[1] "ofn"        "-oTTGCT-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/TGCT-TP/15092576/TGCT-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/TGCT-TP/15101914/transformed.cor.cli.txt"

nPatients in clinical file=133, in cluster file=150, common to both=133
[1] "Reduce the number of clustering variables from 82 to 74."
[1]  74 133
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               32               101 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               32               101 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               54                79 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               54                79 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               39                94 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               39                94 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               38                95 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               38                95 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               23               110 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               23               110 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               31               102 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               31               102 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3               130 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3               130 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                6               127 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                6               127 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3               130 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3               130 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               21               112 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               21               112 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               17               116 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               17               116 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              110                23 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              110                23 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               96                37 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               96                37 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              101                32 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              101                32 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              103                30 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              103                30 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               119 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               119 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               15               118 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               15               118 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                127 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                127 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                125 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                125 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                124 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                124 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                129 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                129 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               129                  4 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               129                  4 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                90                 43 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                90                 43 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                45                 88 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                45                 88 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                47                 86 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                47                 86 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                13                120 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                13                120 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                120 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                120 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                32                101 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                32                101 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                43                 90 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                43                 90 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                129 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                129 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                32                101 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                32                101 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                26                107 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                26                107 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                30                103 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                30                103 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                33                100 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                33                100 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               112                 21 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               112                 21 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                34                 99 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                34                 99 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               18               115 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               18               115 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               18               115 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               18               115 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               17               116 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               17               116 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8               125 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8               125 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5               128 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5               128 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6               127 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6               127 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               30               103 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               30               103 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               22               111 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               22               111 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               83                50 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               83                50 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               98                35 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               98                35 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               92                41 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               92                41 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               90                43 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               90                43 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               11               122 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               11               122 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14               119 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14               119 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10               123 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10               123 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               129 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               129 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               55                78 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               55                78 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               50                83 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               50                83 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                67                 66 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                67                 66 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                63                 70 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                63                 70 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                88                 45 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                88                 45 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               104                 29 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               104                 29 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               103                 30 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               103                 30 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                17                116 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                17                116 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                22                111 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                22                111 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                43                 90 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                43                 90 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                46                 87 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                46                 87 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                34                 99 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                34                 99 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                14                119 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                14                119 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               103                 30 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               103                 30 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               109                 24 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               109                 24 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                40                 93 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                40                 93 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                42                 91 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                42                 91 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                28                105 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                28                105 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                15                118 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                15                118 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                38                 95 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                38                 95 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               23               110 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               23               110 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               23               110 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               23               110 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATION_THERAPY"                     
[12] "RADIATIONS_RADIATION_REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 133 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=4,	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=127,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              12-3-2015 26-3-2015
freq.values   "1"       "132"    
freq.contrast "132"     "1"      
both >= 3     "FALSE"   "FALSE"  
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'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 12:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH_NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER excluded in the analysis because there is no case of (both >= 3) in the table below"
              B430.15.0 B430.16.0
freq.values   "1"       "132"    
freq.contrast "132"     "1"      
both >= 3     "FALSE"   "FALSE"  
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 133 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"        "NEOPLASM_DISEASESTAGE" "PATHOLOGY_T_STAGE"    
[4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "RACE"                 
[7] "ETHNICITY"            
YEARS_TO_BIRTH, nv=38, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 
75 51  6 
[1] "table(vv)"
vv
T1 T2 T3 
75 51  6 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 
75 51  6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T1 T2 T3 
75 51  6 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
46 11  2 
[1] "table(vv)"
vv
   N0 N1+N2 
   46    13 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
46 11  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 46

$Class1_nSamples
[1] 13

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   46    13 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
RACE, nv=3, 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   31  1
  1P GAIN WILD-TYPE 98  3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               32               101 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                 3 
$`1P GAIN MUTATED`
TCGA-2G-AAFI TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG7 
       14.14         9.57        14.86        16.50        36.13        61.71 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGP TCGA-2G-AAGW 
       68.38        79.76        67.96       108.16       120.62        61.45 
TCGA-2G-AAHT TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
        6.08       212.65       161.72       229.22       184.41       131.21 
TCGA-4K-AA1G TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-W4-A7U4 TCGA-XE-A8H1 
        3.52        10.26        17.23        37.18        24.26         6.87 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOD TCGA-XE-AAOL TCGA-YU-A90P TCGA-ZM-AA05 
       12.07         7.89        67.66         0.43        57.90        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B 
       39.35        27.55 

