[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/15092795/THCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/15101916/transformed.cor.cli.txt"

nPatients in clinical file=501, in cluster file=501, 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 
                5               494 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5               494 
[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 
                14                485 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                14                485 
[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 
                9               490 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9               490 
[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 
                88                411 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                88                411 
[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 
                3               496 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               496 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[15] "RADIATIONS_RADIATION_REGIMENINDICATION"
[16] "RADIATION_EXPOSURE"                    
[17] "EXTRATHYROIDAL_EXTENSION"              
[18] "COMPLETENESS_OF_RESECTION"             
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "MULTIFOCALITY"                         
[21] "TUMOR_SIZE"                            
[22] "RACE"                                  
[23] "ETHNICITY"                             
[24] "BATCH_NUMBER"                          

Input Data has 24 rows and 499 columns.

[1] "Batch" "24"   
[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=14,	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=423,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	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:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATION_EXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'EXTRATHYROIDAL_EXTENSION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR_SIZE':	nDistinctValues=70,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'BATCH_NUMBER':	nDistinctValues=25,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL_TYPE"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "RADIATION_EXPOSURE"                    
[10] "EXTRATHYROIDAL_EXTENSION"              
[11] "COMPLETENESS_OF_RESECTION"             
[12] "NUMBER_OF_LYMPH_NODES"                 
[13] "MULTIFOCALITY"                         
[14] "TUMOR_SIZE"                            
[15] "RACE"                                  
[16] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=73, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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 
141 166 167  23 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
141 166 167  23 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
141 166 167  23 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
141 166 167  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
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RADIATION_EXPOSURE, nv=2, binary=FALSE, numeric=FALSE
EXTRATHYROIDAL_EXTENSION, nv=4, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=30, binary=FALSE, numeric=TRUE
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SIZE, nv=70, 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   1
  1P GAIN WILD-TYPE 479  13
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5               492 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                13 
$`1P GAIN MUTATED`
TCGA-4C-A93U TCGA-DO-A2HM TCGA-EL-A3MX TCGA-ET-A3BT TCGA-FY-A3NM 
        4.24         2.33        57.63        24.72         0.99 

$`1P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        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         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
       14.04        31.23        22.29        11.70        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       14.27        13.81        14.07        14.27         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MY TCGA-EL-A3MZ 
       83.57       139.00       131.15       108.66        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       29.65       147.42       130.72       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        78.97        31.50        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        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        37.94        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 
       12.36        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-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        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        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        16.80        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        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        2.43         5.56        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        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 
       81.34        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        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-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        7.82        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         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
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         2.99        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        10.26        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         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 
       86.70         6.02        19.73         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        20.25        12.89 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.99              0.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            57.63            169.32 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            4.240            20.435 
[1] "1.0 - 57.6 (4.2)"   "0.1 - 169.3 (20.4)"
[1] "hr=" "11" 
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  1P GAIN MUTATED         0        0         1        0         3         1
  1P GAIN WILD-TYPE     282       52       108        2        43         5
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 0               282
  STAGE II                0                52
  STAGE III               1               108
  STAGE IV                0                 2
  STAGE IVA               3                43
  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
  1P GAIN MUTATED     1   1   1   2
  1P GAIN WILD-TYPE 140 165 166  21
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               1               140
  T2               1               165
  T3               1               166
  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"
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1   4
  1P GAIN WILD-TYPE 223 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    4
  1P GAIN WILD-TYPE  223  221
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               1               223
  1               4               221
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1   1
  1P GAIN WILD-TYPE 276   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    1
  1P GAIN WILD-TYPE  276    8
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               1               276
  1               1                 8
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     4   1
  1P GAIN WILD-TYPE 362 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4    1
  1P GAIN WILD-TYPE  362  132
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               4               362
  MALE                 1               132
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  1P GAIN MUTATED                0
  1P GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  1P GAIN MUTATED                                               4
  1P GAIN WILD-TYPE                                           352
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  1P GAIN MUTATED                                                                        0
  1P GAIN WILD-TYPE                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  1P GAIN MUTATED                                                                     1
  1P GAIN WILD-TYPE                                                                  35
D1V8, multiclass
                                                                        clus
vv                                                                       1P GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        4
  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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  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"
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0   5
  1P GAIN WILD-TYPE  14 480
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    5
  1P GAIN WILD-TYPE   14  480
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                0                14
  YES               5               480
[1] 2 2
[1] FALSE
D1V10, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     3   1
  1P GAIN WILD-TYPE 418  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    1
  1P GAIN WILD-TYPE  418   16
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                3               418
  YES               1                16
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  1P GAIN MUTATED              1                       1    3
  1P GAIN WILD-TYPE          131                      17  327
                   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                                  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
  1P GAIN MUTATED     3   0   0   2
  1P GAIN WILD-TYPE 378  52   4  28
D1V12, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               3               378
  R1               0                52
  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"
D1V13, continuous
D1V14, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1   4
  1P GAIN WILD-TYPE 224 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    4
  1P GAIN WILD-TYPE  224  260
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  MULTIFOCAL               1               224
  UNIFOCAL                 4               260
[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     4
  1P GAIN WILD-TYPE                        26   321
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                                          4               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"
D1V17, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0   5
  1P GAIN WILD-TYPE  38 353
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    5
  1P GAIN WILD-TYPE   38  353
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               5               353
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    22   3
  1Q GAIN WILD-TYPE 461  11
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               25               472 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                11 
$`1Q GAIN MUTATED`
TCGA-4C-A93U TCGA-BJ-A290 TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DJ-A13U 
        4.24        30.21        11.57        30.02        25.12        23.38 
TCGA-DO-A2HM TCGA-EL-A3GP TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3MX TCGA-EL-A3MZ 
        2.33         1.41       136.01        83.57        57.63        52.50 
TCGA-EL-A3T9 TCGA-EL-A3ZO TCGA-EL-A4JX TCGA-EM-A3O3 TCGA-ET-A39P TCGA-ET-A3BT 
        5.72        47.38        45.96        14.50        58.72        24.72 
TCGA-FE-A231 TCGA-FY-A3NM TCGA-FY-A40L TCGA-IM-A3EB TCGA-J8-A3O1 TCGA-KS-A4IB 
       31.59         0.99         6.58        48.92        27.19        84.72 
TCGA-L6-A4EU 
        9.50 

$`1Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
        1.22        22.88        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 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75        10.88        21.01         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18        21.63         8.98         4.93        23.47         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A69J TCGA-DE-A69K 
       15.85        18.54        18.84        30.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
        2.76         9.96        17.26        14.07       169.32         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
        8.71        56.19        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
       21.53        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ 
       98.53        45.40        57.11       108.36        64.87        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H7 
      139.99        49.32        33.50        43.36        49.71       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MY TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
      131.15       108.66        17.52        29.65       147.42       130.72 
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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       36.03        53.06        52.50        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       59.44        57.47        34.72        37.94        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 
       12.36        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-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        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        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        16.80        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 
       12.07        17.49        17.39        16.18        15.02        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        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        15.62        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        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        98.56        61.02        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 TCGA-FE-A233 
        4.01         1.94        73.74        59.70        44.25        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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82         7.82        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         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.06        17.36        15.16        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
        2.99        20.05        18.61        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83         9.63         2.96         8.65        17.23        43.17 
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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         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 
       86.70         6.02        19.73         6.74        32.45        87.39 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37        21.83        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        20.25        12.89 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.99              0.10 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           136.01            169.32 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           27.190            20.135 
[1] "1.0 - 136.0 (27.2)" "0.1 - 169.3 (20.1)"
[1] "hr=" "4.4"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  1Q GAIN MUTATED         6        0        10        1         8         1
  1Q GAIN WILD-TYPE     276       52        99        1        38         5
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 6               276
  STAGE II                0                52
  STAGE III              10                99
  STAGE IV                1                 1
  STAGE IVA               8                38
  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
  1Q GAIN MUTATED     2   3  15   6
  1Q GAIN WILD-TYPE 139 163 152  17
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               2               139
  T2               3               163
  T3              15               152
  T4               6                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     4  21
  1Q GAIN WILD-TYPE 220 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      4   21
  1Q GAIN WILD-TYPE  220  204
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0               4               220
  1              21               204
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    13   1
  1Q GAIN WILD-TYPE 264   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     13    1
  1Q GAIN WILD-TYPE  264    8
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              13               264
  1               1                 8
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    18   8
  1Q GAIN WILD-TYPE 348 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     18    8
  1Q GAIN WILD-TYPE  348  125
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              18               348
  MALE                 8               125
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  1Q GAIN MUTATED                0
  1Q GAIN WILD-TYPE              9
                   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                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  1Q GAIN MUTATED                                                                     3
  1Q GAIN WILD-TYPE                                                                  33
D2V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        333
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  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"
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     1  25
  1Q GAIN WILD-TYPE  13 460
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1   25
  1Q GAIN WILD-TYPE   13  460
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                1                13
  YES              25               460
[1] 2 2
[1] FALSE
D2V10, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    23   1
  1Q GAIN WILD-TYPE 398  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     23    1
  1Q GAIN WILD-TYPE  398   16
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               23               398
  YES               1                16
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  1Q GAIN MUTATED             11                       4   10
  1Q GAIN WILD-TYPE          121                      14  320
                   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)                         11               121
  MODERATE/ADVANCED (T4A)               4                14
  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
  1Q GAIN MUTATED    15   6   0   4
  1Q GAIN WILD-TYPE 366  46   4  26
D2V12, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              15               366
  R1               6                46
  R2               0                 4
  RX               4                26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, continuous
D2V14, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     6  20
  1Q GAIN WILD-TYPE 219 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6   20
  1Q GAIN WILD-TYPE  219  244
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  MULTIFOCAL               6               219
  UNIFOCAL                20               244
[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   307
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               307
[1] 4 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  34 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      4   20
  1Q GAIN WILD-TYPE   34  338
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                34
  NOT HISPANIC OR LATINO              20               338
[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 481  13
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               494 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                13 
$`3P GAIN MUTATED`
TCGA-EL-A3MX TCGA-EM-A22N TCGA-EM-A2CO 
       57.63        10.65         6.05 

$`3P GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        52.50        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        37.94 
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        12.36        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        11.74        11.15        14.24        16.44 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       17.88        13.18        23.51         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        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        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        16.80        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        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        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        81.34        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-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
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-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         7.82         0.99        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         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        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 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83         9.63         2.96         8.65        17.23 
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-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         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        86.70         6.02        19.73         6.74 
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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       20.25        12.89 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             6.05              0.10 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            57.63            169.32 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           10.650            20.435 
[1] "6.0 - 57.6 (10.7)"  "0.1 - 169.3 (20.4)"
[1] "hr=" "11" 
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       51       109        2        46         5
D3V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 1               281
  STAGE II                1                51
  STAGE III               0               109
  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 140 165 167  22
D3V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               1               140
  T2               1               165
  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 223 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    1
  3P GAIN WILD-TYPE  223  224
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               1               223
  1               1               224
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0   1
  3P GAIN WILD-TYPE 277   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    1
  3P GAIN WILD-TYPE  277    8
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               0               277
  1               1                 8
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3   0
  3P GAIN WILD-TYPE 363 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    0
  3P GAIN WILD-TYPE  363  133
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               3               363
  MALE                 0               133
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  3P GAIN MUTATED                0
  3P GAIN WILD-TYPE              9
                   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                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  3P GAIN MUTATED                                                                     0
  3P GAIN WILD-TYPE                                                                  36
D3V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        355
  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"
D3V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0   3
  3P GAIN WILD-TYPE  14 482
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    3
  3P GAIN WILD-TYPE   14  482
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                0                14
  YES               3               482
[1] 2 2
[1] FALSE
D3V10, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3   0
  3P GAIN WILD-TYPE 418  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    0
  3P GAIN WILD-TYPE  418   17
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                3               418
  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 380  52   4  28
D3V12, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0               1               380
  R1               0                52
  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               381 
       TCGA-4C-A93U        TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        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-A28R        TCGA-BJ-A28T        TCGA-BJ-A28W        TCGA-BJ-A28X 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A45G        TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A3MD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A4M8        TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A4MD        TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13O        TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13V 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13W        TCGA-DJ-A13X        TCGA-DJ-A1QG        TCGA-DJ-A1QH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A1QM        TCGA-DJ-A2PO        TCGA-DJ-A2PP        TCGA-DJ-A2PQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PR        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-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ        TCGA-DJ-A3UR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UU        TCGA-DJ-A3UW        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-A3V4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3VA        TCGA-DJ-A3VB        TCGA-DJ-A3VD        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-A4UL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A4UP        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A4V2        TCGA-DJ-A4V5        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-E3-A3E5        TCGA-E8-A242 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-E8-A414        TCGA-E8-A415 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433        TCGA-E8-A436 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM        TCGA-EL-A3CN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        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-A3GQ        TCGA-EL-A3GS        TCGA-EL-A3GU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0        TCGA-EL-A3T1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3T2        TCGA-EL-A3TB        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-A3ZM        TCGA-EL-A3ZN        TCGA-EL-A3ZO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3ZP        TCGA-EL-A3ZS        TCGA-EL-A4JV        TCGA-EL-A4JW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4KD        TCGA-EL-A4KG        TCGA-EL-A4KI        TCGA-EM-A1CS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A1YE        TCGA-EM-A22I 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L        TCGA-EM-A22M 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A22O        TCGA-EM-A22P        TCGA-EM-A22Q        TCGA-EM-A2CK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2CN        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2CT        TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2OZ        TCGA-EM-A2P0        TCGA-EM-A2P1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2P2        TCGA-EM-A3AJ        TCGA-EM-A3AK        TCGA-EM-A3AL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AQ        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-A3FL        TCGA-EM-A3FM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O8        TCGA-EM-A3O9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST        TCGA-EM-A3SU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3SX        TCGA-EM-A3SZ        TCGA-EM-A4FF        TCGA-EM-A4FM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ        TCGA-EM-A4FR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G        TCGA-ET-A25I 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A2MX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39K        TCGA-ET-A39L        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-A3BO 
"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-A3BV        TCGA-ET-A3BX        TCGA-ET-A3DQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P        TCGA-ET-A40Q 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T        TCGA-ET-A4KN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A 
"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-A3I4        TCGA-FY-A3I5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3NN        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-A3R9        TCGA-FY-A3TY        TCGA-FY-A3W9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A40N        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-A3NZ        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-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-QD-A8IV 
"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   324
D3V16, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1               404 
       TCGA-4C-A93U        TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        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-A192        TCGA-BJ-A28R        TCGA-BJ-A28S 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A28T        TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28X 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N7 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A2N8        TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-BJ-A3PR        TCGA-BJ-A3PT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A45F        TCGA-BJ-A45G        TCGA-BJ-A45H        TCGA-BJ-A45I 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A45J        TCGA-BJ-A45K        TCGA-BJ-A4O8        TCGA-BJ-A4O9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CE-A13K        TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CE-A481        TCGA-CE-A482        TCGA-CE-A483        TCGA-CE-A484 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CE-A485        TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DE-A4M8        TCGA-DE-A4M9 
"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-A69J        TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13P        TCGA-DJ-A13R 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13S        TCGA-DJ-A13T        TCGA-DJ-A13U        TCGA-DJ-A13W 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A1QH        TCGA-DJ-A1QI        TCGA-DJ-A1QM        TCGA-DJ-A1QO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A1QQ        TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PR        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-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX        TCGA-DJ-A3UY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UZ        TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3VD        TCGA-DJ-A3VE        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-A3VM        TCGA-DJ-A4UL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A4UP        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A4UW        TCGA-DJ-A4V0        TCGA-DJ-A4V4        TCGA-DJ-A4V5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DO-A1JZ        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-E3-A3E5        TCGA-E8-A242        TCGA-E8-A2EA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A2JQ        TCGA-E8-A3X7        TCGA-E8-A413        TCGA-E8-A414 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A415        TCGA-E8-A416        TCGA-E8-A417        TCGA-E8-A418 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A419        TCGA-E8-A432        TCGA-E8-A433        TCGA-E8-A434 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A436        TCGA-E8-A437        TCGA-E8-A438        TCGA-E8-A44K 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A44M        TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS 
"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-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ        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-A3H2        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-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3        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-A3BO        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-A3BV        TCGA-ET-A3BW        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-A3SD        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-A3BL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3I5        TCGA-FY-A3NM        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-A3R8        TCGA-FY-A3R9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3RA        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-FY-A76V 
"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-A3NZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A3O0        TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A3YE        TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A42S        TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A41I        TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A4I3        TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A4IB        TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-L6-A4EQ        TCGA-L6-A4ET        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-MK-A84Z        TCGA-QD-A8IV 
"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  38 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    1
  3P GAIN WILD-TYPE   38  357
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               1               357
[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 479  13
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5               492 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                13 
$`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         0.99 

$`4P GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       130.72 
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        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        52.50        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 
       37.94        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        12.36        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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        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        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        29.95        15.62        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        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        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        81.34        39.95        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
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         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
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         2.99        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        10.26        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         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 
       86.70         6.02        19.73         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        20.25        12.89 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.99              0.10 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            57.01            169.32 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           10.650            20.435 
[1] "1.0 - 57.0 (10.7)"  "0.1 - 169.3 (20.4)"
[1] "hr=" "9"  
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       51       106        2        46         6
D4V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 1               281
  STAGE II                1                51
  STAGE III               3               106
  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 140 165 164  23
D4V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               1               140
  T2               1               165
  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 219 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      5    0
  4P GAIN WILD-TYPE  219  225
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               5               219
  1               0               225
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   0
  4P GAIN WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    0
  4P GAIN WILD-TYPE  277    9
D4V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4   1
  4P GAIN WILD-TYPE 362 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    1
  4P GAIN WILD-TYPE  362  132
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               4               362
  MALE                 1               132
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  4P GAIN MUTATED                0
  4P GAIN WILD-TYPE              9
                   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                                                                     95
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  4P GAIN MUTATED                                                                     0
  4P GAIN WILD-TYPE                                                                  36
D4V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  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"
D4V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1   4
  4P GAIN WILD-TYPE  13 481
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    4
  4P GAIN WILD-TYPE   13  481
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                1                13
  YES               4               481
[1] 2 2
[1] FALSE
D4V10, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4   0
  4P GAIN WILD-TYPE 417  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    0
  4P GAIN WILD-TYPE  417   17
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                4               417
  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 377  52   4  29
D4V12, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               4               377
  R1               0                52
  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   322
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               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"
D4V17, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   3
  4P GAIN WILD-TYPE  38 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    3
  4P GAIN WILD-TYPE   38  355
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               355
[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 479  13
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               492 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                13 
$`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         0.99 

$`4Q GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       130.72 
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        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        52.50        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 
       37.94        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        12.36        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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        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        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        29.95        15.62        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        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        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        81.34        39.95        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
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         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
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         2.99        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        10.26        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         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 
       86.70         6.02        19.73         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        20.25        12.89 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.99              0.10 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            57.01            169.32 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           10.650            20.435 
[1] "1.0 - 57.0 (10.7)"  "0.1 - 169.3 (20.4)"
[1] "hr=" "9"  
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       51       106        2        46         6
D5V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 1               281
  STAGE II                1                51
  STAGE III               3               106
  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 140 165 164  23
D5V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               1               140
  T2               1               165
  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 219 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5    0
  4Q GAIN WILD-TYPE  219  225
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               5               219
  1               0               225
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   0
  4Q GAIN WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    0
  4Q GAIN WILD-TYPE  277    9
D5V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4   1
  4Q GAIN WILD-TYPE 362 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    1
  4Q GAIN WILD-TYPE  362  132
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               4               362
  MALE                 1               132
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  4Q GAIN MUTATED                0
  4Q GAIN WILD-TYPE              9
                   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                                                                     95
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  4Q GAIN MUTATED                                                                     0
  4Q GAIN WILD-TYPE                                                                  36
D5V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  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"
D5V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1   4
  4Q GAIN WILD-TYPE  13 481
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    4
  4Q GAIN WILD-TYPE   13  481
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                1                13
  YES               4               481
[1] 2 2
[1] FALSE
D5V10, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4   0
  4Q GAIN WILD-TYPE 417  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    0
  4Q GAIN WILD-TYPE  417   17
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                4               417
  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 377  52   4  29
D5V12, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               4               377
  R1               0                52
  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   322
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               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"
D5V17, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   3
  4Q GAIN WILD-TYPE  38 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    3
  4Q GAIN WILD-TYPE   38  355
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               355
[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 464  12
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               21               476 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                12 
$`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 
       47.38        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        12.26        98.56 
TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       33.63         7.82         0.99 

$`5P GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
        8.25        18.87        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83        44.35        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.21        22.88        18.38        16.57        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
       21.63         8.98         4.93        23.47         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        15.85 
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-A13L TCGA-DJ-A13M TCGA-DJ-A13O 
       14.70        14.27         2.76         9.96        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      169.32         3.39         8.71        56.19        23.38        18.35 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         8.32        11.01       135.91        30.61        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45        42.58        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       17.56        10.09         7.99         5.33        35.41        27.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        12.56         8.28        34.85         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42        34.36        37.74         6.77        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44        37.48        36.46        10.09         7.10        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        35.18        15.88        15.09        31.04        20.45 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        59.57        11.34        21.37        18.51        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        21.47        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        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
        8.32        24.20        17.23        27.62        18.21        21.34 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       19.07        15.42        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       31.23        22.29        11.70        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 
       13.81        14.07        14.27         3.02        25.45        14.43 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       14.70        14.10        14.96         7.69        20.68        13.78 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.58        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
       80.91         4.18        58.82       139.86        98.53        45.40 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       57.11       108.36        64.87         1.41        50.24       115.10 
TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
       65.39        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      131.15       108.66        57.63        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       130.72       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        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       31.50        62.30        53.06        52.50        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        37.94 
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        12.36        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        27.65        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       13.84        19.73        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        29.95        15.62        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        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       29.49        54.05        22.09        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        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         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        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 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83         9.63         2.96         8.65        17.23 
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-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         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        86.70         6.02        19.73         6.74 
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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       20.25        12.89 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.99              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           136.01            169.32 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           20.580            20.235 
[1] "1.0 - 136.0 (20.6)" "0.1 - 169.3 (20.2)"
[1] "hr=" "3.4"
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       47       101        1        44         6
D6V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 5               277
  STAGE II                5                47
  STAGE III               8               101
  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 138 159 158  21
D6V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               3               138
  T2               7               159
  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 213 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11    6
  5P GAIN WILD-TYPE  213  219
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              11               213
  1               6               219
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     5   0
  5P GAIN WILD-TYPE 272   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      5    0
  5P GAIN WILD-TYPE  272    9
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0               5               272
  1               0                 9
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    14   7
  5P GAIN WILD-TYPE 352 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     14    7
  5P GAIN WILD-TYPE  352  126
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              14               352
  MALE                 7               126
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  5P GAIN MUTATED                0
  5P GAIN WILD-TYPE              9
                   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                                                                     90
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  5P GAIN MUTATED                                                                     0
  5P GAIN WILD-TYPE                                                                  36
D6V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        343
  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"
D6V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1  20
  5P GAIN WILD-TYPE  13 465
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   20
  5P GAIN WILD-TYPE   13  465
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                1                13
  YES              20               465
[1] 2 2
[1] FALSE
D6V10, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    20   0
  5P GAIN WILD-TYPE 401  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     20    0
  5P GAIN WILD-TYPE  401   17
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               20               401
  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 366  48   4  28
D6V12, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              15               366
  R1               4                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"
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   312
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               312
[1] 4 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  37 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   12
  5P GAIN WILD-TYPE   37  346
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                37
  NOT HISPANIC OR LATINO              12               346
[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 468  12
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               17               480 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                12 
$`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 
       12.26        98.56        33.63         7.82         0.99 

$`5Q GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        17.69        23.34        20.71         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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75        10.88        21.01         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18        21.63         8.98         4.93        23.47         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       169.32         3.39         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       18.35        14.60         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45        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         5.33        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        12.56         8.28        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24         9.44        37.48        36.46        10.09         7.10 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        12.43        35.18        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       20.45        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        59.57        11.34        21.37        18.51 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        21.47        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        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        24.20        17.23        27.62        18.21 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        19.07        15.42        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
       14.04        31.23        22.29        11.70        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       14.27        13.81        14.07        14.27         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       130.72       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        78.97        31.50        62.30        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       52.50        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        37.94        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        12.36        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        11.74        11.15        14.24        16.44 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       17.88        13.18        23.51         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        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-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        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        13.91         7.82        11.51        29.95 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       15.62        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        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       22.09        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       13.74        71.01        80.02        65.36        84.89        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        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        81.34        39.95        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
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         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
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         2.99        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        10.26        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         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 
       86.70         6.02        19.73         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        20.25        12.89 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.99              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            98.56            169.32 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           20.580            20.235 
[1] "1.0 - 98.6 (20.6)"  "0.1 - 169.3 (20.2)"
[1] "hr=" "4.8"
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       47       104        1        45         6
D7V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 5               277
  STAGE II                5                47
  STAGE III               5               104
  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 138 160 161  21
D7V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               3               138
  T2               6               160
  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 213 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11    2
  5Q GAIN WILD-TYPE  213  223
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              11               213
  1               2               223
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     2   0
  5Q GAIN WILD-TYPE 275   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    0
  5Q GAIN WILD-TYPE  275    9
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               2               275
  1               0                 9
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    11   6
  5Q GAIN WILD-TYPE 355 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11    6
  5Q GAIN WILD-TYPE  355  127
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              11               355
  MALE                 6               127
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  5Q GAIN MUTATED                0
  5Q GAIN WILD-TYPE              9
                   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                                                                     90
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  5Q GAIN MUTATED                                                                     0
  5Q GAIN WILD-TYPE                                                                  36
D7V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        347
  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"
D7V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1  16
  5Q GAIN WILD-TYPE  13 469
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   16
  5Q GAIN WILD-TYPE   13  469
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                1                13
  YES              16               469
[1] 2 2
[1] FALSE
D7V10, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    16   0
  5Q GAIN WILD-TYPE 405  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     16    0
  5Q GAIN WILD-TYPE  405   17
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               16               405
  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 369  49   4  28
D7V12, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              12               369
  R1               3                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"
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   315
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               315
[1] 4 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  38 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   10
  5Q GAIN WILD-TYPE   38  348
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO              10               348
[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 466  13
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18               479 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                1                13 
$`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        12.26        98.56         7.82         0.99 

$`7P GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        17.69        23.34        20.71         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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        5.75        10.88         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
       21.63         8.98         4.93        23.47         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        15.85 
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-A13L TCGA-DJ-A13M TCGA-DJ-A13O 
       14.70        14.27         2.76         9.96        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      169.32         3.39         8.71        56.19        23.38        18.35 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         8.32        11.01       135.91        30.61        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45        42.58        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       17.56        10.09         7.99         5.33        35.41        27.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        12.56         8.28        34.85         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42        37.74         6.77        40.24         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       37.48        36.46        10.09         7.10        35.90        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        15.88        15.09        31.04        20.45        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       59.57        11.34        21.37        18.51        36.99        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        21.47        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        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       24.20        17.23        27.62        18.21        21.34        19.07 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       15.42        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04        31.23 
TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       22.29        11.70        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 
       14.07        14.27         3.02        25.45        14.43        14.70 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       14.10        14.96         7.69        20.68        13.78        13.58 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
       31.66        26.73       155.54        97.74       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
       45.53        60.95       157.15        37.94        57.01        80.91 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        58.82       139.86        98.53        45.40        57.11 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        64.87         1.41        50.24       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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      131.15       108.66        57.63        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       130.72       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        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        62.30        53.06        47.38        52.50        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 
       37.94        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        12.36        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       19.46        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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       13.18        23.51         2.99        12.30        27.65        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        13.84        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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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 
       13.91         7.82        11.51        29.95        15.62        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        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       27.09        18.38        29.49        54.05        22.09        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       80.02        65.36        84.89        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        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 
       81.34        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        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 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        19.73         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        20.25        12.89 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.99              0.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            98.56            169.32 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            20.53             20.25 
[1] "1.0 - 98.6 (20.5)"  "0.1 - 169.3 (20.2)"
[1] "hr=" "2.2"
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       46       106        1        45         6
D8V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 7               275
  STAGE II                6                46
  STAGE III               3               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
  7P GAIN MUTATED     4   7   5   2
  7P GAIN WILD-TYPE 137 159 162  21
D8V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               4               137
  T2               7               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"
D8V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    12   2
  7P GAIN WILD-TYPE 212 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     12    2
  7P GAIN WILD-TYPE  212  223
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              12               212
  1               2               223
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     4   0
  7P GAIN WILD-TYPE 273   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4    0
  7P GAIN WILD-TYPE  273    9
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0               4               273
  1               0                 9
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    13   5
  7P GAIN WILD-TYPE 353 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     13    5
  7P GAIN WILD-TYPE  353  128
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              13               353
  MALE                 5               128
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  7P GAIN MUTATED                0
  7P GAIN WILD-TYPE              9
                   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                                                                     89
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  7P GAIN MUTATED                                                                     0
  7P GAIN WILD-TYPE                                                                  36
D8V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                89
  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"
D8V9, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     0  18
  7P GAIN WILD-TYPE  14 467
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      0   18
  7P GAIN WILD-TYPE   14  467
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                0                14
  YES              18               467
[1] 2 2
[1] FALSE
D8V10, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    16   0
  7P GAIN WILD-TYPE 405  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     16    0
  7P GAIN WILD-TYPE  405   17
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               16               405
  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 369  49   4  28
D8V12, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              12               369
  R1               3                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"
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   315
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               315
[1] 4 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  38 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      0   10
  7P GAIN WILD-TYPE   38  348
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO              10               348
[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 464  13
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               20               477 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                1                13 
$`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        16.44         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        12.26        98.56 
TCGA-FY-A3I5 TCGA-FY-A3NM 
        7.82         0.99 

$`7Q GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28R 
       15.12        17.69        23.34        20.71         4.83        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.21        22.88        18.38        16.57        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
       10.88         3.45         6.35         7.82         6.18        21.63 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93        23.47         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
        0.23        11.38        10.68         0.10         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       20.22        15.42        36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.27         2.76         9.96        17.26        14.07       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        56.19        23.38        18.35        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        11.01       135.91        30.61        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33        35.41        27.45        26.20 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
       38.83        12.56         8.28        34.85         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.42        37.74         6.77        40.24         9.44        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        10.09         7.10        35.90        12.43        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        20.45        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
       19.56        36.33        32.81        24.23        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        21.37        18.51        36.99        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       21.47        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        21.01        18.97         7.76         8.32        24.20 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        18.21        21.34        19.07        15.42 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04        31.23        22.29 
TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       11.70        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.27         3.02        25.45        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        13.78        13.58        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82       139.86        98.53        45.40        57.11       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       64.87         1.41        50.24       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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        49.71        83.57       139.00       131.15 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        29.65       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      130.72       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        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       62.30        53.06        47.38        52.50        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        37.94 
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        12.36        18.05        19.79        19.46 
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-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.74        11.15        14.24        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        27.65        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       13.84        19.73        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        29.95        15.62        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        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       29.49        54.05        22.09        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        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         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        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         2.99        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 
       10.26        16.90        21.83         9.63         2.96         8.65 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         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        86.70         6.02        19.73 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        20.25        12.89 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.99              0.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            98.56            169.32 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            20.53             20.25 
[1] "1.0 - 98.6 (20.5)"  "0.1 - 169.3 (20.2)"
[1] "hr=" "2"  
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       46       105        1        45         6
D9V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 8               274
  STAGE II                6                46
  STAGE III               4               105
  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 136 159 161  21
D9V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               5               136
  T2               7               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"
D9V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    12   2
  7Q GAIN WILD-TYPE 212 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     12    2
  7Q GAIN WILD-TYPE  212  223
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              12               212
  1               2               223
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     5   0
  7Q GAIN WILD-TYPE 272   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5    0
  7Q GAIN WILD-TYPE  272    9
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0               5               272
  1               0                 9
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    15   5
  7Q GAIN WILD-TYPE 351 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     15    5
  7Q GAIN WILD-TYPE  351  128
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              15               351
  MALE                 5               128
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  7Q GAIN MUTATED                0
  7Q GAIN WILD-TYPE              9
                   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                                                                     88
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  7Q GAIN MUTATED                                                                     0
  7Q GAIN WILD-TYPE                                                                  36
D9V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        346
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                88
  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"
D9V9, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     0  20
  7Q GAIN WILD-TYPE  14 465
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      0   20
  7Q GAIN WILD-TYPE   14  465
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                0                14
  YES              20               465
[1] 2 2
[1] FALSE
D9V10, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    18   0
  7Q GAIN WILD-TYPE 403  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     18    0
  7Q GAIN WILD-TYPE  403   17
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               18               403
  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 368  49   4  27
D9V12, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              13               368
  R1               3                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"
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   314
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               314
[1] 4 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  38 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      0   10
  7Q GAIN WILD-TYPE   38  348
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO              10               348
[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 477  14
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6               491 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                0                14 
$`8P GAIN MUTATED`
TCGA-EM-A2CO TCGA-ET-A2MZ TCGA-ET-A39N TCGA-ET-A3BV TCGA-FY-A3I5 TCGA-L6-A4EP 
        6.05        12.26        98.56        42.25         7.82        33.40 

