A4KD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A4KG        TCGA-EL-A4KH        TCGA-EL-A4KI        TCGA-EM-A22M 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A22O        TCGA-EM-A2OV        TCGA-EM-A3AI        TCGA-ET-A25G 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A25R        TCGA-ET-A2MX        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N3        TCGA-ET-A2N4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39K 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39O        TCGA-ET-A39P 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BW        TCGA-ET-A3BX        TCGA-ET-A3DO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A40P        TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40T 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-ET-A4KQ        TCGA-FE-A22Z        TCGA-FE-A230 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA        TCGA-FE-A3PB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3        TCGA-FK-A3SB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FK-A3SE        TCGA-FK-A3SG        TCGA-FK-A3SH        TCGA-FK-A4UB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3I4        TCGA-FY-A3I5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6        TCGA-FY-A3R7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA        TCGA-FY-A3TY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3WA        TCGA-FY-A3YR        TCGA-FY-A40K 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B0 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6        TCGA-H2-A26U 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI        TCGA-H2-A421 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-IM-A3U2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z        TCGA-IM-A420 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IM-A4EB        TCGA-J8-A3O0        TCGA-J8-A3O1        TCGA-J8-A3O2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J8-A3YD        TCGA-J8-A3YE        TCGA-J8-A3YF        TCGA-J8-A3YG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J8-A3YH        TCGA-J8-A42S        TCGA-J8-A4HY        TCGA-KS-A41F 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KS-A41I        TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KS-A4I3        TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KS-A4IB        TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-L6-A4EQ        TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-MK-A4N9        TCGA-QD-A8IV        TCGA-E8-A418 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D59V17, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0   3
  XQ LOSS WILD-TYPE  38 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    3
  XQ LOSS WILD-TYPE   38  357
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               357
[1] 2 2
[1] FALSE