$`1P GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFV 
      154.59       191.31        36.99        14.56        17.16        40.70 
TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 
       36.89        40.01        52.37        71.24        72.20        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM 
       63.32        68.22        72.85        92.09        75.09        59.64 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX 
      106.39       115.00        59.28       124.57       128.94       170.33 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
       80.94        60.16        60.26        59.84        59.90       125.69 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       61.84        98.53        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKL TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      176.15       122.50        95.67        70.59         2.73         0.13 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
        7.00         0.10         4.83        20.68        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SO-A8JP TCGA-VF-A8A9 
       13.58         1.38        16.31         9.63         3.52        36.79 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
        4.90         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B 
       93.93        16.87         8.88        41.69        50.96         8.32 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       12.92        20.12         6.90        54.35        31.92        21.96 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56         5.29        58.88         7.96        40.96         8.15 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.43              0.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           229.22            191.31 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             37.1              38.3 
[1] "0.4 - 229.2 (37.1)" "0.1 - 191.3 (38.3)"
[1] "hr="     "2.7e+08"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         3        5        3        2         4         0
  1P GAIN WILD-TYPE      16       20        8        3         2         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P GAIN MUTATED           1         0          0          1          1
  1P GAIN WILD-TYPE         0         2          1          5          4
                   vv
clus                STAGE IS
  1P GAIN MUTATED         11
  1P GAIN WILD-TYPE       35
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  3                16
  STAGE IA                 5                20
  STAGE IB                 3                 8
  STAGE II                 2                 3
  STAGE IIA                4                 2
  STAGE IIB                0                 1
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               1                 5
  STAGE IIIC               1                 4
  STAGE IS                11                35
[1] 12  2
[1] 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
  1P GAIN MUTATED   13 18  1
  1P GAIN WILD-TYPE 62 33  5
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              13                62
  T2              18                33
  T3               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  1P GAIN MUTATED   12     6
  1P GAIN WILD-TYPE 34     7
D1V5, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0                 12                34
  N1+N2               6                 7
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   30  1
  1P GAIN WILD-TYPE 84  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     30    1
  1P GAIN WILD-TYPE   84    3
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              30                84
  1               1                 3
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       0                         1    31
  1P GAIN WILD-TYPE     4                         5    87
D1V7, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  31                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    4 27
  1P GAIN WILD-TYPE  7 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4   27
  1P GAIN WILD-TYPE    7   84
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 7
  NOT HISPANIC OR LATINO              27                84
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   52  2
  1Q GAIN WILD-TYPE 77  2
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               54                79 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                2                 2 
$`1Q GAIN MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF8 TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFM 
       20.32        30.35       122.40        36.99        14.14         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 
       14.86        16.50        40.70        36.13        40.01        52.37 
TCGA-2G-AAG7 TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGP 
       61.71        68.38        79.76        67.96       108.16       120.62 
TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA 
      124.57        61.45        80.94        60.26        61.84        98.53 
TCGA-2G-AAHT TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-4K-AA1G TCGA-SN-A6IS 
        6.08       229.22       184.41       131.21         3.52        16.31 
TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-W4-A7U4 TCGA-WZ-A7V5 
       10.26        17.23        37.18        36.79        24.26         0.16 
TCGA-XE-A8H1 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
        6.87        40.01        65.98        93.93        12.07         7.89 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90W 
        8.88        67.66         0.43         6.90        57.90        21.96 
TCGA-YU-A94D TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0H TCGA-ZM-AA0N 
       58.88        37.02        39.35        27.55        46.88        10.85 