$`8P GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       130.72 
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        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        52.50        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 
       37.94        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        12.36        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        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP 
       14.24        16.44        17.88        13.18        23.51         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        27.65        10.49        13.15        22.16        13.84 
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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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 
       13.91         7.82        11.51        29.95        15.62        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 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
        2.43         5.56        24.72        38.30         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        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 
       81.34        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        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 
        0.99        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         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
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         2.99        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        10.26        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         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 
       86.70         6.02        19.73         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       84.72        35.28        33.24        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        20.25        12.89 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             6.05              0.10 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            98.56            169.32 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            22.83             20.42 
[1] "6.0 - 98.6 (22.8)"  "0.1 - 169.3 (20.4)"
[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       51       107        2        46         6
D10V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 3               279
  STAGE II                1                51
  STAGE III               2               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
  8P GAIN MUTATED     1   3   2   0
  8P GAIN WILD-TYPE 140 163 165  23
D10V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               1               140
  T2               3               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"
D10V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     3   1
  8P GAIN WILD-TYPE 221 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3    1
  8P GAIN WILD-TYPE  221  224
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               3               221
  1               1               224
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1   0
  8P GAIN WILD-TYPE 276   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1    0
  8P GAIN WILD-TYPE  276    9
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               1               276
  1               0                 9
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     5   1
  8P GAIN WILD-TYPE 361 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    1
  8P GAIN WILD-TYPE  361  132
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               5               361
  MALE                 1               132
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  8P GAIN MUTATED                0
  8P GAIN WILD-TYPE              9
                   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                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  8P GAIN MUTATED                                                                     0
  8P GAIN WILD-TYPE                                                                  36
D10V8, 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                                                                         9
  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"
D10V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     0   6
  8P GAIN WILD-TYPE  14 479
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0    6
  8P GAIN WILD-TYPE   14  479
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                0                14
  YES               6               479
[1] 2 2
[1] FALSE
D10V10, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     5   0
  8P GAIN WILD-TYPE 416  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    0
  8P GAIN WILD-TYPE  416   17
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                5               416
  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 376  52   4  29
D10V12, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0               5               376
  R1               0                52
  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   321
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               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"
D10V17, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     0   5
  8P GAIN WILD-TYPE  38 353
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0    5
  8P GAIN WILD-TYPE   38  353
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               5               353
[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 477  13
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7               490 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                13 
$`8Q GAIN MUTATED`
TCGA-EL-A3T9 TCGA-EM-A2CO TCGA-ET-A2MZ TCGA-ET-A39N TCGA-ET-A3BV TCGA-FY-A3I5 
        5.72         6.05        12.26        98.56        42.25         7.82 
TCGA-L6-A4EP 
       33.40 

$`8Q GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       130.72 
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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        52.50        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        37.94 
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        12.36        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-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        11.74        11.15        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       16.44        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        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        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        29.95        15.62        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        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       27.09        18.38        29.49        54.05        22.09        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       80.02        65.36        84.89        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.56        24.72        38.30         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       117.40        66.77        81.34 
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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        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         0.99 
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 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        19.73         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        20.25        12.89 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             5.72              0.10 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            98.56            169.32 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           12.260            20.435 
[1] "5.7 - 98.6 (12.3)"  "0.1 - 169.3 (20.4)"
[1] "hr=" "5.1"
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       51       107        1        46         6
D11V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 3               279
  STAGE II                1                51
  STAGE III               2               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
  8Q GAIN MUTATED     1   3   2   1
  8Q GAIN WILD-TYPE 140 163 165  22
D11V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               1               140
  T2               3               163
  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 221 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3    2
  8Q GAIN WILD-TYPE  221  223
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0               3               221
  1               2               223
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     1   0
  8Q GAIN WILD-TYPE 276   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1    0
  8Q GAIN WILD-TYPE  276    9
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0               1               276
  1               0                 9
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     6   1
  8Q GAIN WILD-TYPE 360 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6    1
  8Q GAIN WILD-TYPE  360  132
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               6               360
  MALE                 1               132
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  8Q GAIN MUTATED                0
  8Q GAIN WILD-TYPE              9
                   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                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  8Q GAIN MUTATED                                                                     0
  8Q GAIN WILD-TYPE                                                                  36
D11V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        351
  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"
D11V9, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     0   7
  8Q GAIN WILD-TYPE  14 478
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      0    7
  8Q GAIN WILD-TYPE   14  478
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                0                14
  YES               7               478
[1] 2 2
[1] FALSE
D11V10, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     6   0
  8Q GAIN WILD-TYPE 415  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6    0
  8Q GAIN WILD-TYPE  415   17
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                6               415
  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 376  51   4  29
D11V12, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0               5               376
  R1               1                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"
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   320
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               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"
D11V17, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     0   6
  8Q GAIN WILD-TYPE  38 352
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      0    6
  8Q GAIN WILD-TYPE   38  352
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               6               352
[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 480  14
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               494 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                14 
$`9P GAIN MUTATED`
TCGA-EL-A4K9 TCGA-EM-A1YD TCGA-FY-A3I5 
       47.84        57.01         7.82 

$`9P GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       130.72 
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        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        52.50        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 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       41.13        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        12.36        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-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        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        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        29.95        15.62        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        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        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         0.99        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         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        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 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83         9.63         2.96         8.65        17.23 
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-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         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        86.70         6.02        19.73         6.74 
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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       20.25        12.89 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             7.82              0.10 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            57.01            169.32 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           47.840            20.335 
[1] "7.8 - 57.0 (47.8)"  "0.1 - 169.3 (20.3)"
[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       50       108        2        46         6
D12V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 0               282
  STAGE II                2                50
  STAGE III               1               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
  9P GAIN MUTATED     0   2   1   0
  9P GAIN WILD-TYPE 141 164 166  23
D12V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               0               141
  T2               2               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"
D12V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     3   0
  9P GAIN WILD-TYPE 221 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    0
  9P GAIN WILD-TYPE  221  225
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               3               221
  1               0               225
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1   0
  9P GAIN WILD-TYPE 276   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1    0
  9P GAIN WILD-TYPE  276    9
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               1               276
  1               0                 9
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2   1
  9P GAIN WILD-TYPE 364 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    1
  9P GAIN WILD-TYPE  364  132
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               2               364
  MALE                 1               132
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  9P GAIN MUTATED                0
  9P GAIN WILD-TYPE              9
                   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                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  9P GAIN MUTATED                                                                     0
  9P GAIN WILD-TYPE                                                                  36
D12V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        355
  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"
D12V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0   3
  9P GAIN WILD-TYPE  14 482
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    3
  9P GAIN WILD-TYPE   14  482
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                0                14
  YES               3               482
[1] 2 2
[1] FALSE
D12V10, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2   0
  9P GAIN WILD-TYPE 419  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    0
  9P GAIN WILD-TYPE  419   17
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                2               419
  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 378  52   4  30
D12V12, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0               3               378
  R1               0                52
  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               381 
       TCGA-4C-A93U        TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        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-A28R        TCGA-BJ-A28T        TCGA-BJ-A28W        TCGA-BJ-A28X 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A45G        TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A3MD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A4M8        TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A4MD        TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13O        TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13V 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13W        TCGA-DJ-A13X        TCGA-DJ-A1QG        TCGA-DJ-A1QH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A1QM        TCGA-DJ-A2PO        TCGA-DJ-A2PP        TCGA-DJ-A2PQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PR        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-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ        TCGA-DJ-A3UR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UU        TCGA-DJ-A3UW        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-A3V4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3VA        TCGA-DJ-A3VB        TCGA-DJ-A3VD        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-A4UL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A4UP        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A4V2        TCGA-DJ-A4V5        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-E3-A3E5        TCGA-E8-A242 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-E8-A414        TCGA-E8-A415 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433        TCGA-E8-A436 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM        TCGA-EL-A3CN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        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-A3GQ        TCGA-EL-A3GS        TCGA-EL-A3GU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3TB        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-A3ZM        TCGA-EL-A3ZN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3ZO        TCGA-EL-A3ZP        TCGA-EL-A3ZS        TCGA-EL-A4JV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4K7        TCGA-EL-A4KD        TCGA-EL-A4KG        TCGA-EL-A4KI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A1CS        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YC        TCGA-EM-A1YE        TCGA-EM-A22I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L        TCGA-EM-A22M 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A22N        TCGA-EM-A22O        TCGA-EM-A22P        TCGA-EM-A22Q 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CN        TCGA-EM-A2CP        TCGA-EM-A2CQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2CS        TCGA-EM-A2CT        TCGA-EM-A2CU        TCGA-EM-A2OV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2OX        TCGA-EM-A2OY        TCGA-EM-A2OZ        TCGA-EM-A2P0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A2P2        TCGA-EM-A3AJ        TCGA-EM-A3AK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AQ 
"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-A3FL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3FM        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3FQ        TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3O9        TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3SU        TCGA-EM-A3SX        TCGA-EM-A3SZ        TCGA-EM-A4FF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A4FM        TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A4FR        TCGA-EM-A4FV        TCGA-EM-A4G1        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-A2MX        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A39K        TCGA-ET-A39L        TCGA-ET-A39O 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3I4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON        TCGA-FY-A3R6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY        TCGA-FY-A3W9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        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-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-QD-A8IV 
"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   323
D12V16, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2               403 
       TCGA-4C-A93U        TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        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-A192        TCGA-BJ-A28R        TCGA-BJ-A28S 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A28T        TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28X 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A2N8        TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-BJ-A3PR        TCGA-BJ-A3PT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A45F        TCGA-BJ-A45G        TCGA-BJ-A45H        TCGA-BJ-A45I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A45J        TCGA-BJ-A45K        TCGA-BJ-A4O8        TCGA-BJ-A4O9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CE-A13K        TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CE-A481        TCGA-CE-A482        TCGA-CE-A483        TCGA-CE-A484 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CE-A485        TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DE-A4M8        TCGA-DE-A4M9 
"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-A69J        TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13P        TCGA-DJ-A13R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13S        TCGA-DJ-A13T        TCGA-DJ-A13U        TCGA-DJ-A13W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A1QH        TCGA-DJ-A1QI        TCGA-DJ-A1QM        TCGA-DJ-A1QO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A1QQ        TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PR        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-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX        TCGA-DJ-A3UY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UZ        TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3VD        TCGA-DJ-A3VE        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-A3VM        TCGA-DJ-A4UL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A4UP        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A4UW        TCGA-DJ-A4V0        TCGA-DJ-A4V4        TCGA-DJ-A4V5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DO-A1JZ        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-E3-A3E5        TCGA-E8-A242        TCGA-E8-A2EA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A2JQ        TCGA-E8-A3X7        TCGA-E8-A413        TCGA-E8-A414 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A415        TCGA-E8-A416        TCGA-E8-A417        TCGA-E8-A418 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A419        TCGA-E8-A432        TCGA-E8-A433        TCGA-E8-A434 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A436        TCGA-E8-A437        TCGA-E8-A438        TCGA-E8-A44K 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A44M        TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS 
"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-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ        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-A3H2        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-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"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-A3BO        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-A3BV        TCGA-ET-A3BW        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-A3SD        TCGA-FK-A3SE        TCGA-FK-A3SG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA 
"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-FY-A76V        TCGA-GE-A2C6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        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-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-L6-A4ET        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-MK-A84Z        TCGA-QD-A8IV 
"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  38 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    2
  9P GAIN WILD-TYPE   38  356
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               356
[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 479  14
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               493 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                14 
$`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-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
        8.28         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        52.50        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        37.94 
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-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        12.36        18.05        19.79        19.46        78.61 
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-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        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        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        16.80        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        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        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        81.34        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-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
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         0.99        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         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83         9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         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        86.70         6.02        19.73         6.74        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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        20.25 
TCGA-QD-A8IV 
       12.89 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             7.82              0.10 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            57.01            169.32 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           41.345            20.250 
[1] "7.8 - 57.0 (41.3)"  "0.1 - 169.3 (20.2)"
[1] "hr="     "9100000"
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       50       107        2        46         6
D13V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 0               282
  STAGE II                2                50
  STAGE III               2               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
  9Q GAIN MUTATED     0   2   2   0
  9Q GAIN WILD-TYPE 141 164 165  23
D13V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               0               141
  T2               2               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"
D13V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3   1
  9Q GAIN WILD-TYPE 221 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    1
  9Q GAIN WILD-TYPE  221  224
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               3               221
  1               1               224
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2   0
  9Q GAIN WILD-TYPE 275   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    0
  9Q GAIN WILD-TYPE  275    9
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               2               275
  1               0                 9
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2   2
  9Q GAIN WILD-TYPE 364 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    2
  9Q GAIN WILD-TYPE  364  131
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               2               364
  MALE                 2               131
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  9Q GAIN MUTATED                0
  9Q GAIN WILD-TYPE              9
                   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                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  9Q GAIN MUTATED                                                                     0
  9Q GAIN WILD-TYPE                                                                  36
D13V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  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"
D13V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0   4
  9Q GAIN WILD-TYPE  14 481
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    4
  9Q GAIN WILD-TYPE   14  481
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                0                14
  YES               4               481
[1] 2 2
[1] FALSE
D13V10, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3   0
  9Q GAIN WILD-TYPE 418  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    0
  9Q GAIN WILD-TYPE  418   17
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                3               418
  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 377  52   4  30
D13V12, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               4               377
  R1               0                52
  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   322
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               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"
D13V17, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0   3
  9Q GAIN WILD-TYPE  38 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    3
  9Q GAIN WILD-TYPE   38  355
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               355
[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 477  14
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                491 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                 14 
$`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        12.26        98.56 

$`11P GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       130.72 
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        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        52.50        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        37.94 
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        12.36        18.05        19.79        19.46 
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-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AI 
       32.32        33.96        17.59        17.46        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        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        16.80        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        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        29.95        15.62        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        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       29.49        54.05        22.09        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        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         0.99 
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 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        19.73         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        20.25        12.89 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             12.26               0.10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             98.56             169.32 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            38.725             20.420 
[1] "12.3 - 98.6 (38.7)" "0.1 - 169.3 (20.4)"
[1] "hr="     "9300000"
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       51       107        2        46         6
D14V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  3                279
  STAGE II                 1                 51
  STAGE III                2                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
  11P GAIN MUTATED     2   1   3   0
  11P GAIN WILD-TYPE 139 165 164  23
D14V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                2                139
  T2                1                165
  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 220 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4    0
  11P GAIN WILD-TYPE  220  225
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                4                220
  1                0                225
[1] 2 2
[1] FALSE
D14V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1   0
  11P GAIN WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    0
  11P GAIN WILD-TYPE  276    9
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                1                276
  1                0                  9
[1] 2 2
[1] FALSE
D14V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     3   3
  11P GAIN WILD-TYPE 363 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    3
  11P GAIN WILD-TYPE  363  130
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                3                363
  MALE                  3                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  11P GAIN MUTATED                0
  11P GAIN WILD-TYPE              9
                    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                                                                     95
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  11P GAIN MUTATED                                                                     0
  11P GAIN WILD-TYPE                                                                  36
D14V8, 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                                                                          9
  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"
D14V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0   6
  11P GAIN WILD-TYPE  14 479
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    6
  11P GAIN WILD-TYPE   14  479
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 0                 14
  YES                6                479
[1] 2 2
[1] FALSE
D14V10, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     6   0
  11P GAIN WILD-TYPE 415  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6    0
  11P GAIN WILD-TYPE  415   17
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 6                415
  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 376  52   4  29
D14V12, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                5                376
  R1                0                 52
  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   322
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                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"
D14V17, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0   3
  11P GAIN WILD-TYPE  38 355
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    3
  11P GAIN WILD-TYPE   38  355
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                3                355
[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 478  14
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                492 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                 14 
$`11Q GAIN MUTATED`
TCGA-EL-A3ZR TCGA-EM-A1YC TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       60.16        78.61        13.51        12.26        98.56 

$`11Q GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       130.72 
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        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        52.50        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        37.94 
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        12.36        18.05        19.79        19.46 
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-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        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        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       117.40        66.77        81.34 
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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        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 
        0.99        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         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
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         2.99        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        10.26        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         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 
       86.70         6.02        19.73         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        20.25        12.89 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             12.26               0.10 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             98.56             169.32 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            60.160             20.335 
[1] "12.3 - 98.6 (60.2)" "0.1 - 169.3 (20.3)"
[1] "hr="     "9300000"
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       51       108        2        46         6
D15V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  3                279
  STAGE II                 1                 51
  STAGE III                1                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
  11Q GAIN MUTATED     2   1   2   0
  11Q GAIN WILD-TYPE 139 165 165  23
D15V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                2                139
  T2                1                165
  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 221 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    0
  11Q GAIN WILD-TYPE  221  225
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                3                221
  1                0                225
[1] 2 2
[1] FALSE
D15V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1   0
  11Q GAIN WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    0
  11Q GAIN WILD-TYPE  276    9
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                1                276
  1                0                  9
[1] 2 2
[1] FALSE
D15V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3   2
  11Q GAIN WILD-TYPE 363 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    2
  11Q GAIN WILD-TYPE  363  131
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                363
  MALE                  2                131
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  11Q GAIN MUTATED                0
  11Q GAIN WILD-TYPE              9
                    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                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  11Q GAIN MUTATED                                                                     0
  11Q GAIN WILD-TYPE                                                                  36
D15V8, 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                                                                          9
  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"
D15V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0   5
  11Q GAIN WILD-TYPE  14 480
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    5
  11Q GAIN WILD-TYPE   14  480
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 0                 14
  YES                5                480
[1] 2 2
[1] FALSE
D15V10, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     5   0
  11Q GAIN WILD-TYPE 416  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    0
  11Q GAIN WILD-TYPE  416   17
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 5                416
  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 377  52   4  29
D15V12, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                4                377
  R1                0                 52
  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                381 
        TCGA-4C-A93U         TCGA-BJ-A0Z0         TCGA-BJ-A0Z3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A0Z9         TCGA-BJ-A0ZA         TCGA-BJ-A0ZB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZH         TCGA-BJ-A0ZJ         TCGA-BJ-A18Y 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A18Z         TCGA-BJ-A190         TCGA-BJ-A191 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A28R         TCGA-BJ-A28T         TCGA-BJ-A28W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A28X         TCGA-BJ-A28Z         TCGA-BJ-A290 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A291         TCGA-BJ-A2N8         TCGA-BJ-A2N9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A3EZ         TCGA-BJ-A3PR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A3PU         TCGA-BJ-A45C         TCGA-BJ-A45D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A45E         TCGA-BJ-A45G         TCGA-BJ-A45I 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A45J         TCGA-BJ-A45K         TCGA-BJ-A4O8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BJ-A4O9         TCGA-CE-A13K         TCGA-CE-A3MD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DE-A0XZ         TCGA-DE-A0Y2         TCGA-DE-A0Y3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DE-A3KN         TCGA-DE-A4M8         TCGA-DE-A4MA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DE-A4MB         TCGA-DE-A4MC         TCGA-DE-A4MD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DE-A69K         TCGA-DE-A7U5         TCGA-DJ-A13M 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A13O         TCGA-DJ-A13R         TCGA-DJ-A13T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A13V         TCGA-DJ-A13W         TCGA-DJ-A13X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QH         TCGA-DJ-A1QM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PO         TCGA-DJ-A2PP         TCGA-DJ-A2PQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PR         TCGA-DJ-A2PS         TCGA-DJ-A2PT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PU         TCGA-DJ-A2PV         TCGA-DJ-A2PW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PX         TCGA-DJ-A2PY         TCGA-DJ-A2PZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q0         TCGA-DJ-A2Q1         TCGA-DJ-A2Q2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q3         TCGA-DJ-A2Q4         TCGA-DJ-A2Q5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q6         TCGA-DJ-A2Q7         TCGA-DJ-A2Q8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q9         TCGA-DJ-A2QA         TCGA-DJ-A2QB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UK         TCGA-DJ-A3UM         TCGA-DJ-A3UN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UO         TCGA-DJ-A3UP         TCGA-DJ-A3UQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UR         TCGA-DJ-A3UU         TCGA-DJ-A3UW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UX         TCGA-DJ-A3UZ         TCGA-DJ-A3V0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V2         TCGA-DJ-A3V3         TCGA-DJ-A3V4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V5         TCGA-DJ-A3V7         TCGA-DJ-A3V8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V9         TCGA-DJ-A3VA         TCGA-DJ-A3VB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VD         TCGA-DJ-A3VF         TCGA-DJ-A3VG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VJ         TCGA-DJ-A3VL         TCGA-DJ-A4UL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A4UP         TCGA-DJ-A4UQ         TCGA-DJ-A4UR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DJ-A4UW         TCGA-DJ-A4V2         TCGA-DJ-A4V5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-DO-A2HM         TCGA-E3-A3DY 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E3-A3DZ         TCGA-E3-A3E0         TCGA-E3-A3E1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E3-A3E2         TCGA-E3-A3E3         TCGA-E3-A3E5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E8-A242         TCGA-E8-A2EA         TCGA-E8-A2JQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E8-A414         TCGA-E8-A415         TCGA-E8-A417 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E8-A419         TCGA-E8-A433         TCGA-E8-A436 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E8-A438         TCGA-E8-A44K         TCGA-EL-A3CM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3CN         TCGA-EL-A3CO         TCGA-EL-A3CR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3CS         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-A3CY         TCGA-EL-A3CZ         TCGA-EL-A3D0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3D1         TCGA-EL-A3D4         TCGA-EL-A3D5 
"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-A3GQ         TCGA-EL-A3GS         TCGA-EL-A3GU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3GV         TCGA-EL-A3GX         TCGA-EL-A3H3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3H4         TCGA-EL-A3H5         TCGA-EL-A3H7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3H8         TCGA-EL-A3MW         TCGA-EL-A3MX 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3T0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3T1         TCGA-EL-A3T2         TCGA-EL-A3TB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZH         TCGA-EL-A3ZK         TCGA-EL-A3ZL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZM         TCGA-EL-A3ZN         TCGA-EL-A3ZO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZP         TCGA-EL-A3ZS         TCGA-EL-A4JV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A4JW         TCGA-EL-A4JX         TCGA-EL-A4JZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A4K0         TCGA-EL-A4K1         TCGA-EL-A4K2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A4K4         TCGA-EL-A4K6         TCGA-EL-A4K7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EL-A4KD         TCGA-EL-A4KG         TCGA-EL-A4KI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A1CS         TCGA-EM-A1CT         TCGA-EM-A1CU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A1CV         TCGA-EM-A1CW         TCGA-EM-A1YD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A1YE         TCGA-EM-A22I         TCGA-EM-A22J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A22K         TCGA-EM-A22L         TCGA-EM-A22M 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A22N         TCGA-EM-A22O         TCGA-EM-A22P 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A22Q         TCGA-EM-A2CK         TCGA-EM-A2CN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A2CP         TCGA-EM-A2CQ         TCGA-EM-A2CS 
"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-A3AQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3AR         TCGA-EM-A3FJ         TCGA-EM-A3FK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3FL         TCGA-EM-A3FM         TCGA-EM-A3FN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3FO         TCGA-EM-A3FP         TCGA-EM-A3FQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3FR         TCGA-EM-A3O3         TCGA-EM-A3O8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3O9         TCGA-EM-A3OA         TCGA-EM-A3OB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3ST         TCGA-EM-A3SU         TCGA-EM-A3SX 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A3SZ         TCGA-EM-A4FF         TCGA-EM-A4FM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A4FN         TCGA-EM-A4FO         TCGA-EM-A4FQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EM-A4FR         TCGA-EM-A4FV         TCGA-EM-A4G1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25I         TCGA-ET-A25J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A25K         TCGA-ET-A25L         TCGA-ET-A25M 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A25N         TCGA-ET-A25O         TCGA-ET-A25P 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A2MX         TCGA-ET-A2N0         TCGA-ET-A2N1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A2N4         TCGA-ET-A39K         TCGA-ET-A39L 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A39O         TCGA-ET-A39P         TCGA-ET-A39R 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A39S         TCGA-ET-A39T         TCGA-ET-A3BO 
"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-A3BV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A3BX         TCGA-ET-A3DQ         TCGA-ET-A3DR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A3DV         TCGA-ET-A3DW         TCGA-ET-A40P 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A40Q         TCGA-ET-A40R         TCGA-ET-A40S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ET-A40T         TCGA-ET-A4KN         TCGA-FE-A22Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FE-A230         TCGA-FE-A231         TCGA-FE-A232 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FE-A233         TCGA-FE-A234         TCGA-FE-A235 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FE-A236         TCGA-FE-A237         TCGA-FE-A238 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FE-A3PB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FE-A3PC         TCGA-FE-A3PD         TCGA-FK-A3S3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FK-A3SB         TCGA-FK-A3SE         TCGA-FK-A3SG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FK-A3SH         TCGA-FK-A4UB         TCGA-FY-A2QD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FY-A3I4         TCGA-FY-A3I5         TCGA-FY-A3NM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FY-A3NN         TCGA-FY-A3ON         TCGA-FY-A3R6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FY-A3R7         TCGA-FY-A3R9         TCGA-FY-A3TY 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FY-A3W9         TCGA-FY-A3YR         TCGA-FY-A40K 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FY-A40L         TCGA-FY-A40M         TCGA-FY-A40N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FY-A4B3         TCGA-FY-A4B4         TCGA-GE-A2C6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-H2-A26U         TCGA-H2-A2K9         TCGA-H2-A3RH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-H2-A3RI         TCGA-H2-A421         TCGA-H2-A422 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IM-A3EB         TCGA-IM-A3ED         TCGA-IM-A3U2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IM-A3U3         TCGA-IM-A41Y         TCGA-IM-A41Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IM-A420         TCGA-IM-A4EB         TCGA-J8-A3NZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-J8-A3O0         TCGA-J8-A3O1         TCGA-J8-A3O2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-J8-A3YD         TCGA-J8-A3YE         TCGA-J8-A3YF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-J8-A3YG         TCGA-J8-A3YH         TCGA-J8-A42S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-J8-A4HW         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   322
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                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"
D15V17, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0   3
  11Q GAIN WILD-TYPE  38 355
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    3
  11Q GAIN WILD-TYPE   38  355
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                3                355
[1] 2 2
[1] FALSE

Clustering(16) Variable = 12P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    14   0
  12P GAIN WILD-TYPE 469  14
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                14                483 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                 14 
$`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        12.26        98.56         0.30 
TCGA-FY-A3I5 TCGA-FY-A3NM 
        7.82         0.99 

$`12P GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        17.69        23.34        20.71         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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75        10.88        21.01         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18        21.63         8.98         4.93        23.47         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       169.32         3.39         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       18.35        14.60         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45        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         5.33        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        12.56         8.28        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24         9.44        37.48        36.46        10.09         7.10 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        12.43        35.18        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       20.45        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        59.57        11.34        21.37        18.51 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        21.47        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        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        24.20        17.23        27.62        18.21 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        19.07        15.42        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
       14.04        31.23        22.29        11.70        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       14.27        13.81        14.07        14.27         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       130.72       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        78.97        31.50        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        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        37.94        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-A1YE 
       20.91        12.36        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        27.65        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       13.84        19.73        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       69.24        59.87        43.50        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        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         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        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         2.99        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 
       10.26        16.90        21.83         9.63         2.96         8.65 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         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        86.70         6.02        19.73 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        20.25        12.89 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               0.3                0.1 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             98.56             169.32 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            16.995             20.420 
[1] "0.3 - 98.6 (17.0)"  "0.1 - 169.3 (20.4)"
[1] "hr="     "2.5e+07"
D16V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  12P GAIN MUTATED         6        5         3        0         0         0
  12P GAIN WILD-TYPE     276       47       106        2        46         6
D16V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  6                276
  STAGE II                 5                 47
  STAGE III                3                106
  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     4   6   4   0
  12P GAIN WILD-TYPE 137 160 163  23
D16V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                4                137
  T2                6                160
  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 214 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     10    0
  12P GAIN WILD-TYPE  214  225
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               10                214
  1                0                225
[1] 2 2
[1] FALSE
D16V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     1   0
  12P GAIN WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    0
  12P GAIN WILD-TYPE  276    9
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                1                276
  1                0                  9
[1] 2 2
[1] FALSE
D16V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    11   3
  12P GAIN WILD-TYPE 355 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     11    3
  12P GAIN WILD-TYPE  355  130
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               11                355
  MALE                  3                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  12P GAIN MUTATED                0
  12P GAIN WILD-TYPE              9
                    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                                                                        8
  12P GAIN WILD-TYPE                                                                     90
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  12P GAIN MUTATED                                                                     0
  12P GAIN WILD-TYPE                                                                  36
D16V8, multiclass
                                                                        clus
vv                                                                       12P GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       12P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         350
  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"
D16V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0  14
  12P GAIN WILD-TYPE  14 471
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   14
  12P GAIN WILD-TYPE   14  471
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 0                 14
  YES               14                471
[1] 2 2
[1] FALSE
D16V10, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    13   0
  12P GAIN WILD-TYPE 408  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     13    0
  12P GAIN WILD-TYPE  408   17
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                13                408
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  12P GAIN MUTATED              1                       0   13
  12P GAIN WILD-TYPE          131                      18  317
                    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                                  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
  12P GAIN MUTATED    11   1   0   2
  12P GAIN WILD-TYPE 370  51   4  28
D16V12, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               11                370
  R1                1                 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"
D16V13, continuous
D16V14, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     7   7
  12P GAIN WILD-TYPE 218 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7    7
  12P GAIN WILD-TYPE  218  257
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  MULTIFOCAL                7                218
  UNIFOCAL                  7                257
[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     8
  12P GAIN WILD-TYPE                        27   317
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                                           8                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"
D16V17, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0   8
  12P GAIN WILD-TYPE  38 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0    8
  12P GAIN WILD-TYPE   38  350
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                8                350
[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 468  14
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                482 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                 14 
$`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        12.26        98.56         0.30 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3WA 
        7.82         0.99        17.06 