$`1Q GAIN WILD-TYPE`
TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFJ 
       38.30        59.70       102.35       154.59       191.31        14.56 
TCGA-2G-AAFL TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAG9 
       17.16        36.89        71.24        72.20        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGN 
       68.22        72.85        92.09        75.09        59.64       106.39 
TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH2 
      115.00        59.28       128.94       170.33        60.16        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       59.90       125.69        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AALP 
      176.15       122.50       212.65       161.72        95.67        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
        2.73         0.13         7.00         0.10         4.83        20.68 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A84W TCGA-SO-A8JP 
       18.15         9.14        13.58         1.38         9.63         3.52 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H4 
        4.90         3.65         5.06         0.82        28.14        18.38 
TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XE-AAOJ 
       34.22         0.46        53.03        16.87        41.69        50.96 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90Y 
        8.32        12.92        20.12        54.35        31.92         0.56 
TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA0D TCGA-ZM-AA0E 
        5.29         7.96        40.96         8.15        17.39        16.41 
TCGA-ZM-AA0F 
       11.34 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.16              0.10 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           229.22            212.65 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           38.265            37.680 
[1] "0.2 - 229.2 (38.3)" "0.1 - 212.7 (37.7)"
[1] "hr=" "1.4"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         4        9        5        1         4         1
  1Q GAIN WILD-TYPE      15       16        6        4         2         0
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q GAIN MUTATED           1         0          0          2          2
  1Q GAIN WILD-TYPE         0         2          1          4          3
                   vv
clus                STAGE IS
  1Q GAIN MUTATED         24
  1Q GAIN WILD-TYPE       22
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  4                15
  STAGE IA                 9                16
  STAGE IB                 5                 6
  STAGE II                 1                 4
  STAGE IIA                4                 2
  STAGE IIB                1                 0
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               2                 4
  STAGE IIIC               2                 3
  STAGE IS                24                22
[1] 12  2
[1] 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
  1Q GAIN MUTATED   23 28  3
  1Q GAIN WILD-TYPE 52 23  3
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              23                52
  T2              28                23
  T3               3                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  1Q GAIN MUTATED   18     7
  1Q GAIN WILD-TYPE 28     6
D2V5, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0                 18                28
  N1+N2               7                 6
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   49  1
  1Q GAIN WILD-TYPE 65  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     49    1
  1Q GAIN WILD-TYPE   65    3
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              49                65
  1               1                 3
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       1                         1    50
  1Q GAIN WILD-TYPE     3                         5    68
D2V7, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  50                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    8 43
  1Q GAIN WILD-TYPE  3 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      8   43
  1Q GAIN WILD-TYPE    3   68
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                 3
  NOT HISPANIC OR LATINO              43                68
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED   38  1
  2P GAIN WILD-TYPE 91  3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               39                94 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                 3 
$`2P GAIN MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAG3 
       59.70       191.31        14.14        16.50        40.70        52.37 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       61.71        63.22        68.38        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAHC 
      108.16        59.64       120.62       124.57        61.45        59.74 
TCGA-2G-AAKL TCGA-4K-AA1G TCGA-S6-A8JW TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A84X 
       95.67         3.52        20.68        13.58         1.38        10.26 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-A8H4 TCGA-XE-A8H5 
        3.52        37.18         0.16        28.14        18.38        40.01 
TCGA-XE-AAOC TCGA-XE-AAOF TCGA-XY-A8S2 TCGA-YU-A90P TCGA-YU-A90W TCGA-YU-A90Y 
        8.88        41.69        12.92        57.90        21.96         0.56 
TCGA-YU-A94D TCGA-YU-A94I TCGA-ZM-AA06 
       58.88         7.96        39.35 

$`2P GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        38.30       102.35       122.40       154.59 
TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFY 
       36.99        14.56        17.16         9.57        14.86        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG9 TCGA-2G-AAGA 
       36.89        40.01        71.24        72.20        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGV 
       72.85        79.76       106.39       115.00        59.28       128.94 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
      170.33        80.94        60.16        60.26        59.84        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
      125.69        61.84        98.53        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM 
      176.15         6.08       122.50       212.65       161.72       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H 
      184.41       131.21        70.59         2.73         0.13         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SN-A6IS TCGA-SN-A84W 
        0.10         4.83        18.15         9.14        16.31         9.63 
TCGA-SN-A84Y TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       17.23        36.79        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       23.90        41.52         4.90        24.26         3.65         5.06 
TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
        0.82         6.87        34.22        65.98         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOJ 
       93.93        12.07         7.89        16.87        67.66        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S 
        0.43         8.32        20.12         6.90        54.35        31.92 
TCGA-YU-A912 TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D 
        5.29        40.96         8.15        37.02        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.16              0.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           191.31            229.22 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            40.70             36.94 
[1] "0.2 - 191.3 (40.7)" "0.1 - 229.2 (36.9)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         4        9        3        1         2         0
  2P GAIN WILD-TYPE      15       16        8        4         4         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P GAIN MUTATED           0         0          0          1          2
  2P GAIN WILD-TYPE         1         2          1          5          3
                   vv
clus                STAGE IS
  2P GAIN MUTATED         16
  2P GAIN WILD-TYPE       30
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  4                15
  STAGE IA                 9                16
  STAGE IB                 3                 8
  STAGE II                 1                 4
  STAGE IIA                2                 4
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               1                 5
  STAGE IIIC               2                 3
  STAGE IS                16                30
[1] 12  2
[1] 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
  2P GAIN MUTATED   22 13  3
  2P GAIN WILD-TYPE 53 38  3
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              22                53
  T2              13                38
  T3               3                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  2P GAIN MUTATED   16     3
  2P GAIN WILD-TYPE 30    10
D3V5, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0                 16                30
  N1+N2               3                10
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   32  1
  2P GAIN WILD-TYPE 82  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     32    1
  2P GAIN WILD-TYPE   82    3
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              32                82
  1               1                 3
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       1                         2    33
  2P GAIN WILD-TYPE     3                         4    85
D3V7, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               2                 4
  WHITE                                  33                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    3 31
  2P GAIN WILD-TYPE  8 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3   31
  2P GAIN WILD-TYPE    8   80
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              31                80
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED   37  1
  2Q GAIN WILD-TYPE 92  3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               38                95 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                 3 
$`2Q GAIN MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFI TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAG3 TCGA-2G-AAG8 
       59.70        14.14        16.50        40.70        52.37        63.22 
TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGP 
       68.38        67.96        92.09       108.16        59.64       120.62 
TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHT 
      124.57        61.45        98.53        59.74        59.80         6.08 
TCGA-2G-AAKL TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-S6-A8JW TCGA-SO-A8JP TCGA-VF-A8A8 
       95.67         0.13         3.52        20.68         3.52        37.18 
TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AAOC TCGA-XE-AAOF 
        0.16        28.14        18.38        40.01         8.88        41.69 
TCGA-XE-AAOL TCGA-XY-A8S2 TCGA-YU-A90P TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D 
        0.43        12.92        57.90        21.96         0.56        58.88 
TCGA-YU-A94I TCGA-ZM-AA06 
        7.96        39.35 