$`12Q GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        17.69        23.34        20.71         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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75        10.88        21.01         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18        21.63         8.98         4.93        23.47         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       169.32         3.39         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       18.35        14.60         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45        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         5.33        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        12.56         8.28        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24         9.44        37.48        36.46        10.09         7.10 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        12.43        35.18        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       20.45        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        59.57        11.34        21.37        18.51 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        21.47        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        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        24.20        17.23        27.62        18.21 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        19.07        15.42        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
       14.04        31.23        22.29        11.70        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       14.27        13.81        14.07        14.27         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       130.72       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        78.97        31.50        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        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        37.94        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-A1YE 
       20.91        12.36        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        27.65        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       13.84        19.73        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       69.24        59.87        43.50        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        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         0.30         0.76 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        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 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83         9.63         2.96         8.65        17.23 
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-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         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        86.70         6.02        19.73         6.74 
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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       20.25        12.89 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               0.3                0.1 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             98.56             169.32 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            17.060             20.435 
[1] "0.3 - 98.6 (17.1)"  "0.1 - 169.3 (20.4)"
[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       47       106        2        46         6
D17V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  7                275
  STAGE II                 5                 47
  STAGE III                3                106
  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 136 160 163  23
D17V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                5                136
  T2                6                160
  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 214 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     10    0
  12Q GAIN WILD-TYPE  214  225
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               10                214
  1                0                225
[1] 2 2
[1] FALSE
D17V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1   0
  12Q GAIN WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    0
  12Q GAIN WILD-TYPE  276    9
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                1                276
  1                0                  9
[1] 2 2
[1] FALSE
D17V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    12   3
  12Q GAIN WILD-TYPE 354 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     12    3
  12Q GAIN WILD-TYPE  354  130
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               12                354
  MALE                  3                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  12Q GAIN MUTATED                0
  12Q GAIN WILD-TYPE              9
                    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                                                                     89
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  12Q GAIN MUTATED                                                                     0
  12Q GAIN WILD-TYPE                                                                  36
D17V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 89
  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"
D17V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0  15
  12Q GAIN WILD-TYPE  14 470
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   15
  12Q GAIN WILD-TYPE   14  470
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 0                 14
  YES               15                470
[1] 2 2
[1] FALSE
D17V10, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    14   0
  12Q GAIN WILD-TYPE 407  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     14    0
  12Q GAIN WILD-TYPE  407   17
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                14                407
  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 369  51   4  28
D17V12, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               12                369
  R1                1                 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"
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   316
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                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"
D17V17, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0   9
  12Q GAIN WILD-TYPE  38 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0    9
  12Q GAIN WILD-TYPE   38  349
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                9                349
[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 478  14
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                492 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                 14 
$`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-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         5.75        10.88         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        52.50        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        37.94 
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-A1YC 
       20.91        12.36        18.05        19.79        19.46        78.61 
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-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       13.18        23.51         2.99        12.30        27.65        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        13.84        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-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        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        13.91         7.82        11.51        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       15.62        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        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       54.05        22.09        12.26        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89        98.56        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       117.40        66.77        81.34 
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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        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 
        0.99        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         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
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         2.99        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        10.26        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         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 
       86.70         6.02        19.73         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        20.25        12.89 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              6.05               0.10 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             57.01             169.32 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            23.900             20.235 
[1] "6.0 - 57.0 (23.9)"  "0.1 - 169.3 (20.2)"
[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       49       108        2        46         6
D18V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  1                281
  STAGE II                 3                 49
  STAGE III                1                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 GAIN MUTATED     1   3   1   0
  13Q GAIN WILD-TYPE 140 163 166  23
D18V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                1                140
  T2                3                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"
D18V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   0
  13Q GAIN WILD-TYPE 220 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    0
  13Q GAIN WILD-TYPE  220  225
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                4                220
  1                0                225
[1] 2 2
[1] FALSE
D18V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1   0
  13Q GAIN WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1    0
  13Q GAIN WILD-TYPE  276    9
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                1                276
  1                0                  9
[1] 2 2
[1] FALSE
D18V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   1
  13Q GAIN WILD-TYPE 362 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    1
  13Q GAIN WILD-TYPE  362  132
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                4                362
  MALE                  1                132
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  13Q GAIN MUTATED                0
  13Q GAIN WILD-TYPE              9
                    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                                                                     95
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  13Q GAIN MUTATED                                                                     0
  13Q GAIN WILD-TYPE                                                                  36
D18V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         354
  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"
D18V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0   5
  13Q GAIN WILD-TYPE  14 480
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    5
  13Q GAIN WILD-TYPE   14  480
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 0                 14
  YES                5                480
[1] 2 2
[1] FALSE
D18V10, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   0
  13Q GAIN WILD-TYPE 417  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    0
  13Q GAIN WILD-TYPE  417   17
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 4                417
  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 377  52   4  30
D18V12, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0                4                377
  R1                0                 52
  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   323
D18V16, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                403 
        TCGA-4C-A93U         TCGA-BJ-A0YZ         TCGA-BJ-A0Z2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A0Z3         TCGA-BJ-A0Z5         TCGA-BJ-A0Z9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZE         TCGA-BJ-A0ZG         TCGA-BJ-A0ZH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZJ         TCGA-BJ-A18Y         TCGA-BJ-A18Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A190         TCGA-BJ-A191         TCGA-BJ-A192 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A28R         TCGA-BJ-A28S         TCGA-BJ-A28T 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A28V         TCGA-BJ-A28W         TCGA-BJ-A28X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A28Z         TCGA-BJ-A290         TCGA-BJ-A291 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A2N7         TCGA-BJ-A2N8         TCGA-BJ-A2N9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A2P4         TCGA-BJ-A3EZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A3F0         TCGA-BJ-A3PR         TCGA-BJ-A3PT 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A3PU         TCGA-BJ-A45C         TCGA-BJ-A45D 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A45F         TCGA-BJ-A45G         TCGA-BJ-A45H 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A45I         TCGA-BJ-A45J         TCGA-BJ-A45K 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A4O8         TCGA-BJ-A4O9         TCGA-CE-A13K 
"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-A0XZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DE-A0Y2         TCGA-DE-A0Y3         TCGA-DE-A2OL 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DE-A3KN         TCGA-DE-A4M8         TCGA-DE-A4M9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DE-A4MA         TCGA-DE-A4MB         TCGA-DE-A4MC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DE-A4MD         TCGA-DE-A69J         TCGA-DE-A69K 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DE-A7U5         TCGA-DJ-A13L         TCGA-DJ-A13M 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A13O         TCGA-DJ-A13P         TCGA-DJ-A13R 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A13S         TCGA-DJ-A13T         TCGA-DJ-A13U 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A13W         TCGA-DJ-A1QD         TCGA-DJ-A1QE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QF         TCGA-DJ-A1QG         TCGA-DJ-A1QH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QI         TCGA-DJ-A1QM         TCGA-DJ-A1QO 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QQ         TCGA-DJ-A2PN         TCGA-DJ-A2PO 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PQ         TCGA-DJ-A2PR         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-A3UU 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UW         TCGA-DJ-A3UX         TCGA-DJ-A3UY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UZ         TCGA-DJ-A3V2         TCGA-DJ-A3V3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V4         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-E3-A3E5         TCGA-E8-A242         TCGA-E8-A2EA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A2JQ         TCGA-E8-A3X7         TCGA-E8-A413 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A414         TCGA-E8-A415         TCGA-E8-A416 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A417         TCGA-E8-A418         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-A3CR         TCGA-EL-A3CS 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"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-A3H2         TCGA-EL-A3H3         TCGA-EL-A3H4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3N3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3T0         TCGA-EL-A3T1         TCGA-EL-A3T2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3T3         TCGA-EL-A3T6         TCGA-EL-A3T7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3T8         TCGA-EL-A3T9         TCGA-EL-A3TA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3TB         TCGA-EL-A3ZG         TCGA-EL-A3ZH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZK         TCGA-EL-A3ZL         TCGA-EL-A3ZN 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZO         TCGA-EL-A3ZP         TCGA-EL-A3ZQ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZR         TCGA-EL-A3ZS         TCGA-EL-A3ZT 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4JV         TCGA-EL-A4JW         TCGA-EL-A4JX 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4JZ         TCGA-EL-A4K0         TCGA-EL-A4K1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4K2         TCGA-EL-A4K4         TCGA-EL-A4K6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4K7         TCGA-EL-A4K9         TCGA-EL-A4KD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4KG         TCGA-EL-A4KH         TCGA-EM-A22M 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EM-A22O         TCGA-EM-A2OV         TCGA-EM-A3AI 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25I         TCGA-ET-A25J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A25K         TCGA-ET-A25L         TCGA-ET-A25M 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A25N         TCGA-ET-A25O         TCGA-ET-A25P 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A25R         TCGA-ET-A2MX         TCGA-ET-A2MY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A2MZ         TCGA-ET-A2N0         TCGA-ET-A2N1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A2N3         TCGA-ET-A2N4         TCGA-ET-A2N5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A39I         TCGA-ET-A39J         TCGA-ET-A39K 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A39M         TCGA-ET-A39N         TCGA-ET-A39O 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A39P         TCGA-ET-A39R         TCGA-ET-A39S 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A39T         TCGA-ET-A3BN         TCGA-ET-A3BO 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3BQ         TCGA-ET-A3BS         TCGA-ET-A3BT 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3BU         TCGA-ET-A3BV         TCGA-ET-A3BW 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3DO         TCGA-ET-A3DP         TCGA-ET-A3DQ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3DR         TCGA-ET-A3DS         TCGA-ET-A3DT 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3DU         TCGA-ET-A3DV         TCGA-ET-A3DW 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A40P         TCGA-ET-A40Q         TCGA-ET-A40R 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A40S         TCGA-ET-A40T         TCGA-ET-A4KN 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A4KQ         TCGA-FE-A22Z         TCGA-FE-A230 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A231         TCGA-FE-A232         TCGA-FE-A233 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A234         TCGA-FE-A235         TCGA-FE-A236 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A237         TCGA-FE-A238         TCGA-FE-A239 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A23A         TCGA-FE-A3PA         TCGA-FE-A3PB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A3PC         TCGA-FE-A3PD         TCGA-FK-A3S3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FK-A3SB         TCGA-FK-A3SD         TCGA-FK-A3SE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FK-A3SG         TCGA-FK-A3SH         TCGA-FK-A4UB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A2QD         TCGA-FY-A3BL         TCGA-FY-A3I4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A3I5         TCGA-FY-A3NM         TCGA-FY-A3ON 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A3R6         TCGA-FY-A3R7         TCGA-FY-A3R8 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A3R9         TCGA-FY-A3RA         TCGA-FY-A3W9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A3WA         TCGA-FY-A3YR         TCGA-FY-A40K 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A40L         TCGA-FY-A40M         TCGA-FY-A40N 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A4B0         TCGA-FY-A4B3         TCGA-FY-A4B4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A76V         TCGA-GE-A2C6         TCGA-H2-A26U 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-H2-A2K9         TCGA-H2-A3RH         TCGA-H2-A3RI 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-H2-A421         TCGA-H2-A422         TCGA-IM-A3EB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IM-A3ED         TCGA-IM-A3U2         TCGA-IM-A3U3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IM-A41Y         TCGA-IM-A41Z         TCGA-IM-A420 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IM-A4EB         TCGA-J8-A3NZ         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-A4HW 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-J8-A4HY         TCGA-KS-A41F         TCGA-KS-A41I 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-KS-A41J         TCGA-KS-A41L         TCGA-KS-A4I1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-KS-A4I3         TCGA-KS-A4I5         TCGA-KS-A4I7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-KS-A4I9         TCGA-KS-A4IB         TCGA-KS-A4IC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-KS-A4ID         TCGA-L6-A4EP         TCGA-L6-A4EQ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-L6-A4ET         TCGA-L6-A4EU         TCGA-MK-A4N6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-MK-A4N7         TCGA-MK-A4N9         TCGA-MK-A84Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-QD-A8IV 
"13Q GAIN WILD-TYPE" 
D18V17, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0   2
  13Q GAIN WILD-TYPE  38 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    2
  13Q GAIN WILD-TYPE   38  356
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                2                356
[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 472  14
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                486 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 0                 14 
$`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        98.56         7.82         0.99        22.29 

$`14Q GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       130.72 
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        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        52.50        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        37.94 
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-A1YC 
       20.91        12.36        18.05        19.79        19.46        78.61 
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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        27.65        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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 
       13.91         7.82        11.51        29.95        15.62        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 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       13.74        71.01        80.02        65.36        84.89        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        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         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YH 
       27.19        11.24        31.82        27.85        24.69         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         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 
       86.70         6.02        19.73         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        20.25        12.89 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.99               0.10 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             98.56             169.32 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            22.520             20.235 
[1] "1.0 - 98.6 (22.5)"  "0.1 - 169.3 (20.2)"
[1] "hr="     "2.5e+07"
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       47       105        2        46         6
D19V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  2                280
  STAGE II                 5                 47
  STAGE III                4                105
  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 140 160 163  23
D19V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                1                140
  T2                6                160
  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 217 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      7    1
  14Q GAIN WILD-TYPE  217  224
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                7                217
  1                1                224
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2   0
  14Q GAIN WILD-TYPE 275   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    0
  14Q GAIN WILD-TYPE  275    9
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                2                275
  1                0                  9
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    10   1
  14Q GAIN WILD-TYPE 356 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     10    1
  14Q GAIN WILD-TYPE  356  132
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               10                356
  MALE                  1                132
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  14Q GAIN MUTATED                0
  14Q GAIN WILD-TYPE              9
                    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                                                                     92
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  14Q GAIN MUTATED                                                                     0
  14Q GAIN WILD-TYPE                                                                  36
D19V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         351
  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"
D19V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0  11
  14Q GAIN WILD-TYPE  14 474
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   11
  14Q GAIN WILD-TYPE   14  474
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 0                 14
  YES               11                474
[1] 2 2
[1] FALSE
D19V10, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    10   0
  14Q GAIN WILD-TYPE 411  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     10    0
  14Q GAIN WILD-TYPE  411   17
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                10                411
  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 371  52   4  29
D19V12, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               10                371
  R1                0                 52
  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   318
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                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"
D19V17, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0   6
  14Q GAIN WILD-TYPE  38 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    6
  14Q GAIN WILD-TYPE   38  352
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                352
[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 469  13
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                482 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 13 
$`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        12.26        98.56 
TCGA-ET-A3DS TCGA-FY-A3I5 TCGA-FY-A3NM 
        0.30         7.82         0.99 

$`16P GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        20.58         4.83 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75        10.88        21.01         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18        21.63         8.98         4.93        23.47         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       169.32         3.39         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       18.35        14.60         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45        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         5.33        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        12.56         8.28        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        5.52         8.78         8.42        37.74         6.77        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44        37.48        36.46        10.09         7.10        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        35.18        15.88        15.09        31.04        20.45 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        59.57        11.34        21.37        18.51        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        21.47        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        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
        8.32        24.20        17.23        27.62        18.21        21.34 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       19.07        15.42        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       31.23        22.29        11.70        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 
       13.81        14.07        14.27         3.02        25.45        14.43 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       14.70        14.10        14.96         7.69        20.68        13.78 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.58        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
       80.91         4.18        58.82       139.86        98.53        45.40 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       57.11       108.36        64.87         1.41        50.24       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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      139.99        49.32        33.50        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       131.15       108.66        57.63        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       29.65       147.42       130.72       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 
       78.97        31.50        62.30        36.03        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       52.50        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        37.94        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        12.36 
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-A22O TCGA-EM-A22P 
       14.50        15.75        10.45        14.53        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP 
       14.24        16.44        17.88        13.18        23.51         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        27.65        10.49        13.15        22.16        13.84 
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-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        29.95        15.62        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        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       29.49        54.05        22.09        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       59.87        43.50        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        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         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        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 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83         9.63         2.96         8.65        17.23 
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-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         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        86.70         6.02        19.73         6.74 
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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       20.25        12.89 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               0.3                0.1 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             98.56             169.32 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            12.260             20.465 
[1] "0.3 - 98.6 (12.3)"  "0.1 - 169.3 (20.5)"
[1] "hr=" "3.2"
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       48       106        1        46         6
D20V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  7                275
  STAGE II                 4                 48
  STAGE III                3                106
  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 137 161 162  22
D20V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                4                137
  T2                5                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"
D20V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     9   1
  16P GAIN WILD-TYPE 215 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9    1
  16P GAIN WILD-TYPE  215  224
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                9                215
  1                1                224
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     3   0
  16P GAIN WILD-TYPE 274   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    0
  16P GAIN WILD-TYPE  274    9
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                3                274
  1                0                  9
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    12   3
  16P GAIN WILD-TYPE 354 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     12    3
  16P GAIN WILD-TYPE  354  130
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               12                354
  MALE                  3                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  16P GAIN MUTATED                0
  16P GAIN WILD-TYPE              9
                    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                                                                     91
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  16P GAIN MUTATED                                                                     0
  16P GAIN WILD-TYPE                                                                  36
D20V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         348
  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"
D20V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  15
  16P GAIN WILD-TYPE  14 470
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   15
  16P GAIN WILD-TYPE   14  470
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 0                 14
  YES               15                470
[1] 2 2
[1] FALSE
D20V10, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    14   0
  16P GAIN WILD-TYPE 407  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     14    0
  16P GAIN WILD-TYPE  407   17
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                14                407
  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 371  50   4  27
D20V12, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               10                371
  R1                2                 50
  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   315
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                315
[1] 4 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  38 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0    9
  16P GAIN WILD-TYPE   38  349
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                9                349
[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 471  13
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                484 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 13 
$`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        12.26        98.56         7.82 
TCGA-FY-A3NM 
        0.99 

$`16Q GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       34.85         5.52         8.78         8.42        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24         9.44        37.48        36.46        10.09         7.10 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        12.43        35.18        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       20.45        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        59.57        11.34        21.37        18.51 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        21.47        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        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        24.20        17.23        27.62        18.21 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        19.07        15.42        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
       14.04        31.23        22.29        11.70        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       14.27        13.81        14.07        14.27         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       130.72       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        78.97        31.50        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        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        37.94        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 
       12.36        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        27.65        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       13.84        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       117.40        66.77        81.34 
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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        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         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        17.23        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-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       19.73         6.74        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        20.25        12.89 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.99               0.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             98.56             169.32 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            12.260             20.465 
[1] "1.0 - 98.6 (12.3)"  "0.1 - 169.3 (20.5)"
[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       48       107        1        46         6
D21V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  6                276
  STAGE II                 4                 48
  STAGE III                2                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
  16Q GAIN MUTATED     3   5   4   1
  16Q GAIN WILD-TYPE 138 161 163  22
D21V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                3                138
  T2                5                161
  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 216 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      8    1
  16Q GAIN WILD-TYPE  216  224
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                8                216
  1                1                224
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2   0
  16Q GAIN WILD-TYPE 275   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2    0
  16Q GAIN WILD-TYPE  275    9
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                2                275
  1                0                  9
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    10   3
  16Q GAIN WILD-TYPE 356 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     10    3
  16Q GAIN WILD-TYPE  356  130
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               10                356
  MALE                  3                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  16Q GAIN MUTATED                0
  16Q GAIN WILD-TYPE              9
                    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                                                                     91
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  16Q GAIN MUTATED                                                                     0
  16Q GAIN WILD-TYPE                                                                  36
D21V8, 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                                                                          9
  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"
D21V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  13
  16Q GAIN WILD-TYPE  14 472
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   13
  16Q GAIN WILD-TYPE   14  472
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 0                 14
  YES               13                472
[1] 2 2
[1] FALSE
D21V10, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    12   0
  16Q GAIN WILD-TYPE 409  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     12    0
  16Q GAIN WILD-TYPE  409   17
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                12                409
  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 372  50   4  28
D21V12, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                9                372
  R1                2                 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"
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   317
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                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"
D21V17, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0   8
  16Q GAIN WILD-TYPE  38 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0    8
  16Q GAIN WILD-TYPE   38  350
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                8                350
[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 467  14
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                481 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 0                 14 
$`17P GAIN MUTATED`
TCGA-DJ-A2Q0 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1YC 
       34.36        78.97        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        12.26        98.56         7.82 

$`17P GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
        8.28        34.85         5.52         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       66.90        82.82        89.56        31.50        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT 
       53.06        47.38        52.50        61.22         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        37.94        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        12.36        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        11.74        11.15        14.24        16.44 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       17.88        13.18        23.51         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        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-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        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        13.91         7.82        11.51        29.95 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       15.62        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        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       12.33        14.79        27.09        29.49        54.05        22.09 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        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        81.34        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-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
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         0.99        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         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83         9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         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        86.70         6.02        19.73         6.74        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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        20.25 
TCGA-QD-A8IV 
       12.89 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              6.05               0.10 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             98.56             169.32 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             28.11              20.22 
[1] "6.0 - 98.6 (28.1)"  "0.1 - 169.3 (20.2)"
[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       46       106        1        46         6
D22V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  6                276
  STAGE II                 6                 46
  STAGE III                3                106
  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 137 160 162  22
D22V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                4                137
  T2                6                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"
D22V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    10   2
  17P GAIN WILD-TYPE 214 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     10    2
  17P GAIN WILD-TYPE  214  223
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               10                214
  1                2                223
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     3   0
  17P GAIN WILD-TYPE 274   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    0
  17P GAIN WILD-TYPE  274    9
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                3                274
  1                0                  9
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    12   4
  17P GAIN WILD-TYPE 354 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     12    4
  17P GAIN WILD-TYPE  354  129
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               12                354
  MALE                  4                129
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  17P GAIN MUTATED                0
  17P GAIN WILD-TYPE              9
                    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                                                                     90
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  17P GAIN MUTATED                                                                     0
  17P GAIN WILD-TYPE                                                                  36
D22V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         348
  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"
D22V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  16
  17P GAIN WILD-TYPE  14 469
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   16
  17P GAIN WILD-TYPE   14  469
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                 14
  YES               16                469
[1] 2 2
[1] FALSE
D22V10, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    15   0
  17P GAIN WILD-TYPE 406  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     15    0
  17P GAIN WILD-TYPE  406   17
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                15                406
  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 367  52   4  28
D22V12, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               14                367
  R1                0                 52
  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   316
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                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"
D22V17, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  10
  17P GAIN WILD-TYPE  38 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   10
  17P GAIN WILD-TYPE   38  348
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO               10                348
[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 465  14
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                479 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 0                 14 
$`17Q GAIN MUTATED`
TCGA-DJ-A2Q0 TCGA-EL-A3ZH TCGA-EL-A3ZM TCGA-EL-A3ZR TCGA-EL-A4K6 TCGA-EL-A4KI 
       34.36        78.97        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        12.26        98.56         0.30         7.82 

$`17Q GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
        8.28        34.85         5.52         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       66.90        82.82        89.56        31.50        62.30        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       47.38        52.50        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        37.94        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       53.36        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        12.36        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       19.46        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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       13.18        23.51         2.99        12.30        27.65        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        13.84        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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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        13.91         7.82        11.51        29.95        15.62 
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 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       14.79        27.09        29.49        54.05        22.09        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       80.02        65.36        84.89        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU 
       80.81        69.24        59.87        43.50        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       117.40        66.77        81.34 
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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        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         0.99 
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 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        19.73         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        20.25        12.89 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               0.3                0.1 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             98.56             169.32 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             28.11              20.22 
[1] "0.3 - 98.6 (28.1)"  "0.1 - 169.3 (20.2)"
[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       46       106        1        45         6
D23V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  7                275
  STAGE II                 6                 46
  STAGE III                3                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
  17Q GAIN MUTATED     5   6   5   2
  17Q GAIN WILD-TYPE 136 160 162  21
D23V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                5                136
  T2                6                160
  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 213 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     11    3
  17Q GAIN WILD-TYPE  213  222
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               11                213
  1                3                222
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     4   0
  17Q GAIN WILD-TYPE 273   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4    0
  17Q GAIN WILD-TYPE  273    9
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                4                273
  1                0                  9
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    13   5
  17Q GAIN WILD-TYPE 353 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     13    5
  17Q GAIN WILD-TYPE  353  128
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               13                353
  MALE                  5                128
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  17Q GAIN MUTATED                0
  17Q GAIN WILD-TYPE              9
                    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                                                                     90
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  17Q GAIN MUTATED                                                                     0
  17Q GAIN WILD-TYPE                                                                  36
D23V8, 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                                                                          9
  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"
D23V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  18
  17Q GAIN WILD-TYPE  14 467
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   18
  17Q GAIN WILD-TYPE   14  467
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 0                 14
  YES               18                467
[1] 2 2
[1] FALSE
D23V10, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    17   0
  17Q GAIN WILD-TYPE 404  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     17    0
  17Q GAIN WILD-TYPE  404   17
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                17                404
  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 366  51   4  28
D23V12, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               15                366
  R1                1                 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"
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   315
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                315
[1] 4 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  38 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   11
  17Q GAIN WILD-TYPE   38  347
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO               11                347
[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 477  14
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                491 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                 14 
$`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        12.26        98.56         7.82 

$`18P GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         5.75        10.88         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS 
       36.03        53.06        47.38        52.50        61.22         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        37.94        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-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 
       12.36        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-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        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        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        16.80        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        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       117.40        66.77        81.34 
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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        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         0.99 
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 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        19.73         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        20.25        12.89 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              7.82               0.10 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             98.56             169.32 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            22.455             20.250 
[1] "7.8 - 98.6 (22.5)"  "0.1 - 169.3 (20.2)"
[1] "hr="     "9200000"
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       51       107        2        46         6
D24V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  3                279
  STAGE II                 1                 51
  STAGE III                2                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
  18P GAIN MUTATED     2   1   3   0
  18P GAIN WILD-TYPE 139 165 164  23
D24V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                2                139
  T2                1                165
  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 219 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5    0
  18P GAIN WILD-TYPE  219  225
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                5                219
  1                0                225
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2   0
  18P GAIN WILD-TYPE 275   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    0
  18P GAIN WILD-TYPE  275    9
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                2                275
  1                0                  9
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4   2
  18P GAIN WILD-TYPE 362 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    2
  18P GAIN WILD-TYPE  362  131
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                4                362
  MALE                  2                131
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  18P GAIN MUTATED                0
  18P GAIN WILD-TYPE              9
                    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                                                                     97
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  18P GAIN MUTATED                                                                     0
  18P GAIN WILD-TYPE                                                                  36
D24V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         351
  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"
D24V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0   6
  18P GAIN WILD-TYPE  14 479
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0    6
  18P GAIN WILD-TYPE   14  479
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 0                 14
  YES                6                479
[1] 2 2
[1] FALSE
D24V10, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4   0
  18P GAIN WILD-TYPE 417  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    0
  18P GAIN WILD-TYPE  417   17
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 4                417
  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 377  52   4  29
D24V12, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                4                377
  R1                0                 52
  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   319
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                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"
D24V17, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0   6
  18P GAIN WILD-TYPE  38 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0    6
  18P GAIN WILD-TYPE   38  352
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                352
[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 477  14
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                491 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                 14 
$`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        12.26        98.56         7.82 

$`18Q GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         5.75        10.88         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS 
       36.03        53.06        47.38        52.50        61.22         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        37.94        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-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 
       12.36        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-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        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        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        16.80        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        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       117.40        66.77        81.34 
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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        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         0.99 
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 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        19.73         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        20.25        12.89 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              7.82               0.10 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             98.56             169.32 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            22.455             20.250 
[1] "7.8 - 98.6 (22.5)"  "0.1 - 169.3 (20.2)"
[1] "hr="     "9200000"
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       51       107        2        46         6
D25V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  3                279
  STAGE II                 1                 51
  STAGE III                2                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
  18Q GAIN MUTATED     2   1   3   0
  18Q GAIN WILD-TYPE 139 165 164  23
D25V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                2                139
  T2                1                165
  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 219 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    0
  18Q GAIN WILD-TYPE  219  225
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                5                219
  1                0                225
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2   0
  18Q GAIN WILD-TYPE 275   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    0
  18Q GAIN WILD-TYPE  275    9
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                2                275
  1                0                  9
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     4   2
  18Q GAIN WILD-TYPE 362 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    2
  18Q GAIN WILD-TYPE  362  131
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                362
  MALE                  2                131
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  18Q GAIN MUTATED                0
  18Q GAIN WILD-TYPE              9
                    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                                                                     97
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  18Q GAIN MUTATED                                                                     0
  18Q GAIN WILD-TYPE                                                                  36
D25V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         351
  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"
D25V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0   6
  18Q GAIN WILD-TYPE  14 479
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    6
  18Q GAIN WILD-TYPE   14  479
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 0                 14
  YES                6                479
[1] 2 2
[1] FALSE
D25V10, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     4   0
  18Q GAIN WILD-TYPE 417  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    0
  18Q GAIN WILD-TYPE  417   17
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 4                417
  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 377  52   4  29
D25V12, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                4                377
  R1                0                 52
  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   319
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                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"
D25V17, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0   6
  18Q GAIN WILD-TYPE  38 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    6
  18Q GAIN WILD-TYPE   38  352
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                352
[1] 2 2
[1] FALSE

Clustering(26) Variable = 19P GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED     7   0
  19P GAIN WILD-TYPE 476  14
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                490 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                 14 
$`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 
        7.82 

$`19P GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       130.72 
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        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        52.50        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 
       37.94        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-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        12.36        18.05        19.79        19.46 
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-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        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-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        16.80        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        13.91         7.82        11.51        29.95 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       15.62        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        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       98.56        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        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         0.99        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         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        17.23        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-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       19.73         6.74        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        20.25        12.89 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              7.82               0.10 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             78.61             169.32 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            13.510             20.435 
[1] "7.8 - 78.6 (13.5)"  "0.1 - 169.3 (20.4)"
[1] "hr="     "9100000"
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       51       106        2        46         6
D26V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  4                278
  STAGE II                 1                 51
  STAGE III                3                106
  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 138 165 163  23
D26V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                3                138
  T2                1                165
  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 218 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6    0
  19P GAIN WILD-TYPE  218  225
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                6                218
  1                0                225
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0   0
  19P GAIN WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    0
  19P GAIN WILD-TYPE  277    9
D26V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     4   4
  19P GAIN WILD-TYPE 362 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      4    4
  19P GAIN WILD-TYPE  362  129
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                4                362
  MALE                  4                129
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  19P GAIN MUTATED                0
  19P GAIN WILD-TYPE              9
                    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                                                                     92
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  19P GAIN MUTATED                                                                     0
  19P GAIN WILD-TYPE                                                                  36
D26V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         354
  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"
D26V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0   8
  19P GAIN WILD-TYPE  14 477
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    8
  19P GAIN WILD-TYPE   14  477
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 0                 14
  YES                8                477
[1] 2 2
[1] FALSE
D26V10, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     7   0
  19P GAIN WILD-TYPE 414  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7    0
  19P GAIN WILD-TYPE  414   17
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 7                414
  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 375  51   4  29
D26V12, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                6                375
  R1                1                 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"
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   322
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                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"
D26V17, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0   3
  19P GAIN WILD-TYPE  38 355
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    3
  19P GAIN WILD-TYPE   38  355
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                3                355
[1] 2 2
[1] FALSE

Clustering(27) Variable = 19Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED     8   1
  19Q GAIN WILD-TYPE 475  13
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                488 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 13 
$`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 
       33.63         7.82        17.06 

$`19Q GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       130.72 
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        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        52.50        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 
       37.94        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-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        12.36        18.05        19.79        19.46 
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-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        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-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        16.80        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        13.91         7.82        11.51        29.95 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       15.62        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        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       98.56        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        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         0.99        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         0.30         0.76 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        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 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83         9.63         2.96         8.65        17.23 
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-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         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        86.70         6.02        19.73         6.74 
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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       20.25        12.89 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              7.82               0.10 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             78.61             169.32 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            17.060             20.435 
[1] "7.8 - 78.6 (17.1)"  "0.1 - 169.3 (20.4)"
[1] "hr=" "5.6"
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       51       105        2        46         6
D27V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  5                277
  STAGE II                 1                 51
  STAGE III                4                105
  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 137 165 162  23
D27V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                4                137
  T2                1                165
  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 217 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      7    0
  19Q GAIN WILD-TYPE  217  225
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                7                217
  1                0                225
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0   0
  19Q GAIN WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    0
  19Q GAIN WILD-TYPE  277    9
D27V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     5   5
  19Q GAIN WILD-TYPE 361 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      5    5
  19Q GAIN WILD-TYPE  361  128
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                5                361
  MALE                  5                128
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  19Q GAIN MUTATED                0
  19Q GAIN WILD-TYPE              9
                    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                                                                     91
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  19Q GAIN MUTATED                                                                     0
  19Q GAIN WILD-TYPE                                                                  36
D27V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         353
  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"
D27V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1   9
  19Q GAIN WILD-TYPE  13 476
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    9
  19Q GAIN WILD-TYPE   13  476
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 1                 13
  YES                9                476
[1] 2 2
[1] FALSE
D27V10, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     9   0
  19Q GAIN WILD-TYPE 412  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      9    0
  19Q GAIN WILD-TYPE  412   17
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 9                412
  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 373  51   4  29
D27V12, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0                8                373
  R1                1                 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"
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   320
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                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"
D27V17, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0   5
  19Q GAIN WILD-TYPE  38 353
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    5
  19Q GAIN WILD-TYPE   38  353
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                353
[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 472  13
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                485 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                 13 
$`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        12.26        98.56         7.82 

$`20P GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       130.72 
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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        52.50        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        37.94 
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        12.36        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-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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        27.65        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       117.40        66.77        81.34 
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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        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         0.99 
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 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        19.73         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        20.25        12.89 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              5.72               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             98.56             169.32 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            18.015             20.420 
[1] "5.7 - 98.6 (18.0)"  "0.1 - 169.3 (20.4)"
[1] "hr=" "2.7"
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       48       106        1        46         6
D28V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  4                278
  STAGE II                 4                 48
  STAGE III                3                106
  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 139 162 162  22
D28V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                2                139
  T2                4                162
  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 217 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7    1
  20P GAIN WILD-TYPE  217  224
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0                7                217
  1                1                224
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     0   0
  20P GAIN WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      0    0
  20P GAIN WILD-TYPE  277    9
D28V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     8   4
  20P GAIN WILD-TYPE 358 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      8    4
  20P GAIN WILD-TYPE  358  129
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                8                358
  MALE                  4                129
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  20P GAIN MUTATED                0
  20P GAIN WILD-TYPE              9
                    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                                                                     90
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  20P GAIN MUTATED                                                                     0
  20P GAIN WILD-TYPE                                                                  36
D28V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         352
  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"
D28V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     0  12
  20P GAIN WILD-TYPE  14 473
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      0   12
  20P GAIN WILD-TYPE   14  473
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 0                 14
  YES               12                473
[1] 2 2
[1] FALSE
D28V10, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    11   0
  20P GAIN WILD-TYPE 410  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     11    0
  20P GAIN WILD-TYPE  410   17
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                11                410
  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 371  51   4  29
D28V12, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               10                371
  R1                1                 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"
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   319
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                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"
D28V17, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     0   6
  20P GAIN WILD-TYPE  38 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      0    6
  20P GAIN WILD-TYPE   38  352
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                352
[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 472  13
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                485 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                 13 
$`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        12.26        98.56         7.82 

$`20Q GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       130.72 
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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        52.50        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        37.94 
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        12.36        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-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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        27.65        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       117.40        66.77        81.34 
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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        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         0.99 
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 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        19.73         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        20.25        12.89 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              5.72               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             98.56             169.32 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            18.015             20.420 
[1] "5.7 - 98.6 (18.0)"  "0.1 - 169.3 (20.4)"
[1] "hr=" "2.7"
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       48       106        1        46         6
D29V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  4                278
  STAGE II                 4                 48
  STAGE III                3                106
  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 139 162 162  22
D29V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                2                139
  T2                4                162
  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 217 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      7    1
  20Q GAIN WILD-TYPE  217  224
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0                7                217
  1                1                224
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     0   0
  20Q GAIN WILD-TYPE 277   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0    0
  20Q GAIN WILD-TYPE  277    9
D29V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     8   4
  20Q GAIN WILD-TYPE 358 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8    4
  20Q GAIN WILD-TYPE  358  129
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                8                358
  MALE                  4                129
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  20Q GAIN MUTATED                0
  20Q GAIN WILD-TYPE              9
                    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                                                                     90
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  20Q GAIN MUTATED                                                                     0
  20Q GAIN WILD-TYPE                                                                  36
D29V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         352
  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"
D29V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     0  12
  20Q GAIN WILD-TYPE  14 473
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0   12
  20Q GAIN WILD-TYPE   14  473
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 0                 14
  YES               12                473
[1] 2 2
[1] FALSE
D29V10, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    11   0
  20Q GAIN WILD-TYPE 410  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     11    0
  20Q GAIN WILD-TYPE  410   17
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                11                410
  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 371  51   4  29
D29V12, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               10                371
  R1                1                 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"
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   319
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                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"
D29V17, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     0   6
  20Q GAIN WILD-TYPE  38 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0    6
  20Q GAIN WILD-TYPE   38  352
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                352
[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 478  14
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                492 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                 14 
$`21Q GAIN MUTATED`
TCGA-BJ-A45E TCGA-EL-A3ZR TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       21.01        60.16        13.51        12.26        98.56 

$`21Q GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         5.75        10.88         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS 
       36.03        53.06        47.38        52.50        61.22         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        37.94        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        12.36        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-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        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        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       117.40        66.77        81.34 
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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        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 
        0.99        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         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
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         2.99        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        10.26        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         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 
       86.70         6.02        19.73         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        20.25        12.89 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             12.26               0.10 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             98.56             169.32 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            21.010             20.335 
[1] "12.3 - 98.6 (21.0)" "0.1 - 169.3 (20.3)"
[1] "hr="     "9200000"
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       51       109        2        46         6
D30V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  4                278
  STAGE II                 1                 51
  STAGE III                0                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
  21Q GAIN MUTATED     3   1   1   0
  21Q GAIN WILD-TYPE 138 165 166  23
D30V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                138
  T2                1                165
  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 221 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    0
  21Q GAIN WILD-TYPE  221  225
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                3                221
  1                0                225
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     2   0
  21Q GAIN WILD-TYPE 275   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    0
  21Q GAIN WILD-TYPE  275    9
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                2                275
  1                0                  9
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3   2
  21Q GAIN WILD-TYPE 363 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    2
  21Q GAIN WILD-TYPE  363  131
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                3                363
  MALE                  2                131
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  21Q GAIN MUTATED                0
  21Q GAIN WILD-TYPE              9
                    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                                                                     97
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  21Q GAIN MUTATED                                                                     0
  21Q GAIN WILD-TYPE                                                                  36
D30V8, 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                                                                          9
  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"
D30V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0   5
  21Q GAIN WILD-TYPE  14 480
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    5
  21Q GAIN WILD-TYPE   14  480
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 0                 14
  YES                5                480
[1] 2 2
[1] FALSE
D30V10, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     4   0
  21Q GAIN WILD-TYPE 417  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4    0
  21Q GAIN WILD-TYPE  417   17
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 4                417
  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 378  52   4  29
D30V12, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0                3                378
  R1                0                 52
  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                381 
        TCGA-4C-A93U         TCGA-BJ-A0Z0         TCGA-BJ-A0Z3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A0Z9         TCGA-BJ-A0ZA         TCGA-BJ-A0ZB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZH         TCGA-BJ-A0ZJ         TCGA-BJ-A18Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A18Z         TCGA-BJ-A190         TCGA-BJ-A191 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A28R         TCGA-BJ-A28T         TCGA-BJ-A28W 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A28X         TCGA-BJ-A28Z         TCGA-BJ-A290 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A291         TCGA-BJ-A2N8         TCGA-BJ-A2N9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A3EZ         TCGA-BJ-A3PR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A3PU         TCGA-BJ-A45C         TCGA-BJ-A45D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A45G         TCGA-BJ-A45I         TCGA-BJ-A45J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BJ-A45K         TCGA-BJ-A4O8         TCGA-BJ-A4O9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CE-A13K         TCGA-CE-A3MD         TCGA-DE-A0XZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DE-A0Y2         TCGA-DE-A0Y3         TCGA-DE-A3KN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DE-A4M8         TCGA-DE-A4MA         TCGA-DE-A4MB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DE-A4MC         TCGA-DE-A4MD         TCGA-DE-A69K 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DE-A7U5         TCGA-DJ-A13M         TCGA-DJ-A13O 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A13R         TCGA-DJ-A13T         TCGA-DJ-A13V 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A13W         TCGA-DJ-A13X         TCGA-DJ-A1QG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QH         TCGA-DJ-A1QM         TCGA-DJ-A2PO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PP         TCGA-DJ-A2PQ         TCGA-DJ-A2PR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PS         TCGA-DJ-A2PT         TCGA-DJ-A2PU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PV         TCGA-DJ-A2PW         TCGA-DJ-A2PX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q1         TCGA-DJ-A2Q2         TCGA-DJ-A2Q3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q4         TCGA-DJ-A2Q5         TCGA-DJ-A2Q6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q7         TCGA-DJ-A2Q8         TCGA-DJ-A2Q9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A2QA         TCGA-DJ-A2QB         TCGA-DJ-A3UK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UM         TCGA-DJ-A3UN         TCGA-DJ-A3UO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UP         TCGA-DJ-A3UQ         TCGA-DJ-A3UR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UU         TCGA-DJ-A3UW         TCGA-DJ-A3UX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UZ         TCGA-DJ-A3V0         TCGA-DJ-A3V2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V3         TCGA-DJ-A3V4         TCGA-DJ-A3V5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V7         TCGA-DJ-A3V8         TCGA-DJ-A3V9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VA         TCGA-DJ-A3VB         TCGA-DJ-A3VD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VF         TCGA-DJ-A3VG         TCGA-DJ-A3VJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VL         TCGA-DJ-A4UL         TCGA-DJ-A4UP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A4UQ         TCGA-DJ-A4UR         TCGA-DJ-A4UW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DJ-A4V2         TCGA-DJ-A4V5         TCGA-DO-A1K0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DO-A2HM         TCGA-E3-A3DY         TCGA-E3-A3DZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E3-A3E0         TCGA-E3-A3E1         TCGA-E3-A3E2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E3-A3E3         TCGA-E3-A3E5         TCGA-E8-A242 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E8-A2EA         TCGA-E8-A2JQ         TCGA-E8-A414 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E8-A415         TCGA-E8-A417         TCGA-E8-A419 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E8-A433         TCGA-E8-A436         TCGA-E8-A438 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-E8-A44K         TCGA-EL-A3CM         TCGA-EL-A3CN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CO         TCGA-EL-A3CR         TCGA-EL-A3CS 
"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-A3CY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GS         TCGA-EL-A3GU         TCGA-EL-A3GV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3GX         TCGA-EL-A3H3         TCGA-EL-A3H4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3N2         TCGA-EL-A3T0         TCGA-EL-A3T1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3T2         TCGA-EL-A3TB         TCGA-EL-A3ZH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZK         TCGA-EL-A3ZL         TCGA-EL-A3ZM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZN         TCGA-EL-A3ZO         TCGA-EL-A3ZP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZS         TCGA-EL-A4JV         TCGA-EL-A4JW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A4JX         TCGA-EL-A4JZ         TCGA-EL-A4K0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A4K1         TCGA-EL-A4K2         TCGA-EL-A4K4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A4K6         TCGA-EL-A4K7         TCGA-EL-A4KD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EL-A4KG         TCGA-EL-A4KI         TCGA-EM-A1CS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1CT         TCGA-EM-A1CU         TCGA-EM-A1CV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1CW         TCGA-EM-A1YC         TCGA-EM-A1YD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A1YE         TCGA-EM-A22I         TCGA-EM-A22J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A22K         TCGA-EM-A22L         TCGA-EM-A22M 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A22N         TCGA-EM-A22O         TCGA-EM-A22P 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A22Q         TCGA-EM-A2CK         TCGA-EM-A2CN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A2CP         TCGA-EM-A2CQ         TCGA-EM-A2CS 
"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-A3AQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3AR         TCGA-EM-A3FJ         TCGA-EM-A3FK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3FL         TCGA-EM-A3FM         TCGA-EM-A3FN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3FO         TCGA-EM-A3FP         TCGA-EM-A3FQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3FR         TCGA-EM-A3O3         TCGA-EM-A3O8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3O9         TCGA-EM-A3OA         TCGA-EM-A3OB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3ST         TCGA-EM-A3SU         TCGA-EM-A3SX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A3SZ         TCGA-EM-A4FF         TCGA-EM-A4FM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A4FN         TCGA-EM-A4FO         TCGA-EM-A4FQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EM-A4FR         TCGA-EM-A4FV         TCGA-EM-A4G1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25I         TCGA-ET-A25J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A25K         TCGA-ET-A25L         TCGA-ET-A25M 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A25N         TCGA-ET-A25O         TCGA-ET-A25P 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A2MX         TCGA-ET-A2N0         TCGA-ET-A2N1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A2N4         TCGA-ET-A39K         TCGA-ET-A39L 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A39O         TCGA-ET-A39P         TCGA-ET-A39R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A39S         TCGA-ET-A39T         TCGA-ET-A3BO 
"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-A3BV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3BX         TCGA-ET-A3DQ         TCGA-ET-A3DR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A3DV         TCGA-ET-A3DW         TCGA-ET-A40P 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A40Q         TCGA-ET-A40R         TCGA-ET-A40S 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ET-A40T         TCGA-ET-A4KN         TCGA-FE-A22Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A230         TCGA-FE-A231         TCGA-FE-A232 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A233         TCGA-FE-A234         TCGA-FE-A235 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A236         TCGA-FE-A237         TCGA-FE-A238 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FE-A3PB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FE-A3PC         TCGA-FE-A3PD         TCGA-FK-A3S3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FK-A3SB         TCGA-FK-A3SE         TCGA-FK-A3SG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FK-A3SH         TCGA-FK-A4UB         TCGA-FY-A2QD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A3I4         TCGA-FY-A3I5         TCGA-FY-A3NM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A3NN         TCGA-FY-A3ON         TCGA-FY-A3R6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A3R7         TCGA-FY-A3R9         TCGA-FY-A3TY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A3W9         TCGA-FY-A3YR         TCGA-FY-A40K 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A40L         TCGA-FY-A40M         TCGA-FY-A40N 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FY-A4B3         TCGA-FY-A4B4         TCGA-GE-A2C6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-H2-A26U         TCGA-H2-A2K9         TCGA-H2-A3RH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-H2-A3RI         TCGA-H2-A421         TCGA-H2-A422 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IM-A3EB         TCGA-IM-A3ED         TCGA-IM-A3U2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IM-A3U3         TCGA-IM-A41Y         TCGA-IM-A41Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IM-A420         TCGA-IM-A4EB         TCGA-J8-A3NZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-J8-A3O0         TCGA-J8-A3O1         TCGA-J8-A3O2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-J8-A3YD         TCGA-J8-A3YE         TCGA-J8-A3YF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-J8-A3YG         TCGA-J8-A3YH         TCGA-J8-A42S 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-J8-A4HW         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   321
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                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"
D30V17, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0   4
  21Q GAIN WILD-TYPE  38 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    4
  21Q GAIN WILD-TYPE   38  354
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                4                354
[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 476  13
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                8               489 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                13 
$`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 
        5.03         0.99 

$`XP GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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-A3ZM 
       82.82        89.56        78.97        31.50        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        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        37.94        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-A1YE 
       20.91        12.36        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        27.65        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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        13.91         7.82        11.51        29.95        15.62 
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        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       98.56        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN 
       24.72         3.22         7.17         4.80         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82         7.82        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         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        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         2.99        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 
       10.26        16.90        21.83         9.63         2.96         8.65 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         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        86.70         6.02        19.73 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        20.25        12.89 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.99              0.10 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            78.61            169.32 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           15.565            20.420 
[1] "1.0 - 78.6 (15.6)"  "0.1 - 169.3 (20.4)"
[1] "hr=" "5.1"
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       49       107        1        46         6
D31V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 2               280
  STAGE II                3                49
  STAGE III               2               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
  XP GAIN MUTATED     1   4   2   1
  XP GAIN WILD-TYPE 140 162 165  22
D31V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               1               140
  T2               4               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"
D31V5, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     6   1
  XP GAIN WILD-TYPE 218 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      6    1
  XP GAIN WILD-TYPE  218  224
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0               6               218
  1               1               224
[1] 2 2
[1] FALSE
D31V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     1   0
  XP GAIN WILD-TYPE 276   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1    0
  XP GAIN WILD-TYPE  276    9
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0               1               276
  1               0                 9
[1] 2 2
[1] FALSE
D31V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     7   1
  XP GAIN WILD-TYPE 359 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      7    1
  XP GAIN WILD-TYPE  359  132
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               7               359
  MALE                 1               132
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  XP GAIN MUTATED                0
  XP GAIN WILD-TYPE              9
                   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                                                                     94
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  XP GAIN MUTATED                                                                     0
  XP GAIN WILD-TYPE                                                                  36
D31V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        352
  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"
D31V9, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0   8
  XP GAIN WILD-TYPE  14 477
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0    8
  XP GAIN WILD-TYPE   14  477
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                0                14
  YES               8               477
[1] 2 2
[1] FALSE
D31V10, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     7   1
  XP GAIN WILD-TYPE 414  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      7    1
  XP GAIN WILD-TYPE  414   16
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                7               414
  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 377  50   4  28
D31V12, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0               4               377
  R1               2                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"
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   320
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               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"
D31V17, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0   5
  XP GAIN WILD-TYPE  38 353
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0    5
  XP GAIN WILD-TYPE   38  353
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               5               353
[1] 2 2
[1] FALSE

Clustering(32) Variable = XQ GAIN MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     8   1
  XQ GAIN WILD-TYPE 475  13
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9               488 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                13 
$`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-EM-A3FK TCGA-ET-A40S TCGA-FY-A3NM 
       23.77         5.03         0.99 

$`XQ GAIN WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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-A3ZM 
       82.82        89.56        78.97        31.50        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        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        37.94        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-A1YE 
       20.91        12.36        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        27.65        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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 
       13.91         7.82        11.51        29.95        15.62        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 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       13.74        71.01        80.02        65.36        84.89        98.56 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        3.22         7.17         4.80         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        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         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        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 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83         9.63         2.96         8.65        17.23 
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-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         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        86.70         6.02        19.73         6.74 
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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       20.25        12.89 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.99              0.10 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            78.61            169.32 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           20.480            20.335 
[1] "1.0 - 78.6 (20.5)"  "0.1 - 169.3 (20.3)"
[1] "hr=" "4.9"
D32V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  XQ GAIN MUTATED         3        3         2        1         0         0
  XQ GAIN WILD-TYPE     279       49       107        1        46         6
D32V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 3               279
  STAGE II                3                49
  STAGE III               2               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
  XQ GAIN MUTATED     2   4   2   1
  XQ GAIN WILD-TYPE 139 162 165  22
D32V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               2               139
  T2               4               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     6   2
  XQ GAIN WILD-TYPE 218 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6    2
  XQ GAIN WILD-TYPE  218  223
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               6               218
  1               2               223
[1] 2 2
[1] FALSE
D32V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1   0
  XQ GAIN WILD-TYPE 276   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1    0
  XQ GAIN WILD-TYPE  276    9
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               1               276
  1               0                 9
[1] 2 2
[1] FALSE
D32V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     8   1
  XQ GAIN WILD-TYPE 358 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      8    1
  XQ GAIN WILD-TYPE  358  132
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               8               358
  MALE                 1               132
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  XQ GAIN MUTATED                0
  XQ GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  XQ GAIN MUTATED                                               5
  XQ GAIN WILD-TYPE                                           351
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  XQ GAIN MUTATED                                                                        4
  XQ GAIN WILD-TYPE                                                                     94
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  XQ GAIN MUTATED                                                                     0
  XQ GAIN WILD-TYPE                                                                  36
D32V8, multiclass
                                                                        clus
vv                                                                       XQ GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        5
  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                                                                         9
  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"
D32V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0   9
  XQ GAIN WILD-TYPE  14 476
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    9
  XQ GAIN WILD-TYPE   14  476
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                0                14
  YES               9               476
[1] 2 2
[1] FALSE
D32V10, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     8   1
  XQ GAIN WILD-TYPE 413  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      8    1
  XQ GAIN WILD-TYPE  413   16
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                8               413
  YES               1                16
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  XQ GAIN MUTATED              1                       0    7
  XQ GAIN WILD-TYPE          131                      18  323
                   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                                  7               323
  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     5   2   0   2
  XQ GAIN WILD-TYPE 376  50   4  28
D32V12, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0               5               376
  R1               2                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"
D32V13, continuous
D32V14, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     6   3
  XQ GAIN WILD-TYPE 219 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6    3
  XQ GAIN WILD-TYPE  219  261
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  MULTIFOCAL               6               219
  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     5
  XQ GAIN WILD-TYPE                        27   320
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                                          5               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"
D32V17, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0   5
  XQ GAIN WILD-TYPE  38 353
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    5
  XQ GAIN WILD-TYPE   38  353
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               5               353
[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 479  14
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               493 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                0                14 
$`1P LOSS MUTATED`
TCGA-E8-A432 TCGA-EM-A1YE TCGA-ET-A39N TCGA-FY-A3I5 
       14.43        54.08        98.56         7.82 

$`1P LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        25.45        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        52.50        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        37.94 
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        12.36        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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        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        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        29.95        15.62        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        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        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        81.34        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-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
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         0.99        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         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83         9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         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        86.70         6.02        19.73         6.74        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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        20.25 
TCGA-QD-A8IV 
       12.89 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             7.82              0.10 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            98.56            169.32 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           34.255            20.420 
[1] "7.8 - 98.6 (34.3)"  "0.1 - 169.3 (20.4)"
[1] "hr="     "9200000"
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       50       108        2        46         6
D33V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 1               281
  STAGE II                2                50
  STAGE III               1               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
  1P LOSS MUTATED     0   2   2   0
  1P LOSS WILD-TYPE 141 164 165  23
D33V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               0               141
  T2               2               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"
D33V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3   0
  1P LOSS WILD-TYPE 221 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    0
  1P LOSS WILD-TYPE  221  225
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0               3               221
  1               0               225
[1] 2 2
[1] FALSE
D33V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1   0
  1P LOSS WILD-TYPE 276   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    0
  1P LOSS WILD-TYPE  276    9
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0               1               276
  1               0                 9
[1] 2 2
[1] FALSE
D33V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     4   0
  1P LOSS WILD-TYPE 362 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4    0
  1P LOSS WILD-TYPE  362  133
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               4               362
  MALE                 0               133
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  1P LOSS MUTATED                0
  1P LOSS WILD-TYPE              9
                   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                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  1P LOSS MUTATED                                                                     0
  1P LOSS WILD-TYPE                                                                  36
D33V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  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"
D33V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0   4
  1P LOSS WILD-TYPE  14 481
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0    4
  1P LOSS WILD-TYPE   14  481
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                0                14
  YES               4               481
[1] 2 2
[1] FALSE
D33V10, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3   0
  1P LOSS WILD-TYPE 418  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    0
  1P LOSS WILD-TYPE  418   17
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                3               418
  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 377  52   4  30
D33V12, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0               4               377
  R1               0                52
  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               381 
       TCGA-4C-A93U        TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28T        TCGA-BJ-A28W        TCGA-BJ-A28X 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A45G        TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A3MD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DE-A4M8        TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DE-A4MD        TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A13O        TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13V 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A13W        TCGA-DJ-A13X        TCGA-DJ-A1QG        TCGA-DJ-A1QH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A1QM        TCGA-DJ-A2PO        TCGA-DJ-A2PP        TCGA-DJ-A2PQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PT        TCGA-DJ-A2PU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX        TCGA-DJ-A2PY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ        TCGA-DJ-A3UR 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3UU        TCGA-DJ-A3UW        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-A3V4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3VA        TCGA-DJ-A3VB        TCGA-DJ-A3VD        TCGA-DJ-A3VF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A4UL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A4UP        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A4V2        TCGA-DJ-A4V5        TCGA-DO-A1K0        TCGA-DO-A2HM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A242 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-E8-A414        TCGA-E8-A415 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433        TCGA-E8-A436 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM        TCGA-EL-A3CN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        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-A3GQ        TCGA-EL-A3GS        TCGA-EL-A3GU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3TB        TCGA-EL-A3ZH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3ZK        TCGA-EL-A3ZL        TCGA-EL-A3ZM        TCGA-EL-A3ZN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3ZO        TCGA-EL-A3ZP        TCGA-EL-A3ZS        TCGA-EL-A4JV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A4K7        TCGA-EL-A4KD        TCGA-EL-A4KG        TCGA-EL-A4KI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A1CS        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A22I 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L        TCGA-EM-A22M 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A22N        TCGA-EM-A22O        TCGA-EM-A22P        TCGA-EM-A22Q 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CN        TCGA-EM-A2CP        TCGA-EM-A2CQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2CS        TCGA-EM-A2CT        TCGA-EM-A2CU        TCGA-EM-A2OV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2OX        TCGA-EM-A2OY        TCGA-EM-A2OZ        TCGA-EM-A2P0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A2P2        TCGA-EM-A3AJ        TCGA-EM-A3AK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AQ 
"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-A3FL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3FM        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3FQ        TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3O9        TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3SU        TCGA-EM-A3SX        TCGA-EM-A3SZ        TCGA-EM-A4FF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A4FM        TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A4FR        TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A2MX        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A39K        TCGA-ET-A39L        TCGA-ET-A39O 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3I4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON        TCGA-FY-A3R6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY        TCGA-FY-A3W9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        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-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-QD-A8IV 
"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   323
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               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"
D33V17, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0   3
  1P LOSS WILD-TYPE  38 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0    3
  1P LOSS WILD-TYPE   38  355
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               355
[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 480  14
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               494 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                0                14 
$`1Q LOSS MUTATED`
TCGA-EM-A1YE TCGA-ET-A39N TCGA-FY-A3I5 
       54.08        98.56         7.82 

$`1Q LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       130.72 
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        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        52.50        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 
       37.94        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        12.36        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        11.74        11.15        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       16.44        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        27.65        10.49        13.15        22.16        13.84 
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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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 
       13.91         7.82        11.51        29.95        15.62        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 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       13.74        71.01        80.02        65.36        84.89        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        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         0.99        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         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        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 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83         9.63         2.96         8.65        17.23 
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-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         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        86.70         6.02        19.73         6.74 
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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       20.25        12.89 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             7.82              0.10 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            98.56            169.32 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           54.080            20.335 
[1] "7.8 - 98.6 (54.1)"  "0.1 - 169.3 (20.3)"
[1] "hr="     "9200000"
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       51       108        2        46         6
D34V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 1               281
  STAGE II                1                51
  STAGE III               1               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
  1Q LOSS MUTATED     0   1   2   0
  1Q LOSS WILD-TYPE 141 165 165  23
D34V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               0               141
  T2               1               165
  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 222 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    0
  1Q LOSS WILD-TYPE  222  225
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               2               222
  1               0               225
[1] 2 2
[1] FALSE
D34V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   0
  1Q LOSS WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    0
  1Q LOSS WILD-TYPE  277    9
D34V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3   0
  1Q LOSS WILD-TYPE 363 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    0
  1Q LOSS WILD-TYPE  363  133
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               3               363
  MALE                 0               133
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  1Q LOSS MUTATED                0
  1Q LOSS WILD-TYPE              9
                   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                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  1Q LOSS MUTATED                                                                     0
  1Q LOSS WILD-TYPE                                                                  36
D34V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        355
  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"
D34V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   3
  1Q LOSS WILD-TYPE  14 482
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    3
  1Q LOSS WILD-TYPE   14  482
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                0                14
  YES               3               482
[1] 2 2
[1] FALSE
D34V10, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2   0
  1Q LOSS WILD-TYPE 419  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    0
  1Q LOSS WILD-TYPE  419   17
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                2               419
  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 378  52   4  30
D34V12, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               3               378
  R1               0                52
  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               381 
       TCGA-4C-A93U        TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        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-A28R        TCGA-BJ-A28T        TCGA-BJ-A28W        TCGA-BJ-A28X 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A45G        TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A3MD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A4M8        TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A4MD        TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13O        TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13V 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13W        TCGA-DJ-A13X        TCGA-DJ-A1QG        TCGA-DJ-A1QH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QM        TCGA-DJ-A2PO        TCGA-DJ-A2PP        TCGA-DJ-A2PQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PR        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-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ        TCGA-DJ-A3UR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UU        TCGA-DJ-A3UW        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-A3V4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3VA        TCGA-DJ-A3VB        TCGA-DJ-A3VD        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-A4UL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A4UP        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A4V2        TCGA-DJ-A4V5        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-E3-A3E5        TCGA-E8-A242 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-E8-A414        TCGA-E8-A415 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433        TCGA-E8-A436 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM        TCGA-EL-A3CN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        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-A3GQ        TCGA-EL-A3GS        TCGA-EL-A3GU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3TB        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-A3ZM        TCGA-EL-A3ZN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZO        TCGA-EL-A3ZP        TCGA-EL-A3ZS        TCGA-EL-A4JV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4K7        TCGA-EL-A4KD        TCGA-EL-A4KG        TCGA-EL-A4KI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A1CS        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A22I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L        TCGA-EM-A22M 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A22N        TCGA-EM-A22O        TCGA-EM-A22P        TCGA-EM-A22Q 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CN        TCGA-EM-A2CP        TCGA-EM-A2CQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2CS        TCGA-EM-A2CT        TCGA-EM-A2CU        TCGA-EM-A2OV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2OX        TCGA-EM-A2OY        TCGA-EM-A2OZ        TCGA-EM-A2P0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A2P2        TCGA-EM-A3AJ        TCGA-EM-A3AK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AQ 
"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-A3FL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3FM        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3FQ        TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3O9        TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3SU        TCGA-EM-A3SX        TCGA-EM-A3SZ        TCGA-EM-A4FF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A4FM        TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A4FR        TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2MX        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A39K        TCGA-ET-A39L        TCGA-ET-A39O 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3I4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON        TCGA-FY-A3R6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY        TCGA-FY-A3W9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        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-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-QD-A8IV 
"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   323
D34V16, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2               403 
       TCGA-4C-A93U        TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        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-A192        TCGA-BJ-A28R        TCGA-BJ-A28S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A28T        TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28X 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A2N8        TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3F0        TCGA-BJ-A3PR        TCGA-BJ-A3PT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A45F        TCGA-BJ-A45G        TCGA-BJ-A45H        TCGA-BJ-A45I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A45J        TCGA-BJ-A45K        TCGA-BJ-A4O8        TCGA-BJ-A4O9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CE-A13K        TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CE-A481        TCGA-CE-A482        TCGA-CE-A483        TCGA-CE-A484 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CE-A485        TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DE-A4M8        TCGA-DE-A4M9 
"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-A69J        TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13P        TCGA-DJ-A13R 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13S        TCGA-DJ-A13T        TCGA-DJ-A13U        TCGA-DJ-A13W 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QH        TCGA-DJ-A1QI        TCGA-DJ-A1QM        TCGA-DJ-A1QO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QQ        TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PR        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-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX        TCGA-DJ-A3UY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UZ        TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3VD        TCGA-DJ-A3VE        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-A3VM        TCGA-DJ-A4UL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A4UP        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A4UW        TCGA-DJ-A4V0        TCGA-DJ-A4V4        TCGA-DJ-A4V5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DO-A1JZ        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-E3-A3E5        TCGA-E8-A242        TCGA-E8-A2EA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A2JQ        TCGA-E8-A3X7        TCGA-E8-A413        TCGA-E8-A414 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A415        TCGA-E8-A416        TCGA-E8-A417        TCGA-E8-A418 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A419        TCGA-E8-A432        TCGA-E8-A433        TCGA-E8-A434 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A436        TCGA-E8-A437        TCGA-E8-A438        TCGA-E8-A44K 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A44M        TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS 
"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-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ        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-A3H2        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-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"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-A3BO        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-A3BV        TCGA-ET-A3BW        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-A3SD        TCGA-FK-A3SE        TCGA-FK-A3SG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA 
"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-FY-A76V        TCGA-GE-A2C6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        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-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-L6-A4ET        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-MK-A84Z        TCGA-QD-A8IV 
"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  38 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    2
  1Q LOSS WILD-TYPE   38  356
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               356
[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 473  14
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               487 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                14 
$`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         0.30         7.82 

$`2P LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        17.69        23.34        20.71         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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        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         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       34.85         5.52         8.78         8.42        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24         9.44        37.48        36.46        10.09         7.10 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        12.43        35.18        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       20.45        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        59.57        11.34        21.37        18.51 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        21.47        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        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        24.20        17.23        27.62        18.21 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        19.07        15.42        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
       14.04        31.23        22.29        11.70        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       14.27        13.81        14.07        14.27         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       130.72       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        78.97        31.50        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        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        37.94        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        12.36        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       57.01        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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        27.65        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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 
       13.91         7.82        11.51        29.95        15.62        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        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        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        81.34        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-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
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         0.99        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         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83         9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         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        86.70         6.02        19.73         6.74        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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        20.25 
TCGA-QD-A8IV 
       12.89 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              0.3               0.1 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            54.08            169.32 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            12.08             20.45 
[1] "0.3 - 54.1 (12.1)"  "0.1 - 169.3 (20.4)"
[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       47       108        2        46         6
D35V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 4               278
  STAGE II                5                47
  STAGE III               1               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
  2P LOSS MUTATED     3   5   2   0
  2P LOSS WILD-TYPE 138 161 165  23
D35V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               3               138
  T2               5               161
  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 216 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      8    0
  2P LOSS WILD-TYPE  216  225
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               8               216
  1               0               225
[1] 2 2
[1] FALSE
D35V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1   0
  2P LOSS WILD-TYPE 276   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1    0
  2P LOSS WILD-TYPE  276    9
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               1               276
  1               0                 9
[1] 2 2
[1] FALSE
D35V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     7   3
  2P LOSS WILD-TYPE 359 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7    3
  2P LOSS WILD-TYPE  359  130
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               7               359
  MALE                 3               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  2P LOSS MUTATED                0
  2P LOSS WILD-TYPE              9
                   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                                                                     91
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  2P LOSS MUTATED                                                                     0
  2P LOSS WILD-TYPE                                                                  36
D35V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        353
  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"
D35V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  10
  2P LOSS WILD-TYPE  14 475
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   10
  2P LOSS WILD-TYPE   14  475
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                0                14
  YES              10               475
[1] 2 2
[1] FALSE
D35V10, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     9   0
  2P LOSS WILD-TYPE 412  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      9    0
  2P LOSS WILD-TYPE  412   17
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                9               412
  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 372  52   4  29
D35V12, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               9               372
  R1               0                52
  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   321
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               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"
D35V17, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0   4
  2P LOSS WILD-TYPE  38 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    4
  2P LOSS WILD-TYPE   38  354
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               4               354
[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 473  14
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               487 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                0                14 
$`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        98.56         7.82 

$`2Q LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        17.69        23.34        20.71         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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        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         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       34.85         5.52         8.78         8.42        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24         9.44        37.48        36.46        10.09         7.10 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        12.43        35.18        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       20.45        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        59.57        11.34        21.37        18.51 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        21.47        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        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        24.20        17.23        27.62        18.21 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        19.07        15.42        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
       14.04        31.23        22.29        11.70        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       14.27        13.81        14.07        14.27         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       130.72       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        78.97        31.50        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        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        37.94        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        12.36        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       57.01        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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        27.65        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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 
       13.91         7.82        11.51        29.95        15.62        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        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        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        81.34        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-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
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         0.99        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         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83         9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         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        86.70         6.02        19.73         6.74        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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        20.25 
TCGA-QD-A8IV 
       12.89 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             6.05              0.10 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            98.56            169.32 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           17.045            20.420 
[1] "6.0 - 98.6 (17.0)"  "0.1 - 169.3 (20.4)"
[1] "hr="     "9200000"
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       47       108        2        46         6
D36V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 4               278
  STAGE II                5                47
  STAGE III               1               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
  2Q LOSS MUTATED     2   5   3   0
  2Q LOSS WILD-TYPE 139 161 164  23
D36V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               2               139
  T2               5               161
  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 217 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    0
  2Q LOSS WILD-TYPE  217  225
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               7               217
  1               0               225
[1] 2 2
[1] FALSE
D36V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1   0
  2Q LOSS WILD-TYPE 276   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    0
  2Q LOSS WILD-TYPE  276    9
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               1               276
  1               0                 9
[1] 2 2
[1] FALSE
D36V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7   3
  2Q LOSS WILD-TYPE 359 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    3
  2Q LOSS WILD-TYPE  359  130
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               7               359
  MALE                 3               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  2Q LOSS MUTATED                0
  2Q LOSS WILD-TYPE              9
                   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                                                                     91
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  2Q LOSS MUTATED                                                                     0
  2Q LOSS WILD-TYPE                                                                  36
D36V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        353
  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"
D36V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  10
  2Q LOSS WILD-TYPE  14 475
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   10
  2Q LOSS WILD-TYPE   14  475
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                0                14
  YES              10               475
[1] 2 2
[1] FALSE
D36V10, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     9   0
  2Q LOSS WILD-TYPE 412  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      9    0
  2Q LOSS WILD-TYPE  412   17
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                9               412
  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 372  52   4  29
D36V12, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               9               372
  R1               0                52
  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   321
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               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"
D36V17, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0   4
  2Q LOSS WILD-TYPE  38 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    4
  2Q LOSS WILD-TYPE   38  354
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               4               354
[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 480  14
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               494 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                0                14 
$`3P LOSS MUTATED`
TCGA-BJ-A190 TCGA-ET-A39N TCGA-FY-A3I5 
       20.58        98.56         7.82 

$`3P LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        17.69        23.34        20.71         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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        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         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        52.50        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        37.94 
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        12.36        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-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        11.74        11.15        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       16.44        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        27.65        10.49        13.15        22.16        13.84 
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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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 
       13.91         7.82        11.51        29.95        15.62        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 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       13.74        71.01        80.02        65.36        84.89        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        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         0.99        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         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        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 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83         9.63         2.96         8.65        17.23 
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-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         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        86.70         6.02        19.73         6.74 
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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       20.25        12.89 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             7.82              0.10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            98.56            169.32 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           20.580            20.335 
[1] "7.8 - 98.6 (20.6)"  "0.1 - 169.3 (20.3)"
[1] "hr="     "9100000"
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       51       108        2        46         6
D37V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 1               281
  STAGE II                1                51
  STAGE III               1               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
  3P LOSS MUTATED     0   1   2   0
  3P LOSS WILD-TYPE 141 165 165  23
D37V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               0               141
  T2               1               165
  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 222 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    0
  3P LOSS WILD-TYPE  222  225
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               2               222
  1               0               225
[1] 2 2
[1] FALSE
D37V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0   0
  3P LOSS WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    0
  3P LOSS WILD-TYPE  277    9
D37V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2   1
  3P LOSS WILD-TYPE 364 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    1
  3P LOSS WILD-TYPE  364  132
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               2               364
  MALE                 1               132
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  3P LOSS MUTATED                0
  3P LOSS WILD-TYPE              9
                   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                                                                     97
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  3P LOSS MUTATED                                                                     0
  3P LOSS WILD-TYPE                                                                  36
D37V8, 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                                                                         9
  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"
D37V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0   3
  3P LOSS WILD-TYPE  14 482
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    3
  3P LOSS WILD-TYPE   14  482
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                0                14
  YES               3               482
[1] 2 2
[1] FALSE
D37V10, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2   0
  3P LOSS WILD-TYPE 419  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    0
  3P LOSS WILD-TYPE  419   17
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                2               419
  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 378  52   4  30
D37V12, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               3               378
  R1               0                52
  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               381 
       TCGA-4C-A93U        TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A28R 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A28T        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N8        TCGA-BJ-A2N9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR        TCGA-BJ-A3PU 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K        TCGA-BJ-A4O8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A3MD        TCGA-DE-A0XZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN        TCGA-DE-A4M8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13V        TCGA-DJ-A13W 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A13X        TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2PO        TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2PS        TCGA-DJ-A2PT        TCGA-DJ-A2PU        TCGA-DJ-A2PV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2PW        TCGA-DJ-A2PX        TCGA-DJ-A2PY        TCGA-DJ-A2PZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN        TCGA-DJ-A3UO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3UP        TCGA-DJ-A3UQ        TCGA-DJ-A3UR        TCGA-DJ-A3UU 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3UW        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-A3V4        TCGA-DJ-A3V5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9        TCGA-DJ-A3VA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3VB        TCGA-DJ-A3VD        TCGA-DJ-A3VF        TCGA-DJ-A3VG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A4UL        TCGA-DJ-A4UP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW        TCGA-DJ-A4V2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A4V5        TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A242        TCGA-E8-A2EA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E8-A2JQ        TCGA-E8-A414        TCGA-E8-A415        TCGA-E8-A417 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E8-A419        TCGA-E8-A433        TCGA-E8-A436        TCGA-E8-A438 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E8-A44K        TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3D5        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-A3GQ        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0        TCGA-EL-A3T1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3T2        TCGA-EL-A3TB        TCGA-EL-A3ZH        TCGA-EL-A3ZK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3ZL        TCGA-EL-A3ZM        TCGA-EL-A3ZN        TCGA-EL-A3ZO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3ZP        TCGA-EL-A3ZS        TCGA-EL-A4JV        TCGA-EL-A4JW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A4KD        TCGA-EL-A4KG        TCGA-EL-A4KI        TCGA-EM-A1CS 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A1YE        TCGA-EM-A22I 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L        TCGA-EM-A22M 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A22N        TCGA-EM-A22O        TCGA-EM-A22P        TCGA-EM-A22Q 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CN        TCGA-EM-A2CP        TCGA-EM-A2CQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2CS        TCGA-EM-A2CT        TCGA-EM-A2CU        TCGA-EM-A2OV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2OX        TCGA-EM-A2OY        TCGA-EM-A2OZ        TCGA-EM-A2P0 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2P1        TCGA-EM-A2P2        TCGA-EM-A3AJ        TCGA-EM-A3AK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AQ 
"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-A3FL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3FM        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3FQ        TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3O9        TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3SU        TCGA-EM-A3SX        TCGA-EM-A3SZ        TCGA-EM-A4FF 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A4FM        TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A4FR        TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A2MX        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A39K        TCGA-ET-A39L        TCGA-ET-A39O 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3I4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON        TCGA-FY-A3R6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY        TCGA-FY-A3W9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        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-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-QD-A8IV 
"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   322
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               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"
D37V17, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0   3
  3P LOSS WILD-TYPE  38 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    3
  3P LOSS WILD-TYPE   38  355
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               355
[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 479  14
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               493 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                14 
$`3Q LOSS MUTATED`
TCGA-BJ-A190 TCGA-EM-A1YE TCGA-ET-A39N TCGA-FY-A3I5 
       20.58        54.08        98.56         7.82 

$`3Q LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        17.69        23.34        20.71         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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        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         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        52.50        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        37.94 
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        12.36        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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        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        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        29.95        15.62        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        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        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        81.34        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-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
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         0.99        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         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83         9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         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        86.70         6.02        19.73         6.74        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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        20.25 
TCGA-QD-A8IV 
       12.89 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             7.82              0.10 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            98.56            169.32 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            37.33             20.25 
[1] "7.8 - 98.6 (37.3)"  "0.1 - 169.3 (20.2)"
[1] "hr="     "9200000"
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       50       108        2        46         6
D38V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 1               281
  STAGE II                2                50
  STAGE III               1               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
  3Q LOSS MUTATED     0   2   2   0
  3Q LOSS WILD-TYPE 141 164 165  23
D38V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0               141
  T2               2               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"
D38V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3   0
  3Q LOSS WILD-TYPE 221 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    0
  3Q LOSS WILD-TYPE  221  225
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               3               221
  1               0               225
[1] 2 2
[1] FALSE
D38V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   0
  3Q LOSS WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    0
  3Q LOSS WILD-TYPE  277    9
D38V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3   1
  3Q LOSS WILD-TYPE 363 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    1
  3Q LOSS WILD-TYPE  363  132
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               3               363
  MALE                 1               132
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  3Q LOSS MUTATED                0
  3Q LOSS WILD-TYPE              9
                   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                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  3Q LOSS MUTATED                                                                     0
  3Q LOSS WILD-TYPE                                                                  36
D38V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  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"
D38V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   4
  3Q LOSS WILD-TYPE  14 481
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    4
  3Q LOSS WILD-TYPE   14  481
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                0                14
  YES               4               481
[1] 2 2
[1] FALSE
D38V10, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3   0
  3Q LOSS WILD-TYPE 418  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    0
  3Q LOSS WILD-TYPE  418   17
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                3               418
  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 377  52   4  30
D38V12, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               4               377
  R1               0                52
  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   322
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               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"
D38V17, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   3
  3Q LOSS WILD-TYPE  38 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    3
  3Q LOSS WILD-TYPE   38  355
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               355
[1] 2 2
[1] FALSE

Clustering(39) Variable = 6P LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED     3   0
  6P LOSS WILD-TYPE 480  14
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                3               494 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                0                14 
$`6P LOSS MUTATED`
TCGA-ET-A39N TCGA-ET-A3BV TCGA-FY-A3I5 
       98.56        42.25         7.82 

$`6P LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       130.72 
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        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        52.50        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 
       37.94        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        12.36        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        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        16.44        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        27.65        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       13.84        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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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        13.91         7.82        11.51        29.95        15.62 
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        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        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         0.99        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         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        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 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83         9.63         2.96         8.65        17.23 
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-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         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        86.70         6.02        19.73         6.74 
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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       20.25        12.89 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             7.82              0.10 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            98.56            169.32 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           42.250            20.335 
[1] "7.8 - 98.6 (42.2)"  "0.1 - 169.3 (20.3)"
[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       52       107        2        46         6
D39V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 2               280
  STAGE II                0                52
  STAGE III               2               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
  6P LOSS MUTATED     1   1   2   0
  6P LOSS WILD-TYPE 140 165 165  23
D39V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               1               140
  T2               1               165
  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 223 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1    1
  6P LOSS WILD-TYPE  223  224
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0               1               223
  1               1               224
[1] 2 2
[1] FALSE
D39V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0   0
  6P LOSS WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    0
  6P LOSS WILD-TYPE  277    9
D39V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     3   1
  6P LOSS WILD-TYPE 363 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3    1
  6P LOSS WILD-TYPE  363  132
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               3               363
  MALE                 1               132
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  6P LOSS MUTATED                0
  6P LOSS WILD-TYPE              9
                   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                                                                     97
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  6P LOSS MUTATED                                                                     0
  6P LOSS WILD-TYPE                                                                  36
D39V8, 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                                                                         9
  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"
D39V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0   4
  6P LOSS WILD-TYPE  14 481
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    4
  6P LOSS WILD-TYPE   14  481
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                0                14
  YES               4               481
[1] 2 2
[1] FALSE
D39V10, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     3   0
  6P LOSS WILD-TYPE 418  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3    0
  6P LOSS WILD-TYPE  418   17
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                3               418
  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 378  51   4  30
D39V12, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0               3               378
  R1               1                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"
D39V13, continuous
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2               381 
       TCGA-4C-A93U        TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        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-A290        TCGA-BJ-A291        TCGA-BJ-A2N8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A45G        TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A3MD 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DE-A4M8        TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DE-A4MD        TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A13O        TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13V 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A13W        TCGA-DJ-A13X        TCGA-DJ-A1QG        TCGA-DJ-A1QH 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A1QM        TCGA-DJ-A2PO        TCGA-DJ-A2PP        TCGA-DJ-A2PQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PT        TCGA-DJ-A2PU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX        TCGA-DJ-A2PY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ        TCGA-DJ-A3UR 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX        TCGA-DJ-A3UZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3V0        TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3VA        TCGA-DJ-A3VB        TCGA-DJ-A3VD        TCGA-DJ-A3VF 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A4UL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A4UP        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A4V2        TCGA-DJ-A4V5        TCGA-DO-A1K0        TCGA-DO-A2HM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A242 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E8-A2EA        TCGA-E8-A2JQ        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-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GS        TCGA-EL-A3GU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3TB        TCGA-EL-A3ZH 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3ZK        TCGA-EL-A3ZL        TCGA-EL-A3ZM        TCGA-EL-A3ZN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3ZO        TCGA-EL-A3ZP        TCGA-EL-A3ZS        TCGA-EL-A4JV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A4K7        TCGA-EL-A4KD        TCGA-EL-A4KG        TCGA-EL-A4KI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1CS        TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1CW        TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A1YE 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22N        TCGA-EM-A22O        TCGA-EM-A22P 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A22Q        TCGA-EM-A2CK        TCGA-EM-A2CN        TCGA-EM-A2CP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2CQ        TCGA-EM-A2CS        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-A3AQ        TCGA-EM-A3AR        TCGA-EM-A3FJ        TCGA-EM-A3FK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3FL        TCGA-EM-A3FM        TCGA-EM-A3FN        TCGA-EM-A3FO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3FP        TCGA-EM-A3FQ        TCGA-EM-A3FR        TCGA-EM-A3O3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3O8        TCGA-EM-A3O9        TCGA-EM-A3OA        TCGA-EM-A3OB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3ST        TCGA-EM-A3SU        TCGA-EM-A3SX        TCGA-EM-A3SZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A4FF        TCGA-EM-A4FM        TCGA-EM-A4FN        TCGA-EM-A4FO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A4FQ        TCGA-EM-A4FR        TCGA-EM-A4FV        TCGA-EM-A4G1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A25P        TCGA-ET-A2MX        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A39K        TCGA-ET-A39L 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A39O        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39S 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A39T        TCGA-ET-A3BO        TCGA-ET-A3BP        TCGA-ET-A3BQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3I4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON        TCGA-FY-A3R6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY        TCGA-FY-A3W9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        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-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-QD-A8IV 
"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   321
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               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"
D39V17, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0   4
  6P LOSS WILD-TYPE  38 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    4
  6P LOSS WILD-TYPE   38  354
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               4               354
[1] 2 2
[1] FALSE

Clustering(40) Variable = 6Q LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED     4   2
  6Q LOSS WILD-TYPE 479  12
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                6               491 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                12 
$`6Q LOSS MUTATED`
TCGA-EL-A3H2 TCGA-EM-A1YE TCGA-ET-A39N TCGA-ET-A3BV TCGA-FE-A239 TCGA-FY-A3I5 
       33.50        54.08        98.56        42.25        33.63         7.82 

$`6Q LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        50.24       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-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        52.50        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        37.94 
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        12.36        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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        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        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        29.95        15.62        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        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
        2.43         5.56        24.72        38.30         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       81.34        39.95        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        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         0.99 
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 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        19.73         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        20.25        12.89 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             7.82              0.10 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            98.56            169.32 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            37.94             20.22 
[1] "7.8 - 98.6 (37.9)"  "0.1 - 169.3 (20.2)"
[1] "hr=" "7.6"
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       50       106        2        46         6
D40V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 2               280
  STAGE II                2                50
  STAGE III               3               106
  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 140 163 164  23
D40V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               1               140
  T2               3               163
  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 220 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    1
  6Q LOSS WILD-TYPE  220  224
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0               4               220
  1               1               224
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     0   0
  6Q LOSS WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0    0
  6Q LOSS WILD-TYPE  277    9
D40V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     4   3
  6Q LOSS WILD-TYPE 362 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    3
  6Q LOSS WILD-TYPE  362  130
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               4               362
  MALE                 3               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  6Q LOSS MUTATED                0
  6Q LOSS WILD-TYPE              9
                   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                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  6Q LOSS MUTATED                                                                     0
  6Q LOSS WILD-TYPE                                                                  36
D40V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        351
  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"
D40V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1   6
  6Q LOSS WILD-TYPE  13 479
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1    6
  6Q LOSS WILD-TYPE   13  479
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                1                13
  YES               6               479
[1] 2 2
[1] FALSE
D40V10, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     5   1
  6Q LOSS WILD-TYPE 416  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5    1
  6Q LOSS WILD-TYPE  416   16
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                5               416
  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 375  51   4  30
D40V12, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0               6               375
  R1               1                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"
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   319
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               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"
D40V17, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     0   6
  6Q LOSS WILD-TYPE  38 352
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0    6
  6Q LOSS WILD-TYPE   38  352
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               6               352
[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 479  14
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4               493 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                14 
$`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-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        17.69        23.34        20.71         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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        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         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       34.85         5.52         8.78         8.42        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24         9.44        37.48        36.46        10.09         7.10 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        12.43        35.18        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       20.45        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        59.57        11.34        21.37        18.51 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        21.47        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        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        24.20        17.23        27.62        18.21 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        19.07        15.42        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
       14.04        31.23        22.29        11.70        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       14.27        13.81        14.07        14.27         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       130.72       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        78.97        31.50        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        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        37.94        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        12.36        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-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        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        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        29.95        15.62        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        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        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 
       81.34        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        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         0.99        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         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83         9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         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        86.70         6.02        19.73         6.74        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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        20.25 
TCGA-QD-A8IV 
       12.89 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             9.24              0.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            34.36            169.32 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           17.045            20.420 
[1] "9.2 - 34.4 (17.0)"  "0.1 - 169.3 (20.4)"
[1] "hr="     "3300000"
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       50       109        2        46         6
D41V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 2               280
  STAGE II                2                50
  STAGE III               0               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 LOSS MUTATED     1   2   1   0
  8P LOSS WILD-TYPE 140 164 166  23
D41V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               1               140
  T2               2               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"
D41V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     3   0
  8P LOSS WILD-TYPE 221 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    0
  8P LOSS WILD-TYPE  221  225
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               3               221
  1               0               225
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1   0
  8P LOSS WILD-TYPE 276   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    0
  8P LOSS WILD-TYPE  276    9
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               1               276
  1               0                 9
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1   3
  8P LOSS WILD-TYPE 365 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    3
  8P LOSS WILD-TYPE  365  130
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               1               365
  MALE                 3               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  8P LOSS MUTATED                0
  8P LOSS WILD-TYPE              9
                   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                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  8P LOSS MUTATED                                                                     0
  8P LOSS WILD-TYPE                                                                  36
D41V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  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"
D41V9, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     0   4
  8P LOSS WILD-TYPE  14 481
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0    4
  8P LOSS WILD-TYPE   14  481
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                0                14
  YES               4               481
[1] 2 2
[1] FALSE
D41V10, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     4   0
  8P LOSS WILD-TYPE 417  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    0
  8P LOSS WILD-TYPE  417   17
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                4               417
  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 377  52   4  30
D41V12, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0               4               377
  R1               0                52
  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   323
D41V16, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2               403 
       TCGA-4C-A93U        TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZJ        TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4        TCGA-BJ-A3EZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A3F0        TCGA-BJ-A3PR        TCGA-BJ-A3PT        TCGA-BJ-A3PU 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45F 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A45G        TCGA-BJ-A45H        TCGA-BJ-A45I        TCGA-BJ-A45J 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A45K        TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CE-A482        TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DE-A3KN        TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13L        TCGA-DJ-A13M 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A13O        TCGA-DJ-A13P        TCGA-DJ-A13R        TCGA-DJ-A13S 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A13T        TCGA-DJ-A13U        TCGA-DJ-A13W        TCGA-DJ-A1QD 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG        TCGA-DJ-A1QH 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A1QI        TCGA-DJ-A1QM        TCGA-DJ-A1QO        TCGA-DJ-A1QQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PQ        TCGA-DJ-A2PR 
"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-A3UU        TCGA-DJ-A3UW 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3UX        TCGA-DJ-A3UY        TCGA-DJ-A3UZ        TCGA-DJ-A3V2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3V3        TCGA-DJ-A3V4        TCGA-DJ-A3V5        TCGA-DJ-A3V7 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3V8        TCGA-DJ-A3V9        TCGA-DJ-A3VD        TCGA-DJ-A3VE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3VM        TCGA-DJ-A4UL        TCGA-DJ-A4UP        TCGA-DJ-A4UQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A4UR        TCGA-DJ-A4UT        TCGA-DJ-A4UW        TCGA-DJ-A4V0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A4V4        TCGA-DJ-A4V5        TCGA-DO-A1JZ        TCGA-DO-A1K0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DO-A2HM        TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E3-A3E1        TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E3-A3E5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-E8-A3X7 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A413        TCGA-E8-A414        TCGA-E8-A415        TCGA-E8-A416 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A418        TCGA-E8-A419        TCGA-E8-A432 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A433        TCGA-E8-A434        TCGA-E8-A436        TCGA-E8-A437 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-E8-A44M        TCGA-EL-A3CL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        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-A3CY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GQ        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-A3H2        TCGA-EL-A3H3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        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-A3BO 
"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-A3BV        TCGA-ET-A3BW        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-A3SD        TCGA-FK-A3SE        TCGA-FK-A3SG        TCGA-FK-A3SH 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3I4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A3I5        TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA 
"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-FY-A76V        TCGA-GE-A2C6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-L6-A4ET        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-MK-A84Z        TCGA-QD-A8IV 
"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  38 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0    2
  8P LOSS WILD-TYPE   38  356
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               356
[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 479  14
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               493 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                14 
$`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-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        17.69        23.34        20.71         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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        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         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       34.85         5.52         8.78         8.42        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24         9.44        37.48        36.46        10.09         7.10 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        12.43        35.18        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       20.45        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        59.57        11.34        21.37        18.51 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        21.47        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        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        24.20        17.23        27.62        18.21 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        19.07        15.42        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
       14.04        31.23        22.29        11.70        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       14.27        13.81        14.07        14.27         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       130.72       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        78.97        31.50        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        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        37.94        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        12.36        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-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        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        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        29.95        15.62        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        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        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 
       81.34        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        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         0.99        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         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83         9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         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        86.70         6.02        19.73         6.74        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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        20.25 
TCGA-QD-A8IV 
       12.89 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             9.24              0.10 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            34.36            169.32 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           17.045            20.420 
[1] "9.2 - 34.4 (17.0)"  "0.1 - 169.3 (20.4)"
[1] "hr="     "3300000"
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       50       109        2        46         6
D42V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 2               280
  STAGE II                2                50
  STAGE III               0               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
  8Q LOSS MUTATED     1   2   1   0
  8Q LOSS WILD-TYPE 140 164 166  23
D42V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               1               140
  T2               2               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"
D42V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     3   0
  8Q LOSS WILD-TYPE 221 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    0
  8Q LOSS WILD-TYPE  221  225
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               3               221
  1               0               225
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1   0
  8Q LOSS WILD-TYPE 276   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    0
  8Q LOSS WILD-TYPE  276    9
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               1               276
  1               0                 9
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1   3
  8Q LOSS WILD-TYPE 365 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    3
  8Q LOSS WILD-TYPE  365  130
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               1               365
  MALE                 3               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  8Q LOSS MUTATED                0
  8Q LOSS WILD-TYPE              9
                   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                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  8Q LOSS MUTATED                                                                     0
  8Q LOSS WILD-TYPE                                                                  36
D42V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        354
  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"
D42V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0   4
  8Q LOSS WILD-TYPE  14 481
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    4
  8Q LOSS WILD-TYPE   14  481
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                14
  YES               4               481
[1] 2 2
[1] FALSE
D42V10, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     4   0
  8Q LOSS WILD-TYPE 417  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      4    0
  8Q LOSS WILD-TYPE  417   17
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                4               417
  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 377  52   4  30
D42V12, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               4               377
  R1               0                52
  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   323
D42V16, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               403 
       TCGA-4C-A93U        TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A0ZJ        TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4        TCGA-BJ-A3EZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A3F0        TCGA-BJ-A3PR        TCGA-BJ-A3PT        TCGA-BJ-A3PU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A45G        TCGA-BJ-A45H        TCGA-BJ-A45I        TCGA-BJ-A45J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A45K        TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CE-A482        TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DE-A3KN        TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13L        TCGA-DJ-A13M 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A13O        TCGA-DJ-A13P        TCGA-DJ-A13R        TCGA-DJ-A13S 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A13T        TCGA-DJ-A13U        TCGA-DJ-A13W        TCGA-DJ-A1QD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG        TCGA-DJ-A1QH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QI        TCGA-DJ-A1QM        TCGA-DJ-A1QO        TCGA-DJ-A1QQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PQ        TCGA-DJ-A2PR 
"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-A3UU        TCGA-DJ-A3UW 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UX        TCGA-DJ-A3UY        TCGA-DJ-A3UZ        TCGA-DJ-A3V2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V3        TCGA-DJ-A3V4        TCGA-DJ-A3V5        TCGA-DJ-A3V7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V8        TCGA-DJ-A3V9        TCGA-DJ-A3VD        TCGA-DJ-A3VE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3VM        TCGA-DJ-A4UL        TCGA-DJ-A4UP        TCGA-DJ-A4UQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A4UR        TCGA-DJ-A4UT        TCGA-DJ-A4UW        TCGA-DJ-A4V0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A4V4        TCGA-DJ-A4V5        TCGA-DO-A1JZ        TCGA-DO-A1K0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DO-A2HM        TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E3-A3E1        TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E3-A3E5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-E8-A3X7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A413        TCGA-E8-A414        TCGA-E8-A415        TCGA-E8-A416 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A418        TCGA-E8-A419        TCGA-E8-A432 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A433        TCGA-E8-A434        TCGA-E8-A436        TCGA-E8-A437 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-E8-A44M        TCGA-EL-A3CL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        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-A3CY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GQ        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-A3H2        TCGA-EL-A3H3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        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-A3BO 
"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-A3BV        TCGA-ET-A3BW        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-A3SD        TCGA-FK-A3SE        TCGA-FK-A3SG        TCGA-FK-A3SH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3I4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A3I5        TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA 
"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-FY-A76V        TCGA-GE-A2C6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-L6-A4ET        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-MK-A84Z        TCGA-QD-A8IV 
"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  38 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    2
  8Q LOSS WILD-TYPE   38  356
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               356
[1] 2 2
[1] FALSE

Clustering(43) Variable = 9P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    17   1
  9P LOSS WILD-TYPE 466  13
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               18               479 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                1                13 
$`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        14.43         1.41        57.63 
TCGA-EL-A3ZK TCGA-EL-A3ZO TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1YE TCGA-EM-A2OY 
       31.50        47.38        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        98.56         0.92        22.49 

$`9P LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N9 
       17.52         1.22        30.21        22.88        18.38        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       34.85         5.52         8.78         8.42        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24         9.44        37.48        36.46        10.09         7.10 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        12.43        35.18        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       20.45        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        59.57        11.34        21.37        18.51 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        21.47        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        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        24.20        17.23        27.62        18.21 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        19.07        15.42        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY 
        3.12        15.81        24.33        54.90        21.53        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       31.23        22.29        11.70        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 
       13.81        14.07        14.27         3.02        25.45        14.70 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       14.10        14.96         7.69        20.68        13.78        13.58 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
       31.66        26.73       155.54        97.74       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
       45.53        60.95       157.15        37.94        57.01        80.91 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        58.82       139.86        98.53        45.40        57.11 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        50.24       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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        49.71        83.57       139.00       131.15 
TCGA-EL-A3MW TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
      108.66        17.52        52.50        29.65       147.42       130.72 
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-A3ZL 
        5.72        66.90        82.82        89.56        78.97        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       36.03        53.06        52.50        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        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       34.39        30.51        53.36        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        12.36 
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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        27.65        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       16.18        15.02        15.06         7.33        12.53        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       80.02        65.36        84.89        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        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 
       81.34        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        22.03 
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 
        0.99        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         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        6.58        19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        19.73         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        20.25        12.89 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.92              0.10 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            98.56            169.32 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           23.195            20.250 
[1] "0.9 - 98.6 (23.2)"  "0.1 - 169.3 (20.2)"
[1] "hr=" "2.2"
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       48       105        1        45         5
D43V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 8               274
  STAGE II                4                48
  STAGE III               4               105
  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 136 159 162  21
D43V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               5               136
  T2               7               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"
D43V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     8   8
  9P LOSS WILD-TYPE 216 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      8    8
  9P LOSS WILD-TYPE  216  217
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0               8               216
  1               8               217
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     6   1
  9P LOSS WILD-TYPE 271   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6    1
  9P LOSS WILD-TYPE  271    8
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0               6               271
  1               1                 8
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    12   7
  9P LOSS WILD-TYPE 354 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     12    7
  9P LOSS WILD-TYPE  354  126
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              12               354
  MALE                 7               126
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  9P LOSS MUTATED                0
  9P LOSS WILD-TYPE              9
                   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                                                                     94
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  9P LOSS MUTATED                                                                     0
  9P LOSS WILD-TYPE                                                                  36
D43V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        341
  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"
D43V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     0  19
  9P LOSS WILD-TYPE  14 466
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0   19
  9P LOSS WILD-TYPE   14  466
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                0                14
  YES              19               466
[1] 2 2
[1] FALSE
D43V10, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    18   0
  9P LOSS WILD-TYPE 403  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     18    0
  9P LOSS WILD-TYPE  403   17
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               18               403
  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 366  51   4  28
D43V12, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              15               366
  R1               1                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"
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   313
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               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"
D43V17, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     0  14
  9P LOSS WILD-TYPE  38 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0   14
  9P LOSS WILD-TYPE   38  344
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO              14               344
[1] 2 2
[1] FALSE

Clustering(44) Variable = 9Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    22   2
  9Q LOSS WILD-TYPE 461  12
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               24               473 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                12 
$`9Q LOSS MUTATED`
TCGA-4C-A93U TCGA-BJ-A2N8 TCGA-DE-A4MB TCGA-DJ-A13L TCGA-DJ-A2Q0 TCGA-DO-A2HM 
        4.24        16.57        11.57         9.96        34.36         2.33 
TCGA-E8-A432 TCGA-EL-A3GP TCGA-EL-A3MX TCGA-EL-A3T9 TCGA-EL-A3ZK TCGA-EL-A3ZO 
       14.43         1.41        57.63         5.72        31.50        47.38 
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        98.56        31.59         0.92        22.49 

$`9Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
        1.22        30.21        22.88        18.38        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75        10.88        21.01         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18        21.63         8.98         4.93        23.47         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A4MD 
       15.85        18.54        18.84        30.12        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        17.26        14.07       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        56.19        23.38        18.35        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        11.01       135.91        30.61        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33        35.41        27.45        26.20 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
       38.83        12.56         8.28        34.85         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.42        37.74         6.77        40.24         9.44        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        10.09         7.10        35.90        12.43        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        20.45        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
       19.56        36.33        32.81        24.23        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        21.37        18.51        36.99        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       21.47        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        21.01        18.97         7.76         8.32        24.20 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        18.21        21.34        19.07        15.42 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       54.90        21.53        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        25.45        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ 
       98.53        45.40        57.11       108.36        64.87        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MY TCGA-EL-A3MZ 
       83.57       139.00       131.15       108.66        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       29.65       147.42       130.72       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-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       78.97        62.30        36.03        53.06        52.50        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-A4K7 
       37.94        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-A1YC TCGA-EM-A1YD 
       20.91        12.36        18.05        19.79        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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        27.65        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        13.84        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-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        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 
       13.91         7.82        11.51        29.95        15.62        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        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       59.70        44.25        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 
       81.34        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        22.03 
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 
        0.99        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         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        6.58        19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        19.73         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        20.25        12.89 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.92              0.10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            98.56            169.32 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           18.015            20.450 
[1] "0.9 - 98.6 (18.0)"  "0.1 - 169.3 (20.4)"
[1] "hr=" "4.4"
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       47       105        0        42         5
D44V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 9               273
  STAGE II                5                47
  STAGE III               4               105
  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 135 158 160  19
D44V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               6               135
  T2               8               158
  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 215 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9   12
  9Q LOSS WILD-TYPE  215  213
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0               9               215
  1              12               213
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     9   1
  9Q LOSS WILD-TYPE 268   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9    1
  9Q LOSS WILD-TYPE  268    8
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0               9               268
  1               1                 8
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    16   9
  9Q LOSS WILD-TYPE 350 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     16    9
  9Q LOSS WILD-TYPE  350  124
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              16               350
  MALE                 9               124
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  9Q LOSS MUTATED                0
  9Q LOSS WILD-TYPE              9
                   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                                                                     93
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  9Q LOSS MUTATED                                                                     1
  9Q LOSS WILD-TYPE                                                                  35
D44V8, 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                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        337
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                93
  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"
D44V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     1  24
  9Q LOSS WILD-TYPE  13 461
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   24
  9Q LOSS WILD-TYPE   13  461
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                1                13
  YES              24               461
[1] 2 2
[1] FALSE
D44V10, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    23   1
  9Q LOSS WILD-TYPE 398  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     23    1
  9Q LOSS WILD-TYPE  398   16
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               23               398
  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 362  49   4  28
D44V12, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              19               362
  R1               3                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"
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   309
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               309
[1] 4 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  37 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   18
  9Q LOSS WILD-TYPE   37  340
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                37
  NOT HISPANIC OR LATINO              18               340
[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 476  14
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                490 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 0                 14 
$`10P LOSS MUTATED`
TCGA-BJ-A190 TCGA-E8-A432 TCGA-EL-A4KI TCGA-EM-A1YE TCGA-EM-A3O9 TCGA-ET-A39N 
       20.58        14.43        23.90        54.08         9.24        98.56 
TCGA-FY-A3I5 
        7.82 

$`10P LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        17.69        23.34        20.71         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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        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         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       25.45        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       130.72       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        78.97        31.50        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        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        37.94        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-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 
       12.36        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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        27.65        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        32.32        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-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        16.80        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        13.91         7.82        11.51        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       15.62        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        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       54.05        22.09        12.26        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        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         0.99        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         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        17.23        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-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       19.73         6.74        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        20.25        12.89 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              7.82               0.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             98.56             169.32 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            20.580             20.335 
[1] "7.8 - 98.6 (20.6)"  "0.1 - 169.3 (20.3)"
[1] "hr="     "9200000"
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       49       107        2        46         6
D45V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  2                280
  STAGE II                 3                 49
  STAGE III                2                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
  10P LOSS MUTATED     0   3   4   0
  10P LOSS WILD-TYPE 141 163 163  23
D45V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                0                141
  T2                3                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"
D45V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     6   0
  10P LOSS WILD-TYPE 218 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6    0
  10P LOSS WILD-TYPE  218  225
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                6                218
  1                0                225
[1] 2 2
[1] FALSE
D45V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1   0
  10P LOSS WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    0
  10P LOSS WILD-TYPE  276    9
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                1                276
  1                0                  9
[1] 2 2
[1] FALSE
D45V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4   3
  10P LOSS WILD-TYPE 362 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4    3
  10P LOSS WILD-TYPE  362  130
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                4                362
  MALE                  3                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  10P LOSS MUTATED                0
  10P LOSS WILD-TYPE              9
                    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                                                                     95
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  10P LOSS MUTATED                                                                     0
  10P LOSS WILD-TYPE                                                                  36
D45V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         352
  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"
D45V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     0   7
  10P LOSS WILD-TYPE  14 478
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0    7
  10P LOSS WILD-TYPE   14  478
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 0                 14
  YES                7                478
[1] 2 2
[1] FALSE
D45V10, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     6   0
  10P LOSS WILD-TYPE 415  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6    0
  10P LOSS WILD-TYPE  415   17
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 6                415
  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 374  52   4  30
D45V12, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0                7                374
  R1                0                 52
  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   321
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                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"
D45V17, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     0   5
  10P LOSS WILD-TYPE  38 353
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0    5
  10P LOSS WILD-TYPE   38  353
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                353
[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 477  14
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                491 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 0                 14 
$`10Q LOSS MUTATED`
TCGA-BJ-A190 TCGA-E8-A432 TCGA-EL-A4KI TCGA-EM-A3O9 TCGA-ET-A39N TCGA-FY-A3I5 
       20.58        14.43        23.90         9.24        98.56         7.82 

$`10Q LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        17.69        23.34        20.71         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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        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         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       25.45        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       130.72       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        78.97        31.50        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        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        37.94        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-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 
       12.36        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-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        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        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        16.80        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        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        15.62        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        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       117.40        66.77        81.34 
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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        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         0.99 
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 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        19.73         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        20.25        12.89 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              7.82               0.10 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             98.56             169.32 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            17.505             20.420 
[1] "7.8 - 98.6 (17.5)"  "0.1 - 169.3 (20.4)"
[1] "hr="     "9100000"
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       50       107        2        46         6
D46V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  2                280
  STAGE II                 2                 50
  STAGE III                2                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
  10Q LOSS MUTATED     0   2   4   0
  10Q LOSS WILD-TYPE 141 164 163  23
D46V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                0                141
  T2                2                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"
D46V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     5   0
  10Q LOSS WILD-TYPE 219 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5    0
  10Q LOSS WILD-TYPE  219  225
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                5                219
  1                0                225
[1] 2 2
[1] FALSE
D46V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1   0
  10Q LOSS WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1    0
  10Q LOSS WILD-TYPE  276    9
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                1                276
  1                0                  9
[1] 2 2
[1] FALSE
D46V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     3   3
  10Q LOSS WILD-TYPE 363 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3    3
  10Q LOSS WILD-TYPE  363  130
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                3                363
  MALE                  3                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  10Q LOSS MUTATED                0
  10Q LOSS WILD-TYPE              9
                    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                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  10Q LOSS MUTATED                                                                     0
  10Q LOSS WILD-TYPE                                                                  36
D46V8, 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                                                                          9
  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"
D46V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     0   6
  10Q LOSS WILD-TYPE  14 479
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0    6
  10Q LOSS WILD-TYPE   14  479
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 0                 14
  YES                6                479
[1] 2 2
[1] FALSE
D46V10, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     5   0
  10Q LOSS WILD-TYPE 416  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5    0
  10Q LOSS WILD-TYPE  416   17
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 5                416
  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 375  52   4  30
D46V12, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0                6                375
  R1                0                 52
  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   321
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                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"
D46V17, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     0   5
  10Q LOSS WILD-TYPE  38 353
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0    5
  10Q LOSS WILD-TYPE   38  353
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                353
[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 477  13
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                490 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 13 
$`11P LOSS MUTATED`
TCGA-BJ-A190 TCGA-EL-A3GP TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A22N TCGA-FE-A239 
       20.58         1.41        44.15        23.90        10.65        33.63 
TCGA-FY-A3I5 
        7.82 

$`11P LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        17.69        23.34        20.71         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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        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         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ 
       98.53        45.40        57.11       108.36        64.87        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       130.72       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        78.97        31.50        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        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        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       34.39        30.51        53.36        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        12.36 
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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        27.65        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        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-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        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        13.91         7.82        11.51        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       15.62        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        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       54.05        22.09        12.26        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89        98.56        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       117.40        66.77        81.34 
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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        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         0.99        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         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        17.23        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-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       19.73         6.74        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        20.25        12.89 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              1.41               0.10 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             44.15             169.32 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            20.580             20.335 
[1] "1.4 - 44.1 (20.6)"  "0.1 - 169.3 (20.3)"
[1] "hr=" "12" 
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       51       105        1        46         6
D47V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  1                281
  STAGE II                 1                 51
  STAGE III                4                105
  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 140 165 163  22
D47V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                1                140
  T2                1                165
  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 219 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5    2
  11P LOSS WILD-TYPE  219  223
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                5                219
  1                2                223
[1] 2 2
[1] FALSE
D47V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     1   0
  11P LOSS WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1    0
  11P LOSS WILD-TYPE  276    9
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                1                276
  1                0                  9
[1] 2 2
[1] FALSE
D47V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2   5
  11P LOSS WILD-TYPE 364 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2    5
  11P LOSS WILD-TYPE  364  128
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                2                364
  MALE                  5                128
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  11P LOSS MUTATED                0
  11P LOSS WILD-TYPE              9
                    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                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  11P LOSS MUTATED                                                                     0
  11P LOSS WILD-TYPE                                                                  36
D47V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         351
  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"
D47V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     1   6
  11P LOSS WILD-TYPE  13 479
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1    6
  11P LOSS WILD-TYPE   13  479
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 1                 13
  YES                6                479
[1] 2 2
[1] FALSE
D47V10, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     6   0
  11P LOSS WILD-TYPE 415  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6    0
  11P LOSS WILD-TYPE  415   17
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 6                415
  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 375  52   4  29
D47V12, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0                6                375
  R1                0                 52
  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   320
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                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"
D47V17, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0   6
  11P LOSS WILD-TYPE  38 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0    6
  11P LOSS WILD-TYPE   38  352
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                352
[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 475  13
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                488 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                 13 
$`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         1.41        44.15        23.90 
TCGA-EM-A22N TCGA-FE-A239 TCGA-FY-A3I5 
       10.65        33.63         7.82 

$`11Q LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        24.79        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83        44.35        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        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 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75        10.88        21.01         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18        21.63         8.98         4.93        23.47         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O 
       14.70        14.27         2.76         9.96        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      169.32         3.39         8.71        56.19        23.38        18.35 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         8.32        11.01       135.91        30.61        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45        42.58        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       17.56        10.09         7.99         5.33        35.41        27.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        12.56         8.28        34.85         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42        34.36        37.74         6.77        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44        37.48        36.46        10.09         7.10        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        35.18        15.88        15.09        31.04        20.45 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        59.57        11.34        21.37        18.51        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        21.47        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        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
        8.32        24.20        17.23        27.62        18.21        21.34 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       19.07        15.42        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       31.23        22.29        11.70        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 
       13.81        14.07        14.27         3.02        25.45        14.43 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       14.70        14.10        14.96         7.69        20.68        13.78 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.58        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
       80.91         4.18        58.82       139.86        98.53        45.40 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
       57.11       108.36        64.87        50.24       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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      131.15       108.66        57.63        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       130.72       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 
       78.97        31.50        62.30        36.03        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       52.50        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        37.94        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       53.36        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        12.36        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-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       15.75        10.45        14.53        11.74        11.15        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       16.44        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        27.65        10.49        13.15        22.16        13.84 
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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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 
       13.91         7.82        11.51        29.95        15.62        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 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       13.74        71.01        80.02        65.36        84.89        98.56 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        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         0.99        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         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        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 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83         9.63         2.96         8.65        17.23 
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-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         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        86.70         6.02        19.73         6.74 
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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       20.25        12.89 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              1.41               0.10 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             44.15             169.32 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            20.580             20.335 
[1] "1.4 - 44.1 (20.6)"  "0.1 - 169.3 (20.3)"
[1] "hr=" "11" 
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       50       105        1        45         6
D48V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  1                281
  STAGE II                 2                 50
  STAGE III                4                105
  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 140 164 162  22
D48V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                1                140
  T2                2                164
  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 218 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6    3
  11Q LOSS WILD-TYPE  218  222
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                6                218
  1                3                222
[1] 2 2
[1] FALSE
D48V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     2   0
  11Q LOSS WILD-TYPE 275   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    0
  11Q LOSS WILD-TYPE  275    9
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                2                275
  1                0                  9
[1] 2 2
[1] FALSE
D48V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     2   7
  11Q LOSS WILD-TYPE 364 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    7
  11Q LOSS WILD-TYPE  364  126
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                2                364
  MALE                  7                126
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  11Q LOSS MUTATED                0
  11Q LOSS WILD-TYPE              9
                    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                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  11Q LOSS MUTATED                                                                     0
  11Q LOSS WILD-TYPE                                                                  36
D48V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         349
  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"
D48V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1   8
  11Q LOSS WILD-TYPE  13 477
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1    8
  11Q LOSS WILD-TYPE   13  477
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 1                 13
  YES                8                477
[1] 2 2
[1] FALSE
D48V10, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     7   0
  11Q LOSS WILD-TYPE 414  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      7    0
  11Q LOSS WILD-TYPE  414   17
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 7                414
  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 373  52   4  29
D48V12, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0                8                373
  R1                0                 52
  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   319
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                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"
D48V17, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     0   8
  11Q LOSS WILD-TYPE  38 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    8
  11Q LOSS WILD-TYPE   38  350
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                8                350
[1] 2 2
[1] FALSE

Clustering(49) Variable = 13Q LOSS MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    12   1
  13Q LOSS WILD-TYPE 471  13
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                13                484 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                 13 
$`13Q LOSS MUTATED`
TCGA-BJ-A3F0 TCGA-CE-A13K TCGA-DJ-A13P TCGA-DJ-A1QN TCGA-DJ-A2Q2 TCGA-EM-A1YB 
       13.94         0.53       169.32        42.58         6.77        19.46 
TCGA-EM-A22M TCGA-EM-A22Q TCGA-ET-A39N TCGA-ET-A40S TCGA-FE-A239 TCGA-FY-A3I5 
       14.53        14.24        98.56         5.03        33.63         7.82 
TCGA-FY-A3W9 
        0.76 

$`13Q LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        17.26 
TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
       14.07         3.39         8.71        56.19        23.38        18.35 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         8.32        11.01       135.91        30.61        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ 
        7.99        14.96         7.20         1.45        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33        35.41        27.45        26.20 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
       38.83        12.56         8.28        34.85         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.42        34.36        37.74        40.24         9.44        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        10.09         7.10        35.90        12.43        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        20.45        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
       19.56        36.33        32.81        24.23        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        21.37        18.51        36.99        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       21.47        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        21.01        18.97         7.76         8.32        24.20 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        18.21        21.34        19.07        15.42 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04        31.23        22.29 
TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       11.70        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.27         3.02        25.45        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        13.78        13.58        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82       139.86        98.53        45.40        57.11       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       64.87         1.41        50.24       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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        49.71        83.57       139.00       131.15 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        29.65       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      130.72       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        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       31.50        62.30        36.03        53.06        47.38        52.50 
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        37.94        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        12.36        18.05 
TCGA-EM-A1YA TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.79        78.61        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2CJ 
       15.75        10.45        10.65        11.74        11.15        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        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        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        29.95        15.62        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        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        4.80         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       81.34        39.95        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        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         0.99 
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-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.30        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        17.23        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-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       19.73         6.74        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        20.25        12.89 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.53               0.10 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            169.32             158.83 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             14.24              20.48 
[1] "0.5 - 169.3 (14.2)" "0.1 - 158.8 (20.5)"
[1] "hr=" "2.8"
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       48       106        2        46         6
D49V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  7                275
  STAGE II                 4                 48
  STAGE III                3                106
  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 137 162 161  23
D49V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                4                137
  T2                4                162
  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 214 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     10    1
  13Q LOSS WILD-TYPE  214  224
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               10                214
  1                1                224
[1] 2 2
[1] FALSE
D49V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     5   0
  13Q LOSS WILD-TYPE 272   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      5    0
  13Q LOSS WILD-TYPE  272    9
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0                5                272
  1                0                  9
[1] 2 2
[1] FALSE
D49V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     9   5
  13Q LOSS WILD-TYPE 357 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9    5
  13Q LOSS WILD-TYPE  357  128
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                9                357
  MALE                  5                128
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  13Q LOSS MUTATED                0
  13Q LOSS WILD-TYPE              9
                    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                                                                     93
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  13Q LOSS MUTATED                                                                     0
  13Q LOSS WILD-TYPE                                                                  36
D49V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         347
  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"
D49V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     1  13
  13Q LOSS WILD-TYPE  13 472
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   13
  13Q LOSS WILD-TYPE   13  472
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 1                 13
  YES               13                472
[1] 2 2
[1] FALSE
D49V10, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     8   4
  13Q LOSS WILD-TYPE 413  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8    4
  13Q LOSS WILD-TYPE  413   13
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 8                413
  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 370  50   4  29
D49V12, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               11                370
  R1                2                 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"
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   316
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                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"
D49V17, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     0  12
  13Q LOSS WILD-TYPE  38 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0   12
  13Q LOSS WILD-TYPE   38  346
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO               12                346
[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 475  14
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                489 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 0                 14 
$`15Q LOSS MUTATED`
TCGA-BJ-A3F0 TCGA-DJ-A4UR TCGA-EL-A3GO TCGA-EM-A1YE TCGA-EM-A2OY TCGA-EM-A3O9 
       13.94        15.42        64.87        54.08        32.32         9.24 
TCGA-ET-A39N TCGA-FY-A3I5 
       98.56         7.82 

$`15Q LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       18.21        21.34        19.07        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
       14.04        31.23        22.29        11.70        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       14.27        13.81        14.07        14.27         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       45.40        57.11       108.36         1.41        50.24       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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      139.99        49.32        33.50        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       131.15       108.66        57.63        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       29.65       147.42       130.72       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        78.97        31.50        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        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        37.94        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 
       12.36        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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        27.65        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        13.84        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-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        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        13.91         7.82        11.51        29.95        15.62 
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        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        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         0.99        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         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        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         2.99        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 
       10.26        16.90        21.83         9.63         2.96         8.65 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         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        86.70         6.02        19.73 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        20.25        12.89 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              7.82               0.10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             98.56             169.32 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             23.87              20.42 
[1] "7.8 - 98.6 (23.9)"  "0.1 - 169.3 (20.4)"
[1] "hr="     "9300000"
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       49       108        2        46         6
D50V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  4                278
  STAGE II                 3                 49
  STAGE III                1                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
  15Q LOSS MUTATED     1   3   4   0
  15Q LOSS WILD-TYPE 140 163 163  23
D50V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                1                140
  T2                3                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"
D50V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     6   1
  15Q LOSS WILD-TYPE 218 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6    1
  15Q LOSS WILD-TYPE  218  224
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0                6                218
  1                1                224
[1] 2 2
[1] FALSE
D50V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2   1
  15Q LOSS WILD-TYPE 275   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    1
  15Q LOSS WILD-TYPE  275    8
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0                2                275
  1                1                  8
[1] 2 2
[1] FALSE
D50V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     7   1
  15Q LOSS WILD-TYPE 359 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7    1
  15Q LOSS WILD-TYPE  359  132
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                7                359
  MALE                  1                132
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  15Q LOSS MUTATED                0
  15Q LOSS WILD-TYPE              9
                    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                                                                     93
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  15Q LOSS MUTATED                                                                     0
  15Q LOSS WILD-TYPE                                                                  36
D50V8, 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                                                                          9
  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"
D50V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     0   8
  15Q LOSS WILD-TYPE  14 477
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0    8
  15Q LOSS WILD-TYPE   14  477
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 0                 14
  YES                8                477
[1] 2 2
[1] FALSE
D50V10, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     7   0
  15Q LOSS WILD-TYPE 414  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7    0
  15Q LOSS WILD-TYPE  414   17
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 7                414
  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 373  52   4  30
D50V12, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0                8                373
  R1                0                 52
  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   321
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                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"
D50V17, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1   4
  15Q LOSS WILD-TYPE  37 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    4
  15Q LOSS WILD-TYPE   37  354
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 37
  NOT HISPANIC OR LATINO                4                354
[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 475  14
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                489 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 0                 14 
$`17P LOSS MUTATED`
TCGA-E8-A432 TCGA-EL-A3D5 TCGA-EL-A3ZM TCGA-EM-A1YE TCGA-EM-A3O9 TCGA-EM-A3OB 
       14.43        57.11        36.03        54.08         9.24         7.82 
TCGA-FE-A22Z TCGA-FE-A238 
       73.74        39.95 

$`17P LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        25.45        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       98.53        45.40       108.36        64.87         1.41        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       130.72       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-A3ZN 
       82.82        89.56        78.97        31.50        62.30        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        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        37.94        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 
       12.36        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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        27.65        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        32.32        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-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        16.80        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        7.33        12.53        13.91        11.51        29.95        15.62 
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        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       98.56        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        4.01         1.94        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A239 TCGA-FE-A23A 
       68.22       117.40        66.77        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        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         0.99        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         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        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         2.99        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 
       10.26        16.90        21.83         9.63         2.96         8.65 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         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        86.70         6.02        19.73 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        20.25        12.89 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              7.82               0.10 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             73.74             169.32 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             37.99              20.25 
[1] "7.8 - 73.7 (38.0)"  "0.1 - 169.3 (20.2)"
[1] "hr="     "9300000"
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       50       109        2        44         6
D51V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  4                278
  STAGE II                 2                 50
  STAGE III                0                109
  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 141 163 164  21
D51V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                0                141
  T2                3                163
  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 219 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5    3
  17P LOSS WILD-TYPE  219  222
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0                5                219
  1                3                222
[1] 2 2
[1] FALSE
D51V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     3   0
  17P LOSS WILD-TYPE 274   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3    0
  17P LOSS WILD-TYPE  274    9
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0                3                274
  1                0                  9
[1] 2 2
[1] FALSE
D51V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     6   2
  17P LOSS WILD-TYPE 360 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6    2
  17P LOSS WILD-TYPE  360  131
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                6                360
  MALE                  2                131
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  17P LOSS MUTATED                0
  17P LOSS WILD-TYPE              9
                    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                                                                     94
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  17P LOSS MUTATED                                                                     0
  17P LOSS WILD-TYPE                                                                  36
D51V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         352
  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"
D51V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     2   6
  17P LOSS WILD-TYPE  12 479
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2    6
  17P LOSS WILD-TYPE   12  479
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 2                 12
  YES                6                479
[1] 2 2
[1] FALSE
D51V10, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     7   1
  17P LOSS WILD-TYPE 414  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      7    1
  17P LOSS WILD-TYPE  414   16
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 7                414
  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 375  50   4  30
D51V12, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0                6                375
  R1                2                 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"
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   322
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                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"
D51V17, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     0   4
  17P LOSS WILD-TYPE  38 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      0    4
  17P LOSS WILD-TYPE   38  354
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                4                354
[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 479  14
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                493 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 0                 14 
$`17Q LOSS MUTATED`
TCGA-E8-A432 TCGA-EM-A3O9 TCGA-EM-A3OB TCGA-FE-A238 
       14.43         9.24         7.82        39.95 

$`17Q LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28        34.85         5.52         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         6.77        40.24         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        18.51        36.99        20.22        30.61        21.47 
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 
       21.01        18.97         7.76         8.32        24.20        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        18.21        21.34        19.07        15.42        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       63.19        30.31        14.04        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        25.45        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        52.50        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        37.94 
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        12.36        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-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        11.74        11.15        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       16.44        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        27.65        10.49        13.15        22.16        13.84 
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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        13.91 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       66.77        81.34        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        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         0.99        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         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83         9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         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        86.70         6.02        19.73         6.74        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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        20.25 
TCGA-QD-A8IV 
       12.89 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              7.82               0.10 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             39.95             169.32 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            11.835             20.450 
[1] "7.8 - 40.0 (11.8)"  "0.1 - 169.3 (20.4)"
[1] "hr="     "1200000"
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       51       109        2        46         6
D52V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  3                279
  STAGE II                 1                 51
  STAGE III                0                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
  17Q LOSS MUTATED     0   2   2   0
  17Q LOSS WILD-TYPE 141 164 165  23
D52V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                141
  T2                2                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"
D52V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4   0
  17Q LOSS WILD-TYPE 220 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    0
  17Q LOSS WILD-TYPE  220  225
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0                4                220
  1                0                225
[1] 2 2
[1] FALSE
D52V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1   0
  17Q LOSS WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    0
  17Q LOSS WILD-TYPE  276    9
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0                1                276
  1                0                  9
[1] 2 2
[1] FALSE
D52V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3   1
  17Q LOSS WILD-TYPE 363 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3    1
  17Q LOSS WILD-TYPE  363  132
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                3                363
  MALE                  1                132
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  17Q LOSS MUTATED                0
  17Q LOSS WILD-TYPE              9
                    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                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  17Q LOSS MUTATED                                                                     0
  17Q LOSS WILD-TYPE                                                                  36
D52V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         354
  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"
D52V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1   3
  17Q LOSS WILD-TYPE  13 482
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    3
  17Q LOSS WILD-TYPE   13  482
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 1                 13
  YES                3                482
[1] 2 2
[1] FALSE
D52V10, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4   0
  17Q LOSS WILD-TYPE 417  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    0
  17Q LOSS WILD-TYPE  417   17
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 4                417
  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 377  52   4  30
D52V12, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                4                377
  R1                0                 52
  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   324
D52V16, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                403 
        TCGA-4C-A93U         TCGA-BJ-A0YZ         TCGA-BJ-A0Z2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A0Z3         TCGA-BJ-A0Z5         TCGA-BJ-A0Z9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZE         TCGA-BJ-A0ZG         TCGA-BJ-A0ZH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZJ         TCGA-BJ-A18Y         TCGA-BJ-A18Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A190         TCGA-BJ-A191         TCGA-BJ-A192 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A28R         TCGA-BJ-A28S         TCGA-BJ-A28T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A28V         TCGA-BJ-A28W         TCGA-BJ-A28X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A28Z         TCGA-BJ-A290         TCGA-BJ-A291 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A2N7         TCGA-BJ-A2N8         TCGA-BJ-A2N9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A2P4         TCGA-BJ-A3EZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A3F0         TCGA-BJ-A3PR         TCGA-BJ-A3PT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A3PU         TCGA-BJ-A45C         TCGA-BJ-A45D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A45E         TCGA-BJ-A45F         TCGA-BJ-A45G 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A45H         TCGA-BJ-A45I         TCGA-BJ-A45J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A45K         TCGA-BJ-A4O8         TCGA-BJ-A4O9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CE-A13K         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-A0XZ         TCGA-DE-A0Y2         TCGA-DE-A0Y3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DE-A2OL         TCGA-DE-A3KN         TCGA-DE-A4M8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DE-A4M9         TCGA-DE-A4MA         TCGA-DE-A4MB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DE-A4MC         TCGA-DE-A4MD         TCGA-DE-A69J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DE-A69K         TCGA-DE-A7U5         TCGA-DJ-A13L 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A13M         TCGA-DJ-A13O         TCGA-DJ-A13P 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A13R         TCGA-DJ-A13S         TCGA-DJ-A13T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A13U         TCGA-DJ-A13W         TCGA-DJ-A1QD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QE         TCGA-DJ-A1QF         TCGA-DJ-A1QG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QH         TCGA-DJ-A1QI         TCGA-DJ-A1QM 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QO         TCGA-DJ-A1QQ         TCGA-DJ-A2PN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PO         TCGA-DJ-A2PQ         TCGA-DJ-A2PR 
"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-A3UU         TCGA-DJ-A3UW         TCGA-DJ-A3UX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UY         TCGA-DJ-A3UZ         TCGA-DJ-A3V2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3V3         TCGA-DJ-A3V4         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-E3-A3E5         TCGA-E8-A242 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E8-A2EA         TCGA-E8-A2JQ         TCGA-E8-A3X7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E8-A413         TCGA-E8-A414         TCGA-E8-A415 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E8-A416         TCGA-E8-A417         TCGA-E8-A418 
"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-A3CR         TCGA-EL-A3CS 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CY 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"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-A3H2         TCGA-EL-A3H3         TCGA-EL-A3H4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MY 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3N3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3T0         TCGA-EL-A3T1         TCGA-EL-A3T2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3T3         TCGA-EL-A3T6         TCGA-EL-A3T7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3T8         TCGA-EL-A3T9         TCGA-EL-A3TA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3TB         TCGA-EL-A3ZG         TCGA-EL-A3ZH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZK         TCGA-EL-A3ZL         TCGA-EL-A3ZN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZO         TCGA-EL-A3ZP         TCGA-EL-A3ZQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZR         TCGA-EL-A3ZS         TCGA-EL-A3ZT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4JV         TCGA-EL-A4JW         TCGA-EL-A4JX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4JZ         TCGA-EL-A4K0         TCGA-EL-A4K1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4K2         TCGA-EL-A4K4         TCGA-EL-A4K6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4K7         TCGA-EL-A4K9         TCGA-EL-A4KD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4KG         TCGA-EL-A4KH         TCGA-EL-A4KI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22O         TCGA-EM-A2OV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EM-A3AI         TCGA-ET-A25G         TCGA-ET-A25I 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A25J         TCGA-ET-A25K         TCGA-ET-A25L 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25N         TCGA-ET-A25O 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A25P         TCGA-ET-A25R         TCGA-ET-A2MX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A2MY         TCGA-ET-A2MZ         TCGA-ET-A2N0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N3         TCGA-ET-A2N4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A2N5         TCGA-ET-A39I         TCGA-ET-A39J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A39K         TCGA-ET-A39M         TCGA-ET-A39N 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A39O         TCGA-ET-A39P         TCGA-ET-A39R 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A39S         TCGA-ET-A39T         TCGA-ET-A3BN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3BO         TCGA-ET-A3BQ         TCGA-ET-A3BS 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3BT         TCGA-ET-A3BU         TCGA-ET-A3BV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3BW         TCGA-ET-A3DO         TCGA-ET-A3DP 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3DQ         TCGA-ET-A3DR         TCGA-ET-A3DS 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DU         TCGA-ET-A3DV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-ET-A40P         TCGA-ET-A40Q 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A40R         TCGA-ET-A40S         TCGA-ET-A40T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A4KN         TCGA-ET-A4KQ         TCGA-FE-A22Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A230         TCGA-FE-A231         TCGA-FE-A232 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A233         TCGA-FE-A234         TCGA-FE-A235 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A236         TCGA-FE-A237         TCGA-FE-A239 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A23A         TCGA-FE-A3PA         TCGA-FE-A3PB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A3PC         TCGA-FE-A3PD         TCGA-FK-A3S3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FK-A3SB         TCGA-FK-A3SD         TCGA-FK-A3SE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FK-A3SG         TCGA-FK-A3SH         TCGA-FK-A4UB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A2QD         TCGA-FY-A3BL         TCGA-FY-A3I4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A3I5         TCGA-FY-A3NM         TCGA-FY-A3ON 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A3R6         TCGA-FY-A3R7         TCGA-FY-A3R8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A3R9         TCGA-FY-A3RA         TCGA-FY-A3W9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A3WA         TCGA-FY-A3YR         TCGA-FY-A40K 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A40L         TCGA-FY-A40M         TCGA-FY-A40N 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A4B0         TCGA-FY-A4B3         TCGA-FY-A4B4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A76V         TCGA-GE-A2C6         TCGA-H2-A26U 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-H2-A2K9         TCGA-H2-A3RH         TCGA-H2-A3RI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-H2-A421         TCGA-H2-A422         TCGA-IM-A3EB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IM-A3ED         TCGA-IM-A3U2         TCGA-IM-A3U3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IM-A41Y         TCGA-IM-A41Z         TCGA-IM-A420 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IM-A4EB         TCGA-J8-A3NZ         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-A4HW 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-J8-A4HY         TCGA-KS-A41F         TCGA-KS-A41I 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-KS-A41J         TCGA-KS-A41L         TCGA-KS-A4I1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-KS-A4I3         TCGA-KS-A4I5         TCGA-KS-A4I7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-KS-A4I9         TCGA-KS-A4IB         TCGA-KS-A4IC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-KS-A4ID         TCGA-L6-A4EP         TCGA-L6-A4EQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-L6-A4ET         TCGA-L6-A4EU         TCGA-MK-A4N6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MK-A4N7         TCGA-MK-A4N9         TCGA-MK-A84Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-QD-A8IV 
"17Q LOSS WILD-TYPE" 
D52V17, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0   2
  17Q LOSS WILD-TYPE  38 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0    2
  17Q LOSS WILD-TYPE   38  356
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                2                356
[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 479  14
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                493 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 0                 14 
$`18P LOSS MUTATED`
TCGA-DJ-A2Q0 TCGA-EM-A1YE TCGA-EM-A3SY TCGA-ET-A3BP 
       34.36        54.08        13.51         4.18 

$`18P LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
        8.28        34.85         5.52         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        52.50        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        37.94 
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        12.36        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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        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        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BQ 
       57.11        55.10        59.15        28.24         5.85         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        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 
       81.34        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        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         0.99        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         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83         9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         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        86.70         6.02        19.73         6.74        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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        20.25 
TCGA-QD-A8IV 
       12.89 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              4.18               0.10 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             54.08             169.32 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            23.935             20.420 
[1] "4.2 - 54.1 (23.9)"  "0.1 - 169.3 (20.4)"
[1] "hr="     "3300000"
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       50       109        2        46         6
D53V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  2                280
  STAGE II                 2                 50
  STAGE III                0                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 LOSS MUTATED     1   3   0   0
  18P LOSS WILD-TYPE 140 163 167  23
D53V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                1                140
  T2                3                163
  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 222 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    1
  18P LOSS WILD-TYPE  222  224
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0                2                222
  1                1                224
[1] 2 2
[1] FALSE
D53V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1   0
  18P LOSS WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    0
  18P LOSS WILD-TYPE  276    9
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0                1                276
  1                0                  9
[1] 2 2
[1] FALSE
D53V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3   1
  18P LOSS WILD-TYPE 363 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3    1
  18P LOSS WILD-TYPE  363  132
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                3                363
  MALE                  1                132
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  18P LOSS MUTATED                0
  18P LOSS WILD-TYPE              9
                    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                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  18P LOSS MUTATED                                                                     0
  18P LOSS WILD-TYPE                                                                  36
D53V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         354
  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"
D53V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     0   4
  18P LOSS WILD-TYPE  14 481
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0    4
  18P LOSS WILD-TYPE   14  481
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 0                 14
  YES                4                481
[1] 2 2
[1] FALSE
D53V10, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     4   0
  18P LOSS WILD-TYPE 417  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    0
  18P LOSS WILD-TYPE  417   17
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 4                417
  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 377  52   4  30
D53V12, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0                4                377
  R1                0                 52
  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     1
  18P LOSS WILD-TYPE                        27   324
D53V16, multiclass
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                404 
        TCGA-4C-A93U         TCGA-BJ-A0YZ         TCGA-BJ-A0Z2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A0Z3         TCGA-BJ-A0Z5         TCGA-BJ-A0Z9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A0ZE         TCGA-BJ-A0ZG         TCGA-BJ-A0ZH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A0ZJ         TCGA-BJ-A18Y         TCGA-BJ-A18Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A190         TCGA-BJ-A191         TCGA-BJ-A192 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A28R         TCGA-BJ-A28S         TCGA-BJ-A28T 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A28V         TCGA-BJ-A28W         TCGA-BJ-A28X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A28Z         TCGA-BJ-A290         TCGA-BJ-A291 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A2N7         TCGA-BJ-A2N8         TCGA-BJ-A2N9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A2P4         TCGA-BJ-A3EZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A3F0         TCGA-BJ-A3PR         TCGA-BJ-A3PT 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A3PU         TCGA-BJ-A45C         TCGA-BJ-A45D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A45E         TCGA-BJ-A45F         TCGA-BJ-A45G 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A45H         TCGA-BJ-A45I         TCGA-BJ-A45J 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A45K         TCGA-BJ-A4O8         TCGA-BJ-A4O9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CE-A13K         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-A0XZ         TCGA-DE-A0Y2         TCGA-DE-A0Y3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DE-A2OL         TCGA-DE-A3KN         TCGA-DE-A4M8 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DE-A4M9         TCGA-DE-A4MA         TCGA-DE-A4MB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DE-A4MC         TCGA-DE-A4MD         TCGA-DE-A69J 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DE-A69K         TCGA-DE-A7U5         TCGA-DJ-A13L 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A13M         TCGA-DJ-A13O         TCGA-DJ-A13P 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A13R         TCGA-DJ-A13S         TCGA-DJ-A13T 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A13U         TCGA-DJ-A13W         TCGA-DJ-A1QD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A1QE         TCGA-DJ-A1QF         TCGA-DJ-A1QG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A1QH         TCGA-DJ-A1QI         TCGA-DJ-A1QM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A1QO         TCGA-DJ-A1QQ         TCGA-DJ-A2PN 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2PO         TCGA-DJ-A2PQ         TCGA-DJ-A2PR 
"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-A3UU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3UW         TCGA-DJ-A3UX         TCGA-DJ-A3UY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3UZ         TCGA-DJ-A3V2         TCGA-DJ-A3V3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3V4         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-E3-A3E5         TCGA-E8-A242         TCGA-E8-A2EA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A2JQ         TCGA-E8-A3X7         TCGA-E8-A413 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A414         TCGA-E8-A415         TCGA-E8-A416 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A417         TCGA-E8-A418         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-A3CR         TCGA-EL-A3CS 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"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-A3H2         TCGA-EL-A3H3         TCGA-EL-A3H4 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3N3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3T0         TCGA-EL-A3T1         TCGA-EL-A3T2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3T3         TCGA-EL-A3T6         TCGA-EL-A3T7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3T8         TCGA-EL-A3T9         TCGA-EL-A3TA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3TB         TCGA-EL-A3ZG         TCGA-EL-A3ZH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3ZK         TCGA-EL-A3ZL         TCGA-EL-A3ZN 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3ZO         TCGA-EL-A3ZP         TCGA-EL-A3ZQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3ZR         TCGA-EL-A3ZS         TCGA-EL-A3ZT 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4JV         TCGA-EL-A4JW         TCGA-EL-A4JX 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4JZ         TCGA-EL-A4K0         TCGA-EL-A4K1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4K2         TCGA-EL-A4K4         TCGA-EL-A4K6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4K7         TCGA-EL-A4K9         TCGA-EL-A4KD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4KG         TCGA-EL-A4KH         TCGA-EL-A4KI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22O         TCGA-EM-A2OV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EM-A3AI         TCGA-ET-A25G         TCGA-ET-A25I 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A25J         TCGA-ET-A25K         TCGA-ET-A25L 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25N         TCGA-ET-A25O 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A25P         TCGA-ET-A25R         TCGA-ET-A2MX 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A2MY         TCGA-ET-A2MZ         TCGA-ET-A2N0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N3         TCGA-ET-A2N4 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A2N5         TCGA-ET-A39I         TCGA-ET-A39J 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A39K         TCGA-ET-A39M         TCGA-ET-A39N 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A39O         TCGA-ET-A39P         TCGA-ET-A39R 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A39S         TCGA-ET-A39T         TCGA-ET-A3BN 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3BO         TCGA-ET-A3BQ         TCGA-ET-A3BS 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3BT         TCGA-ET-A3BU         TCGA-ET-A3BV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3BW         TCGA-ET-A3DO         TCGA-ET-A3DP 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3DQ         TCGA-ET-A3DR         TCGA-ET-A3DS 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DU         TCGA-ET-A3DV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-ET-A40P         TCGA-ET-A40Q 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A40R         TCGA-ET-A40S         TCGA-ET-A40T 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A4KN         TCGA-ET-A4KQ         TCGA-FE-A22Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A230         TCGA-FE-A231         TCGA-FE-A232 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A233         TCGA-FE-A234         TCGA-FE-A235 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A236         TCGA-FE-A237         TCGA-FE-A238 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FE-A3PA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A3PB         TCGA-FE-A3PC         TCGA-FE-A3PD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FK-A3S3         TCGA-FK-A3SB         TCGA-FK-A3SD 
"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-A3W9         TCGA-FY-A3WA         TCGA-FY-A3YR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A40K         TCGA-FY-A40L         TCGA-FY-A40M 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A40N         TCGA-FY-A4B0         TCGA-FY-A4B3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A4B4         TCGA-FY-A76V         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-A3NZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-J8-A3O0         TCGA-J8-A3O1         TCGA-J8-A3O2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-J8-A3YD         TCGA-J8-A3YE         TCGA-J8-A3YF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-J8-A3YG         TCGA-J8-A3YH         TCGA-J8-A42S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-J8-A4HW         TCGA-J8-A4HY         TCGA-KS-A41F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KS-A41I         TCGA-KS-A41J         TCGA-KS-A41L 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KS-A4I1         TCGA-KS-A4I3         TCGA-KS-A4I5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KS-A4I7         TCGA-KS-A4I9         TCGA-KS-A4IB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KS-A4IC         TCGA-KS-A4ID         TCGA-L6-A4EP 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L6-A4EQ         TCGA-L6-A4ET         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-MK-A84Z         TCGA-QD-A8IV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
D53V17, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1   1
  18P LOSS WILD-TYPE  37 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    1
  18P LOSS WILD-TYPE   37  357
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 37
  NOT HISPANIC OR LATINO                1                357
[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 479  14
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                493 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 0                 14 
$`18Q LOSS MUTATED`
TCGA-DJ-A2Q0 TCGA-EM-A1YE TCGA-EM-A3SY TCGA-ET-A3BP 
       34.36        54.08        13.51         4.18 

$`18Q LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        17.69        23.34        20.71        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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        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         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         5.75        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
        6.35         7.82         6.18        21.63         8.98         4.93 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47         0.53         0.10         0.20         0.23        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68         0.10         0.39         0.10        20.22        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       36.46         5.98        15.85        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-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        17.26        14.07       169.32         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        18.35        14.60         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33        35.41        27.45        26.20        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
        8.28        34.85         5.52         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       130.72       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        78.97        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        52.50        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        37.94 
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        12.36        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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       27.65        10.49        13.15        22.16        13.84        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        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        16.80 
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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BQ 
       57.11        55.10        59.15        28.24         5.85         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        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 
       81.34        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        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         0.99        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         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83         9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         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        86.70         6.02        19.73         6.74        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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        20.25 
TCGA-QD-A8IV 
       12.89 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              4.18               0.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             54.08             169.32 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            23.935             20.420 
[1] "4.2 - 54.1 (23.9)"  "0.1 - 169.3 (20.4)"
[1] "hr="     "3300000"
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       50       109        2        46         6
D54V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  2                280
  STAGE II                 2                 50
  STAGE III                0                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 LOSS MUTATED     1   3   0   0
  18Q LOSS WILD-TYPE 140 163 167  23
D54V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                1                140
  T2                3                163
  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 222 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2    1
  18Q LOSS WILD-TYPE  222  224
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0                2                222
  1                1                224
[1] 2 2
[1] FALSE
D54V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     1   0
  18Q LOSS WILD-TYPE 276   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    0
  18Q LOSS WILD-TYPE  276    9
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0                1                276
  1                0                  9
[1] 2 2
[1] FALSE
D54V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3   1
  18Q LOSS WILD-TYPE 363 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    1
  18Q LOSS WILD-TYPE  363  132
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                3                363
  MALE                  1                132
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  18Q LOSS MUTATED                0
  18Q LOSS WILD-TYPE              9
                    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                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  18Q LOSS MUTATED                                                                     0
  18Q LOSS WILD-TYPE                                                                  36
D54V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         354
  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"
D54V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     0   4
  18Q LOSS WILD-TYPE  14 481
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      0    4
  18Q LOSS WILD-TYPE   14  481
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 0                 14
  YES                4                481
[1] 2 2
[1] FALSE
D54V10, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     4   0
  18Q LOSS WILD-TYPE 417  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4    0
  18Q LOSS WILD-TYPE  417   17
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 4                417
  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 377  52   4  30
D54V12, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0                4                377
  R1                0                 52
  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     1
  18Q LOSS WILD-TYPE                        27   324
D54V16, multiclass
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                404 
        TCGA-4C-A93U         TCGA-BJ-A0YZ         TCGA-BJ-A0Z2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A0Z3         TCGA-BJ-A0Z5         TCGA-BJ-A0Z9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZE         TCGA-BJ-A0ZG         TCGA-BJ-A0ZH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZJ         TCGA-BJ-A18Y         TCGA-BJ-A18Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A190         TCGA-BJ-A191         TCGA-BJ-A192 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A28R         TCGA-BJ-A28S         TCGA-BJ-A28T 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A28V         TCGA-BJ-A28W         TCGA-BJ-A28X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A28Z         TCGA-BJ-A290         TCGA-BJ-A291 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A2N7         TCGA-BJ-A2N8         TCGA-BJ-A2N9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A2P4         TCGA-BJ-A3EZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A3F0         TCGA-BJ-A3PR         TCGA-BJ-A3PT 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A3PU         TCGA-BJ-A45C         TCGA-BJ-A45D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A45E         TCGA-BJ-A45F         TCGA-BJ-A45G 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A45H         TCGA-BJ-A45I         TCGA-BJ-A45J 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A45K         TCGA-BJ-A4O8         TCGA-BJ-A4O9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CE-A13K         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-A0XZ         TCGA-DE-A0Y2         TCGA-DE-A0Y3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DE-A2OL         TCGA-DE-A3KN         TCGA-DE-A4M8 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DE-A4M9         TCGA-DE-A4MA         TCGA-DE-A4MB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DE-A4MC         TCGA-DE-A4MD         TCGA-DE-A69J 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DE-A69K         TCGA-DE-A7U5         TCGA-DJ-A13L 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A13M         TCGA-DJ-A13O         TCGA-DJ-A13P 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A13R         TCGA-DJ-A13S         TCGA-DJ-A13T 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A13U         TCGA-DJ-A13W         TCGA-DJ-A1QD 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QE         TCGA-DJ-A1QF         TCGA-DJ-A1QG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QH         TCGA-DJ-A1QI         TCGA-DJ-A1QM 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QO         TCGA-DJ-A1QQ         TCGA-DJ-A2PN 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PO         TCGA-DJ-A2PQ         TCGA-DJ-A2PR 
"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-A3UU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UW         TCGA-DJ-A3UX         TCGA-DJ-A3UY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UZ         TCGA-DJ-A3V2         TCGA-DJ-A3V3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3V4         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-E3-A3E5         TCGA-E8-A242         TCGA-E8-A2EA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A2JQ         TCGA-E8-A3X7         TCGA-E8-A413 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A414         TCGA-E8-A415         TCGA-E8-A416 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A417         TCGA-E8-A418         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-A3CR         TCGA-EL-A3CS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3CT         TCGA-EL-A3CU         TCGA-EL-A3CV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3CW         TCGA-EL-A3CX         TCGA-EL-A3CY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3CZ         TCGA-EL-A3D0         TCGA-EL-A3D1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3D4         TCGA-EL-A3D5         TCGA-EL-A3D6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"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-A3H2         TCGA-EL-A3H3         TCGA-EL-A3H4 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3MZ         TCGA-EL-A3N2         TCGA-EL-A3N3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3T0         TCGA-EL-A3T1         TCGA-EL-A3T2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3T3         TCGA-EL-A3T6         TCGA-EL-A3T7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3T8         TCGA-EL-A3T9         TCGA-EL-A3TA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3TB         TCGA-EL-A3ZG         TCGA-EL-A3ZH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZK         TCGA-EL-A3ZL         TCGA-EL-A3ZN 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZO         TCGA-EL-A3ZP         TCGA-EL-A3ZQ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZR         TCGA-EL-A3ZS         TCGA-EL-A3ZT 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4JV         TCGA-EL-A4JW         TCGA-EL-A4JX 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4JZ         TCGA-EL-A4K0         TCGA-EL-A4K1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4K2         TCGA-EL-A4K4         TCGA-EL-A4K6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4K7         TCGA-EL-A4K9         TCGA-EL-A4KD 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4KG         TCGA-EL-A4KH         TCGA-EL-A4KI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22O         TCGA-EM-A2OV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EM-A3AI         TCGA-ET-A25G         TCGA-ET-A25I 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A25J         TCGA-ET-A25K         TCGA-ET-A25L 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25N         TCGA-ET-A25O 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A25P         TCGA-ET-A25R         TCGA-ET-A2MX 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A2MY         TCGA-ET-A2MZ         TCGA-ET-A2N0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N3         TCGA-ET-A2N4 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A2N5         TCGA-ET-A39I         TCGA-ET-A39J 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A39K         TCGA-ET-A39M         TCGA-ET-A39N 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A39O         TCGA-ET-A39P         TCGA-ET-A39R 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A39S         TCGA-ET-A39T         TCGA-ET-A3BN 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3BO         TCGA-ET-A3BQ         TCGA-ET-A3BS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3BT         TCGA-ET-A3BU         TCGA-ET-A3BV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3BW         TCGA-ET-A3DO         TCGA-ET-A3DP 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3DQ         TCGA-ET-A3DR         TCGA-ET-A3DS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DU         TCGA-ET-A3DV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-ET-A40P         TCGA-ET-A40Q 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A40R         TCGA-ET-A40S         TCGA-ET-A40T 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A4KN         TCGA-ET-A4KQ         TCGA-FE-A22Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A230         TCGA-FE-A231         TCGA-FE-A232 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A233         TCGA-FE-A234         TCGA-FE-A235 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A236         TCGA-FE-A237         TCGA-FE-A238 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FE-A3PA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A3PB         TCGA-FE-A3PC         TCGA-FE-A3PD 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FK-A3S3         TCGA-FK-A3SB         TCGA-FK-A3SD 
"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-A3W9         TCGA-FY-A3WA         TCGA-FY-A3YR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A40K         TCGA-FY-A40L         TCGA-FY-A40M 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A40N         TCGA-FY-A4B0         TCGA-FY-A4B3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A4B4         TCGA-FY-A76V         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-A3NZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-J8-A3O0         TCGA-J8-A3O1         TCGA-J8-A3O2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-J8-A3YD         TCGA-J8-A3YE         TCGA-J8-A3YF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-J8-A3YG         TCGA-J8-A3YH         TCGA-J8-A42S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-J8-A4HW         TCGA-J8-A4HY         TCGA-KS-A41F 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KS-A41I         TCGA-KS-A41J         TCGA-KS-A41L 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KS-A4I1         TCGA-KS-A4I3         TCGA-KS-A4I5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KS-A4I7         TCGA-KS-A4I9         TCGA-KS-A4IB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KS-A4IC         TCGA-KS-A4ID         TCGA-L6-A4EP 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-L6-A4EQ         TCGA-L6-A4ET         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-MK-A84Z         TCGA-QD-A8IV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D54V17, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     1   1
  18Q LOSS WILD-TYPE  37 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    1
  18Q LOSS WILD-TYPE   37  357
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 37
  NOT HISPANIC OR LATINO                1                357
[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 479  13
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                492 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 13 
$`19P LOSS MUTATED`
TCGA-BJ-A0YZ TCGA-EL-A3D5 TCGA-EL-A3H2 TCGA-ET-A39N TCGA-FY-A3WA 
       24.79        57.11        33.50        98.56        17.06 

$`19P LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        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         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        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-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       169.32         3.39         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        18.35        14.60         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        13.12         7.99        14.96         7.20         1.45 
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         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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 
        6.77        40.24         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        20.45        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        59.57        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       18.51        36.99        20.22        30.61        21.47        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        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       18.21        21.34        19.07        15.42        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       30.31        14.04        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       98.53        45.40       108.36        64.87         1.41        50.24 
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-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       131.15       108.66        57.63        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       29.65       147.42       130.72       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        78.97        31.50        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        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        37.94        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 
       12.36        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-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        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        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        16.80        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        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       80.02        65.36        84.89        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        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 
       81.34        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        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         0.99        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         0.30         0.76        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
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         2.99        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        10.26        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         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 
       86.70         6.02        19.73         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        20.25        12.89 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             17.06               0.10 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             98.56             169.32 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            33.500             20.235 
[1] "17.1 - 98.6 (33.5)" "0.1 - 169.3 (20.2)"
[1] "hr=" "4.1"
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       50       109        2        46         6
D55V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  3                279
  STAGE II                 2                 50
  STAGE III                0                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
  19P LOSS MUTATED     1   2   2   0
  19P LOSS WILD-TYPE 140 164 165  23
D55V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                1                140
  T2                2                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"
D55V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2   1
  19P LOSS WILD-TYPE 222 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    1
  19P LOSS WILD-TYPE  222  224
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                2                222
  1                1                224
[1] 2 2
[1] FALSE
D55V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2   0
  19P LOSS WILD-TYPE 275   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    0
  19P LOSS WILD-TYPE  275    9
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                2                275
  1                0                  9
[1] 2 2
[1] FALSE
D55V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3   2
  19P LOSS WILD-TYPE 363 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    2
  19P LOSS WILD-TYPE  363  131
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                3                363
  MALE                  2                131
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  19P LOSS MUTATED                0
  19P LOSS WILD-TYPE              9
                    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                                                                     97
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  19P LOSS MUTATED                                                                     0
  19P LOSS WILD-TYPE                                                                  36
D55V8, 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                                                                          9
  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"
D55V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0   5
  19P LOSS WILD-TYPE  14 480
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    5
  19P LOSS WILD-TYPE   14  480
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 0                 14
  YES                5                480
[1] 2 2
[1] FALSE
D55V10, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3   2
  19P LOSS WILD-TYPE 418  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    2
  19P LOSS WILD-TYPE  418   15
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 3                418
  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 377  51   4  30
D55V12, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0                4                377
  R1                1                 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"
D55V13, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                382 
        TCGA-4C-A93U         TCGA-BJ-A0Z0         TCGA-BJ-A0Z3 
"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-A290 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A291         TCGA-BJ-A2N8         TCGA-BJ-A2N9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A2NA         TCGA-BJ-A3EZ         TCGA-BJ-A3PR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A3PU         TCGA-BJ-A45C         TCGA-BJ-A45D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A45E         TCGA-BJ-A45G         TCGA-BJ-A45I 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A45J         TCGA-BJ-A45K         TCGA-BJ-A4O8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A4O9         TCGA-CE-A13K         TCGA-CE-A3MD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DE-A0XZ         TCGA-DE-A0Y2         TCGA-DE-A0Y3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DE-A3KN         TCGA-DE-A4M8         TCGA-DE-A4MA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DE-A4MB         TCGA-DE-A4MC         TCGA-DE-A4MD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DE-A69K         TCGA-DE-A7U5         TCGA-DJ-A13M 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A13O         TCGA-DJ-A13R         TCGA-DJ-A13T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A13V         TCGA-DJ-A13W         TCGA-DJ-A13X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QH         TCGA-DJ-A1QM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2PO         TCGA-DJ-A2PP         TCGA-DJ-A2PQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2PR         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-A3UU         TCGA-DJ-A3UW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3UX         TCGA-DJ-A3UZ         TCGA-DJ-A3V0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3V2         TCGA-DJ-A3V3         TCGA-DJ-A3V4 
"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-E3-A3E5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E8-A242         TCGA-E8-A2EA         TCGA-E8-A2JQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E8-A414         TCGA-E8-A415         TCGA-E8-A417 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E8-A419         TCGA-E8-A433         TCGA-E8-A436 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E8-A438         TCGA-E8-A44K         TCGA-EL-A3CM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3CN         TCGA-EL-A3CO         TCGA-EL-A3CR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3CS         TCGA-EL-A3CT         TCGA-EL-A3CU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3CY         TCGA-EL-A3CZ         TCGA-EL-A3D0 
"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-A3GQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3GS         TCGA-EL-A3GU         TCGA-EL-A3GV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3GX         TCGA-EL-A3H3         TCGA-EL-A3H4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3N2         TCGA-EL-A3T0         TCGA-EL-A3T1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3T2         TCGA-EL-A3TB         TCGA-EL-A3ZH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3ZK         TCGA-EL-A3ZL         TCGA-EL-A3ZM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3ZN         TCGA-EL-A3ZO         TCGA-EL-A3ZP 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3ZS         TCGA-EL-A4JV         TCGA-EL-A4JW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A4JX         TCGA-EL-A4JZ         TCGA-EL-A4K0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A4K1         TCGA-EL-A4K2         TCGA-EL-A4K4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A4K6         TCGA-EL-A4K7         TCGA-EL-A4KD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A4KG         TCGA-EL-A4KI         TCGA-EM-A1CS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A1CT         TCGA-EM-A1CU         TCGA-EM-A1CV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A1CW         TCGA-EM-A1YC         TCGA-EM-A1YD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A1YE         TCGA-EM-A22I         TCGA-EM-A22J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A22K         TCGA-EM-A22L         TCGA-EM-A22M 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A22N         TCGA-EM-A22O         TCGA-EM-A22P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A22Q         TCGA-EM-A2CK         TCGA-EM-A2CN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A2CP         TCGA-EM-A2CQ         TCGA-EM-A2CS 
"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-A3AQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3AR         TCGA-EM-A3FJ         TCGA-EM-A3FK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3FL         TCGA-EM-A3FM         TCGA-EM-A3FN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3FO         TCGA-EM-A3FP         TCGA-EM-A3FQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3FR         TCGA-EM-A3O3         TCGA-EM-A3O8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3O9         TCGA-EM-A3OA         TCGA-EM-A3OB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3ST         TCGA-EM-A3SU         TCGA-EM-A3SX 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3SZ         TCGA-EM-A4FF         TCGA-EM-A4FM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A4FN         TCGA-EM-A4FO         TCGA-EM-A4FQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A4FR         TCGA-EM-A4FV         TCGA-EM-A4G1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A25G         TCGA-ET-A25I         TCGA-ET-A25J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A25K         TCGA-ET-A25L         TCGA-ET-A25M 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A25N         TCGA-ET-A25O         TCGA-ET-A25P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A2MX         TCGA-ET-A2MZ         TCGA-ET-A2N0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N4         TCGA-ET-A39K 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A39L         TCGA-ET-A39O         TCGA-ET-A39P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39S         TCGA-ET-A39T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A3BO         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-A3BV         TCGA-ET-A3BX         TCGA-ET-A3DQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A3DR         TCGA-ET-A3DS         TCGA-ET-A3DT 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A3DU         TCGA-ET-A3DV         TCGA-ET-A3DW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A40P         TCGA-ET-A40Q         TCGA-ET-A40R 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A40S         TCGA-ET-A40T         TCGA-ET-A4KN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A238         TCGA-FE-A239         TCGA-FE-A23A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A3PB         TCGA-FE-A3PC         TCGA-FE-A3PD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FK-A3S3         TCGA-FK-A3SB         TCGA-FK-A3SE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FK-A3SG         TCGA-FK-A3SH         TCGA-FK-A4UB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A2QD         TCGA-FY-A3I4         TCGA-FY-A3I5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A3NM         TCGA-FY-A3NN         TCGA-FY-A3ON 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A3R6         TCGA-FY-A3R7         TCGA-FY-A3R9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A3TY         TCGA-FY-A3W9         TCGA-FY-A3YR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A40K         TCGA-FY-A40L         TCGA-FY-A40M 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A40N         TCGA-FY-A4B3         TCGA-FY-A4B4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GE-A2C6         TCGA-H2-A26U         TCGA-H2-A2K9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-H2-A3RH         TCGA-H2-A3RI         TCGA-H2-A421 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-H2-A422         TCGA-IM-A3EB         TCGA-IM-A3ED 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IM-A3U2         TCGA-IM-A3U3         TCGA-IM-A41Y 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IM-A41Z         TCGA-IM-A420         TCGA-IM-A4EB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A3O0         TCGA-J8-A3O1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-J8-A3O2         TCGA-J8-A3YD         TCGA-J8-A3YE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-J8-A3YF         TCGA-J8-A3YG         TCGA-J8-A3YH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-J8-A42S         TCGA-J8-A4HW         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   320
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                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"
D55V17, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0   5
  19P LOSS WILD-TYPE  38 353
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    5
  19P LOSS WILD-TYPE   38  353
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                353
[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 475  14
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                489 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 0                 14 
$`21Q LOSS MUTATED`
TCGA-BJ-A190 TCGA-CE-A485 TCGA-DJ-A2Q0 TCGA-E8-A432 TCGA-EM-A22P TCGA-EM-A2OY 
       20.58         0.10        34.36        14.43        11.15        32.32 
TCGA-FY-A3I5 TCGA-J8-A4HW 
        7.82         2.60 

$`21Q LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        18.21        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
        8.25        18.87         4.01        11.57        16.73         7.56 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        17.69        23.34        20.71         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         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        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         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75        10.88        21.01         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.10         0.39        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       169.32         3.39         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       18.35        14.60         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45        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         5.33        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        12.56         8.28        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        5.52         8.78         8.42        37.74         6.77        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44        37.48        36.46        10.09         7.10        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        35.18        15.88        15.09        31.04        20.45 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        59.57        11.34        21.37        18.51        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        21.47        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        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
        8.32        24.20        17.23        27.62        18.21        21.34 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       19.07        15.42        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       31.23        22.29        11.70        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 
       13.81        14.07        14.27         3.02        25.45        14.70 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       14.10        14.96         7.69        20.68        13.78        13.58 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
       31.66        26.73       155.54        97.74       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
       45.53        60.95       157.15        37.94        57.01        80.91 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        58.82       139.86        98.53        45.40        57.11 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        64.87         1.41        50.24       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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      131.15       108.66        57.63        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       130.72       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 
       78.97        31.50        62.30        36.03        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       52.50        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        37.94        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        12.36 
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-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.74        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        27.65        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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        13.91         7.82        11.51        29.95        15.62 
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        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       98.56        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
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        81.34        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-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        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         0.99        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         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        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         2.99        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        10.26        16.90        21.83         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        17.23        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        86.70         6.02        19.73 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        20.25        12.89 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               0.1                0.1 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             34.36             169.32 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             12.79              20.45 
[1] "0.1 - 34.4 (12.8)"  "0.1 - 169.3 (20.4)"
[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       48       107        2        45         6
D56V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  1                281
  STAGE II                 4                 48
  STAGE III                2                107
  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 140 160 166  23
D56V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                1                140
  T2                6                160
  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 219 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5    3
  21Q LOSS WILD-TYPE  219  222
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0                5                219
  1                3                222
[1] 2 2
[1] FALSE
D56V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4   0
  21Q LOSS WILD-TYPE 273   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4    0
  21Q LOSS WILD-TYPE  273    9
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0                4                273
  1                0                  9
[1] 2 2
[1] FALSE
D56V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     5   3
  21Q LOSS WILD-TYPE 361 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5    3
  21Q LOSS WILD-TYPE  361  130
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                5                361
  MALE                  3                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  21Q LOSS MUTATED                0
  21Q LOSS WILD-TYPE              9
                    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                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  21Q LOSS MUTATED                                                                     0
  21Q LOSS WILD-TYPE                                                                  36
D56V8, 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                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         350
  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"
D56V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     0   8
  21Q LOSS WILD-TYPE  14 477
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      0    8
  21Q LOSS WILD-TYPE   14  477
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 0                 14
  YES                8                477
[1] 2 2
[1] FALSE
D56V10, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     7   0
  21Q LOSS WILD-TYPE 414  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      7    0
  21Q LOSS WILD-TYPE  414   17
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 7                414
  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 374  51   4  30
D56V12, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0                7                374
  R1                1                 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"
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   321
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                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"
D56V17, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     0   5
  21Q LOSS WILD-TYPE  38 353
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      0    5
  21Q LOSS WILD-TYPE   38  353
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                353
[1] 2 2
[1] FALSE

Clustering(57) Variable = 22Q LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    87   1
  22Q LOSS WILD-TYPE 396  13
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                88                409 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 13 
$`22Q LOSS MUTATED`
TCGA-4C-A93U TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 
        4.24        18.21        14.73        15.12        23.34        20.58 
TCGA-BJ-A2P4 TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A0XZ 
        7.04        23.31        10.88         3.45         0.39        20.22 
TCGA-DE-A4M8 TCGA-DJ-A13M TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS 
       18.54        17.26        56.19        13.12        42.58        26.20 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN 
       34.36        10.09        12.43        35.18        15.09        20.45 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E3-A3E5 
       31.46        16.41        27.62        15.42        12.07        14.04 
TCGA-E8-A432 TCGA-E8-A434 TCGA-EL-A3CL TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
       14.43        14.10        31.66       139.86        98.53        45.40 
TCGA-EL-A3GP TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL TCGA-EL-A3ZR TCGA-EL-A4JV 
        1.41        50.20        32.48        62.30        60.16        57.47 
TCGA-EL-A4JZ TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A22K 
       37.94        44.15        47.84        23.90        26.86        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2OY TCGA-EM-A3AP 
       10.45        14.53        11.15        16.44        32.32         8.35 
TCGA-EM-A3FO TCGA-EM-A3O9 TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FO TCGA-EM-A4FR 
       17.49         9.24        15.62        12.79        26.37        21.53 
TCGA-EM-A4FU TCGA-ET-A25L TCGA-ET-A25O TCGA-ET-A2N4 TCGA-ET-A39L TCGA-ET-A39M 
       60.49        14.79        27.09         2.66        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P TCGA-ET-A40T TCGA-FE-A237 
       98.56         4.18         0.30         3.22         2.14        81.34 
TCGA-FE-A3PB TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A4B4 TCGA-GE-A2C6 
       85.15        16.27         0.76        17.06        21.60        12.53 
TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YH TCGA-KS-A41I 
       16.90         9.63        43.17        31.82         5.75        15.98 
TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        84.72        20.25        12.89 

$`22Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB 
       24.79        13.78        16.34         8.25        18.87         4.01 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Z TCGA-BJ-A191 
       11.57        16.73         7.56        17.69        20.71         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         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PU 
       20.48        18.97        16.01        13.94        15.48        18.64 
TCGA-BJ-A45C TCGA-BJ-A45E TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        5.75        21.01         6.35         7.82         6.18        21.63 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93        23.47         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 
        0.23        11.38        10.68         0.10         0.10        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       36.46         5.98        15.85        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V 
       14.07       169.32         3.39         8.71        23.38        18.35 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH 
       14.60         8.32        11.01       135.91        30.61         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       14.96         7.20         1.45        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99         5.33        35.41        27.45        38.83        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
        8.28        34.85         5.52         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 
        6.77        40.24         9.44        37.48        36.46         7.10 
TCGA-DJ-A2Q9 TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       35.90        15.88        31.04        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        59.57        11.34        21.37        18.51 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        21.47        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        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UP 
        7.76         8.32        24.20        17.23        18.21        21.34 
TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       19.07        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3E0 
       24.33        54.90        21.53         2.33        31.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       40.21        63.19        30.31        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
        3.02        25.45        14.70        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.78        13.58        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
       80.91         4.18        58.82        57.11       108.36        64.87 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX 
       50.24       115.10        65.39       136.01        50.37       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T3 
       52.50        29.65       147.42       130.72       129.57       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-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       89.56        78.97        31.50        36.03        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JX 
       52.50        61.22         7.07        59.44        34.72        45.96 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4KD 
       31.04        34.39        30.51        53.36        41.13        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       24.30        27.06        18.18        20.91        12.36        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-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK TCGA-EM-A2CL 
       14.50        10.65        11.74        14.24        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        27.65        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        13.84        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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        13.38        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ 
       23.77        16.80        21.01        12.07        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        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SY TCGA-EM-A4FF TCGA-EM-A4FH 
        7.82        11.51        29.95        13.51        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-EM-A4G1 
       21.34         5.33        26.37        22.45        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M TCGA-ET-A25N 
       47.47        48.20        29.69        32.35        12.33        14.79 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       29.19        19.76        58.22        13.74        71.01        80.02 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        5.85         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R 
       17.98        25.32       132.36        24.72         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        5.03         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 
       44.25        24.69        68.22       117.40        66.77        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       33.63        81.83       106.36        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        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         0.99        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3YR 
       13.91        15.68        16.57        18.08         0.30        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A76V 
       15.16         6.58        22.49        19.04         1.35         1.68 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A41Y TCGA-IM-A420 TCGA-IM-A4EB 
       48.92        47.41        10.26        21.83         2.96         8.65 
TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       17.23        27.19        11.24        27.85        24.69        22.29 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A41L 
        2.47         2.60         0.20       143.57        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID 
        6.02        19.73         6.74        87.39        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 
       30.21 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               0.3                0.1 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            139.86             169.32 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             17.85              20.71 
[1] "0.3 - 139.9 (17.9)" "0.1 - 169.3 (20.7)"
[1] "hr=" "2.3"
D57V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  22Q LOSS MUTATED        49       11        17        1         9         1
  22Q LOSS WILD-TYPE     233       41        92        1        37         5
D57V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                 49                233
  STAGE II                11                 41
  STAGE III               17                 92
  STAGE IV                 1                  1
  STAGE IVA                9                 37
  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  34  26   4
  22Q LOSS WILD-TYPE 117 132 141  19
D57V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               24                117
  T2               34                132
  T3               26                141
  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    44  36
  22Q LOSS WILD-TYPE 180 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     44   36
  22Q LOSS WILD-TYPE  180  189
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               44                180
  1               36                189
[1] 2 2
[1] FALSE
D57V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    44   2
  22Q LOSS WILD-TYPE 233   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     44    2
  22Q LOSS WILD-TYPE  233    7
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               44                233
  1                2                  7
[1] 2 2
[1] FALSE
D57V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    62  26
  22Q LOSS WILD-TYPE 304 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     62   26
  22Q LOSS WILD-TYPE  304  107
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               62                304
  MALE                 26                107
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  22Q LOSS MUTATED                1
  22Q LOSS WILD-TYPE              8
                    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                                                                       23
  22Q LOSS WILD-TYPE                                                                     75
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  22Q LOSS MUTATED                                                                     3
  22Q LOSS WILD-TYPE                                                                  33
D57V8, multiclass
                                                                        clus
vv                                                                       22Q LOSS MUTATED
  OTHER  SPECIFY                                                                        1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        61
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               23
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   3
                                                                        clus
vv                                                                       22Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                          8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         295
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 75
  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"
D57V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     1  87
  22Q LOSS WILD-TYPE  13 398
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   87
  22Q LOSS WILD-TYPE   13  398
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 1                 13
  YES               87                398
[1] 2 2
[1] FALSE
D57V10, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    79   1
  22Q LOSS WILD-TYPE 342  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     79    1
  22Q LOSS WILD-TYPE  342   16
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                79                342
  YES                1                 16
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  22Q LOSS MUTATED             18                       2   63
  22Q LOSS WILD-TYPE          114                      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)                          18                114
  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    67   6   1   8
  22Q LOSS WILD-TYPE 314  46   3  22
D57V12, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               67                314
  R1                6                 46
  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  41
  22Q LOSS WILD-TYPE 180 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     45   41
  22Q LOSS WILD-TYPE  180  223
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  MULTIFOCAL               45                180
  UNIFOCAL                 41                223
[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    52
  22Q LOSS WILD-TYPE                        20   273
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                                          52                273
[1] 4 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  62
  22Q LOSS WILD-TYPE  32 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6   62
  22Q LOSS WILD-TYPE   32  296
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 32
  NOT HISPANIC OR LATINO               62                296
[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 479  14
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                4               493 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                0                14 
$`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-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        24.79        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83        44.35        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        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 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75        10.88        21.01         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18        21.63         8.98         4.93        23.47         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       169.32         3.39         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       18.35        14.60         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45        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         5.33        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        12.56         8.28        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24         9.44        37.48        36.46        10.09         7.10 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        12.43        35.18        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       20.45        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        59.57        11.34        21.37        18.51 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        21.47        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        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        24.20        17.23        27.62        18.21 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        19.07        15.42        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
       14.04        31.23        22.29        11.70        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       14.27        13.81        14.07        14.27         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       130.72       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        78.97        31.50        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        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        37.94        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        12.36        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       57.01        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        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        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       29.72        37.25        27.95        16.80        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        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        15.62        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        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        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 
       81.34        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        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         0.99        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         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83         9.63         2.96         8.65        17.23        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-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         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        86.70         6.02        19.73         6.74        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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        20.25 
TCGA-QD-A8IV 
       12.89 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
            13.78              0.10 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            54.08            169.32 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           22.175            20.250 
[1] "13.8 - 54.1 (22.2)" "0.1 - 169.3 (20.2)"
[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       49       109        2        46         6
D58V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 1               281
  STAGE II                3                49
  STAGE III               0               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
  XP LOSS MUTATED     1   3   0   0
  XP LOSS WILD-TYPE 140 163 167  23
D58V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               1               140
  T2               3               163
  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 221 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      3    1
  XP LOSS WILD-TYPE  221  224
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0               3               221
  1               1               224
[1] 2 2
[1] FALSE
D58V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     0   0
  XP LOSS WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0    0
  XP LOSS WILD-TYPE  277    9
D58V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     2   2
  XP LOSS WILD-TYPE 364 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2    2
  XP LOSS WILD-TYPE  364  131
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE               2               364
  MALE                 2               131
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  XP LOSS MUTATED                0
  XP LOSS WILD-TYPE              9
                   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                                                                     97
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  XP LOSS MUTATED                                                                     0
  XP LOSS WILD-TYPE                                                                  36
D58V8, 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                                                                         9
  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"
D58V9, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     0   4
  XP LOSS WILD-TYPE  14 481
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0    4
  XP LOSS WILD-TYPE   14  481
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                0                14
  YES               4               481
[1] 2 2
[1] FALSE
D58V10, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     3   0
  XP LOSS WILD-TYPE 418  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      3    0
  XP LOSS WILD-TYPE  418   17
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                3               418
  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 377  52   4  30
D58V12, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0               4               377
  R1               0                52
  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-4C-A93U        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC        TCGA-BJ-A0ZE 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ        TCGA-BJ-A18Y 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192        TCGA-BJ-A28R 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V        TCGA-BJ-A28W 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N8 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A2N9        TCGA-BJ-A2P4        TCGA-BJ-A3PU        TCGA-BJ-A45C 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45F        TCGA-BJ-A45G 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A45H        TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K        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-A0XZ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL        TCGA-DE-A3KN 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA        TCGA-DE-A4MB 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J        TCGA-DE-A69K 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A7U5        TCGA-DJ-A13L        TCGA-DJ-A13M        TCGA-DJ-A13O 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13U        TCGA-DJ-A13V 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A13W        TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A1QF        TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QI 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A1QL        TCGA-DJ-A1QM        TCGA-DJ-A1QN        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-A2PP 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        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-A3UU        TCGA-DJ-A3UW 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3UX        TCGA-DJ-A3UY        TCGA-DJ-A3V0        TCGA-DJ-A3V2 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3V3        TCGA-DJ-A3V4        TCGA-DJ-A3V5        TCGA-DJ-A3V7 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3V8        TCGA-DJ-A3VA        TCGA-DJ-A3VB        TCGA-DJ-A3VD 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3VE        TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3VL        TCGA-DJ-A3VM        TCGA-DJ-A4UL        TCGA-DJ-A4UP 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A4UQ        TCGA-DJ-A4UT        TCGA-DJ-A4V0        TCGA-DJ-A4V2 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A4V4        TCGA-DJ-A4V5        TCGA-DO-A1JZ        TCGA-DO-A1K0 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DO-A2HM        TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-E3-A3E1        TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E8-A419 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CR        TCGA-EL-A3CS 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        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-A3GQ        TCGA-EL-A3GR 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H2 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EL-A3T1 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3T2        TCGA-EL-A3T3        TCGA-EL-A3T6        TCGA-EL-A3T7 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3T8        TCGA-EL-A3T9        TCGA-EL-A3TA        TCGA-EL-A3TB 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3ZG        TCGA-EL-A3ZH        TCGA-EL-A3ZK        TCGA-EL-A3ZL 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3ZM        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-A1CS 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A22N        TCGA-EM-A22O        TCGA-EM-A22P        TCGA-EM-A22Q 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A2CT        TCGA-EM-A2CU        TCGA-EM-A2OW        TCGA-EM-A2OX 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P0        TCGA-EM-A2P1        TCGA-EM-A2P2 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A2P3        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AK 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A3AQ        TCGA-EM-A3AR        TCGA-EM-A3FJ        TCGA-EM-A3FM 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FR 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A3O3        TCGA-EM-A3O6        TCGA-EM-A3O7        TCGA-EM-A3O8 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A3O9        TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A3SU        TCGA-EM-A3SX        TCGA-EM-A3SY        TCGA-EM-A3SZ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A4FF        TCGA-EM-A4FH        TCGA-EM-A4FK        TCGA-EM-A4FM 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A4FN        TCGA-EM-A4FQ        TCGA-EM-A4FR        TCGA-EM-A4FU 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G        TCGA-ET-A25I 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A25R 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N5 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39O 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BO 
"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-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A40P 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A4KN 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-ET-A4KQ        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A232 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FE-A3PA        TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FY-A2QD        TCGA-FY-A3I4        TCGA-FY-A3I5        TCGA-FY-A3ON 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FY-A3R8        TCGA-FY-A3TY        TCGA-FY-A3W9        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-A4B3        TCGA-FY-A76V        TCGA-GE-A2C6        TCGA-H2-A421 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-IM-A3U2        TCGA-IM-A3U3 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-IM-A41Y        TCGA-IM-A41Z        TCGA-IM-A420        TCGA-IM-A4EB 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-J8-A3O0        TCGA-J8-A3YD        TCGA-J8-A3YG        TCGA-KS-A41F 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-KS-A41I        TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I3 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-L6-A4ET        TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-MK-A4N9        TCGA-MK-A84Z        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   324
D58V16, multiclass
[1] "Remove cluster labels:" "XP LOSS MUTATED"       
clus
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                1               404 
       TCGA-4C-A93U        TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A0ZJ        TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N8 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4        TCGA-BJ-A3EZ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-BJ-A3F0        TCGA-BJ-A3PR        TCGA-BJ-A3PT        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-A45K        TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-CE-A482        TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A3KN        TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13L        TCGA-DJ-A13M 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A13O        TCGA-DJ-A13P        TCGA-DJ-A13R        TCGA-DJ-A13S 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A13T        TCGA-DJ-A13U        TCGA-DJ-A13W        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-A1QM        TCGA-DJ-A1QO        TCGA-DJ-A1QQ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PQ        TCGA-DJ-A2PR 
"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-A3UU 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3UW        TCGA-DJ-A3UX        TCGA-DJ-A3UY        TCGA-DJ-A3UZ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V4        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-A3V9        TCGA-DJ-A3VD 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3VE        TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A3VL        TCGA-DJ-A3VM        TCGA-DJ-A4UL        TCGA-DJ-A4UP 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UT        TCGA-DJ-A4UW 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DJ-A4V0        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-E3-A3E5        TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A2JQ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-E8-A3X7        TCGA-E8-A413        TCGA-E8-A414        TCGA-E8-A415 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-E8-A416        TCGA-E8-A417        TCGA-E8-A418        TCGA-E8-A419 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-E8-A432        TCGA-E8-A433        TCGA-E8-A434        TCGA-E8-A436 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-E8-A437        TCGA-E8-A438        TCGA-E8-A44K        TCGA-E8-A44M 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS        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-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GQ        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-A3H2 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3        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-A3BO        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-A3BV        TCGA-ET-A3BW        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-A3SD        TCGA-FK-A3SE        TCGA-FK-A3SG 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3I5        TCGA-FY-A3NM        TCGA-FY-A3ON 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FY-A3R6        TCGA-FY-A3R7        TCGA-FY-A3R8        TCGA-FY-A3R9 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FY-A3RA        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-FY-A76V 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-H2-A3RI        TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-IM-A3ED        TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-IM-A41Z        TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-J8-A3O0        TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-J8-A3YE        TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-J8-A42S        TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-KS-A41I        TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-KS-A4I3        TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-KS-A4IB        TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-L6-A4EQ        TCGA-L6-A4ET        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-MK-A84Z        TCGA-QD-A8IV 
"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  38 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0    2
  XP LOSS WILD-TYPE   38  356
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               356
[1] 2 2
[1] FALSE

Clustering(59) Variable = XQ LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED     3   0
  XQ LOSS WILD-TYPE 480  14
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               494 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                0                14 
$`XQ LOSS MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A190 TCGA-EM-A1YE 
       13.78        20.58        54.08 

$`XQ LOSS WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        24.79        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83        44.35        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        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 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75        10.88        21.01         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18        21.63         8.98         4.93        23.47         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       169.32         3.39         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       18.35        14.60         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45        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         5.33        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        12.56         8.28        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24         9.44        37.48        36.46        10.09         7.10 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        12.43        35.18        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       20.45        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        59.57        11.34        21.37        18.51 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        21.47        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        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        24.20        17.23        27.62        18.21 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        19.07        15.42        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
       14.04        31.23        22.29        11.70        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       14.27        13.81        14.07        14.27         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        50.24 
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-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       130.72       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        78.97        31.50        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        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        37.94        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        12.36        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       57.01        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        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        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        16.80        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        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        29.95        15.62        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        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        81.34        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-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
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-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         7.82         0.99        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         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        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 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83         9.63         2.96         8.65        17.23 
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-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         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        86.70         6.02        19.73         6.74 
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-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       20.25        12.89 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            13.78              0.10 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            54.08            169.32 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           20.580            20.335 
[1] "13.8 - 54.1 (20.6)" "0.1 - 169.3 (20.3)"
[1] "hr="     "3300000"
D59V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  XQ LOSS MUTATED         0        3         0        0         0         0
  XQ LOSS WILD-TYPE     282       49       109        2        46         6
D59V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 0               282
  STAGE II                3                49
  STAGE III               0               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
  XQ LOSS MUTATED     0   3   0   0
  XQ LOSS WILD-TYPE 141 163 167  23
D59V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               0               141
  T2               3               163
  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     3   0
  XQ LOSS WILD-TYPE 221 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    0
  XQ LOSS WILD-TYPE  221  225
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0               3               221
  1               0               225
[1] 2 2
[1] FALSE
D59V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0   0
  XQ LOSS WILD-TYPE 277   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    0
  XQ LOSS WILD-TYPE  277    9
D59V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     1   2
  XQ LOSS WILD-TYPE 365 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    2
  XQ LOSS WILD-TYPE  365  131
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               1               365
  MALE                 2               131
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  XQ LOSS MUTATED                0
  XQ LOSS WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  XQ LOSS MUTATED                                               2
  XQ LOSS WILD-TYPE                                           354
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  XQ LOSS MUTATED                                                                        1
  XQ LOSS WILD-TYPE                                                                     97
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  XQ LOSS MUTATED                                                                     0
  XQ LOSS WILD-TYPE                                                                  36
D59V8, multiclass
                                                                        clus
vv                                                                       XQ 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                                                                       XQ LOSS WILD-TYPE
  OTHER  SPECIFY                                                                         9
  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"
D59V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0   3
  XQ LOSS WILD-TYPE  14 482
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    3
  XQ LOSS WILD-TYPE   14  482
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                0                14
  YES               3               482
[1] 2 2
[1] FALSE
D59V10, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2   0
  XQ LOSS WILD-TYPE 419  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2    0
  XQ LOSS WILD-TYPE  419   17
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                2               419
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  XQ LOSS MUTATED              0                       0    3
  XQ LOSS WILD-TYPE          132                      18  327
                   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                                  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
  XQ LOSS MUTATED     3   0   0   0
  XQ LOSS WILD-TYPE 378  52   4  30
D59V12, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0               3               378
  R1               0                52
  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"
D59V13, continuous
D59V14, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     1   2
  XQ LOSS WILD-TYPE 224 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    2
  XQ LOSS WILD-TYPE  224  262
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  MULTIFOCAL               1               224
  UNIFOCAL                 2               262
[1] 2 2
[1] FALSE
D59V15, continuous
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2               399 
       TCGA-4C-A93U        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC        TCGA-BJ-A0ZE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ        TCGA-BJ-A18Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192        TCGA-BJ-A28R 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V        TCGA-BJ-A28W 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A28Z        TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A2N9        TCGA-BJ-A2P4        TCGA-BJ-A3PU        TCGA-BJ-A45C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45F        TCGA-BJ-A45G 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A45H        TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K        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-A0XZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL        TCGA-DE-A3KN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA        TCGA-DE-A4MB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J        TCGA-DE-A69K 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A7U5        TCGA-DJ-A13L        TCGA-DJ-A13M        TCGA-DJ-A13O 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13U        TCGA-DJ-A13V 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A13W        TCGA-DJ-A13X        TCGA-DJ-A1QD        TCGA-DJ-A1QE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A1QF        TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QI 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A1QL        TCGA-DJ-A1QM        TCGA-DJ-A1QN        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-A2PP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2QC        TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ        TCGA-DJ-A3UR 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3US        TCGA-DJ-A3UT        TCGA-DJ-A3UU        TCGA-DJ-A3UW 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3UX        TCGA-DJ-A3UY        TCGA-DJ-A3V0        TCGA-DJ-A3V2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3V3        TCGA-DJ-A3V4        TCGA-DJ-A3V5        TCGA-DJ-A3V7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3V8        TCGA-DJ-A3VA        TCGA-DJ-A3VB        TCGA-DJ-A3VD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3VE        TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3VL        TCGA-DJ-A3VM        TCGA-DJ-A4UL        TCGA-DJ-A4UP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A4UQ        TCGA-DJ-A4UT        TCGA-DJ-A4V0        TCGA-DJ-A4V2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A4V4        TCGA-DJ-A4V5        TCGA-DO-A1JZ        TCGA-DO-A1K0 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DO-A2HM        TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E3-A3E1        TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E8-A419 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CR        TCGA-EL-A3CS 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        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-A3GQ        TCGA-EL-A3GR 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EL-A3T1 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3T2        TCGA-EL-A3T3        TCGA-EL-A3T6        TCGA-EL-A3T7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3T8        TCGA-EL-A3T9        TCGA-EL-A3TA        TCGA-EL-A3TB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3ZG        TCGA-EL-A3ZH        TCGA-EL-A3ZK        TCGA-EL-A3ZL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3ZM        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-A1CS 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A22N        TCGA-EM-A22O        TCGA-EM-A22P        TCGA-EM-A22Q 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A2CT        TCGA-EM-A2CU        TCGA-EM-A2OW        TCGA-EM-A2OX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P0        TCGA-EM-A2P1        TCGA-EM-A2P2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A2P3        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A3AQ        TCGA-EM-A3AR        TCGA-EM-A3FJ        TCGA-EM-A3FM 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FR 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A3O3        TCGA-EM-A3O6        TCGA-EM-A3O7        TCGA-EM-A3O8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A3O9        TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A3SU        TCGA-EM-A3SX        TCGA-EM-A3SY        TCGA-EM-A3SZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A4FF        TCGA-EM-A4FH        TCGA-EM-A4FK        TCGA-EM-A4FM 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A4FN        TCGA-EM-A4FQ        TCGA-EM-A4FR        TCGA-EM-A4FU 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G        TCGA-ET-A25I 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A25R 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39O 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BO 
"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-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A40P 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A4KN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A4KQ        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A232 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A3PA        TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A2QD        TCGA-FY-A3I4        TCGA-FY-A3I5        TCGA-FY-A3ON 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A3R8        TCGA-FY-A3TY        TCGA-FY-A3W9        TCGA-FY-A3YR 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A4B3        TCGA-FY-A76V        TCGA-GE-A2C6        TCGA-H2-A421 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-IM-A3U2        TCGA-IM-A3U3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IM-A41Y        TCGA-IM-A41Z        TCGA-IM-A420        TCGA-IM-A4EB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J8-A3O0        TCGA-J8-A3YD        TCGA-J8-A3YG        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-A4I3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-L6-A4ET        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-MK-A84Z        TCGA-QD-A8IV 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
                   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     1
  XQ LOSS WILD-TYPE                        27   324
D59V16, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1               404 
       TCGA-4C-A93U        TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A0Z5        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A0ZJ        TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4        TCGA-BJ-A3EZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A3F0        TCGA-BJ-A3PR        TCGA-BJ-A3PT        TCGA-BJ-A3PU 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45F 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A45G        TCGA-BJ-A45H        TCGA-BJ-A45I        TCGA-BJ-A45J 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A45K        TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CE-A482        TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A3KN        TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13L        TCGA-DJ-A13M 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A13O        TCGA-DJ-A13P        TCGA-DJ-A13R        TCGA-DJ-A13S 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A13T        TCGA-DJ-A13U        TCGA-DJ-A13W        TCGA-DJ-A1QD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG        TCGA-DJ-A1QH 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A1QI        TCGA-DJ-A1QM        TCGA-DJ-A1QO        TCGA-DJ-A1QQ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2PN        TCGA-DJ-A2PO        TCGA-DJ-A2PQ        TCGA-DJ-A2PR 
"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-A3UU 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3UW        TCGA-DJ-A3UX        TCGA-DJ-A3UY        TCGA-DJ-A3UZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V4        TCGA-DJ-A3V5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9        TCGA-DJ-A3VD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3VE        TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3VL        TCGA-DJ-A3VM        TCGA-DJ-A4UL        TCGA-DJ-A4UP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UT        TCGA-DJ-A4UW 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A4V0        TCGA-DJ-A4V4        TCGA-DJ-A4V5        TCGA-DO-A1JZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY        TCGA-E3-A3DZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2        TCGA-E3-A3E3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A2JQ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E8-A3X7        TCGA-E8-A413        TCGA-E8-A414        TCGA-E8-A415 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E8-A416        TCGA-E8-A417        TCGA-E8-A418        TCGA-E8-A419 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E8-A432        TCGA-E8-A433        TCGA-E8-A434        TCGA-E8-A436 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E8-A437        TCGA-E8-A438        TCGA-E8-A44K        TCGA-E8-A44M 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS        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-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GQ        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-A3H2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3        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-A3BO        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-A3BV        TCGA-ET-A3BW        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-A40S 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A40T        TCGA-ET-A4KN        TCGA-ET-A4KQ        TCGA-FE-A22Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FK-A3SB        TCGA-FK-A3SD        TCGA-FK-A3SE        TCGA-FK-A3SG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3I5        TCGA-FY-A3NM        TCGA-FY-A3ON 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A3R6        TCGA-FY-A3R7        TCGA-FY-A3R8        TCGA-FY-A3R9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A3RA        TCGA-FY-A3W9        TCGA-FY-A3WA        TCGA-FY-A3YR 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A4B0        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-FY-A76V 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-H2-A3RI        TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IM-A3ED        TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IM-A41Z        TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J8-A3O0        TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J8-A3YE        TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J8-A42S        TCGA-J8-A4HW        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-A4ET        TCGA-L6-A4EU        TCGA-MK-A4N6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-MK-A4N7        TCGA-MK-A4N9        TCGA-MK-A84Z        TCGA-QD-A8IV 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D59V17, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0   2
  XQ LOSS WILD-TYPE  38 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    2
  XQ LOSS WILD-TYPE   38  356
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               356
[1] 2 2
[1] FALSE