$`2Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        38.30       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      191.31        36.99        14.56        17.16         9.57        14.86 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 
       36.13        36.89        40.01        71.24        72.20        61.71 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGN 
       63.32        68.22        72.85        79.76        75.09       106.39 
TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      115.00        59.28       128.94       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHG 
       60.26        59.84        59.90       125.69        61.84        59.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM 
       91.43       176.15       122.50       212.65       161.72       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1H TCGA-4K-AA1I 
      184.41       131.21        70.59         2.73         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
        4.83        18.15         9.14        13.58         1.38        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
        9.63        10.26        17.23        36.79        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 
       35.61        33.07        23.90        41.52         4.90        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-AANI TCGA-XE-AANJ 
        3.65         5.06         0.82         6.87        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        53.03        93.93        12.07         7.89        16.87 
TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q 
       67.66        50.96         8.32        20.12         6.90        54.35 
TCGA-YU-A90S TCGA-YU-A912 TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0B 
       31.92         5.29        40.96         8.15        37.02        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.13              0.10 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           124.57            229.22 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           40.355            36.990 
[1] "0.1 - 124.6 (40.4)" "0.1 - 229.2 (37.0)"
[1] "hr=" "1.3"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         7        7        4        1         2         0
  2Q GAIN WILD-TYPE      12       18        7        4         4         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q GAIN MUTATED           0         0          0          1          2
  2Q GAIN WILD-TYPE         1         2          1          5          3
                   vv
clus                STAGE IS
  2Q GAIN MUTATED         14
  2Q GAIN WILD-TYPE       32
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  7                12
  STAGE IA                 7                18
  STAGE IB                 4                 7
  STAGE II                 1                 4
  STAGE IIA                2                 4
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               1                 5
  STAGE IIIC               2                 3
  STAGE IS                14                32
[1] 12  2
[1] 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
  2Q GAIN MUTATED   19 15  3
  2Q GAIN WILD-TYPE 56 36  3
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              19                56
  T2              15                36
  T3               3                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  2Q GAIN MUTATED   15     3
  2Q GAIN WILD-TYPE 31    10
D4V5, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0                 15                31
  N1+N2               3                10
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   31  1
  2Q GAIN WILD-TYPE 83  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     31    1
  2Q GAIN WILD-TYPE   83    3
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              31                83
  1               1                 3
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       1                         2    32
  2Q GAIN WILD-TYPE     3                         4    86
D4V7, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               2                 4
  WHITE                                  32                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    2 31
  2Q GAIN WILD-TYPE  9 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   31
  2Q GAIN WILD-TYPE    9   80
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              31                80
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    23   0
  3P GAIN WILD-TYPE 106   4
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               23               110 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                0                 4 
$`3P GAIN MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAGA TCGA-2G-AAGF TCGA-2G-AAGG 
       59.70        40.70        36.89        68.22        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAKG TCGA-2G-AAKH TCGA-4K-AAAL 
       92.09       108.16        59.64       212.65       161.72         4.83 
TCGA-SB-A6J6 TCGA-SN-A84X TCGA-VF-A8A8 TCGA-W4-A7U3 TCGA-WZ-A7V5 TCGA-X3-A8G4 
       13.58        10.26        37.18         4.90         0.16        28.14 
TCGA-XE-A8H1 TCGA-XE-AANV TCGA-XE-AAOC TCGA-XY-A8S2 TCGA-YU-A94I 
        6.87        53.03         8.88        12.92         7.96 

$`3P GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        38.30       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 
       14.86        16.50        36.13        40.01        52.37        71.24 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE 
       72.20        61.71        63.22        63.32        72.85        68.38 
TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       75.09       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
       95.67       229.22       184.41       131.21        70.59         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JW TCGA-S6-A8JX 
        0.13         3.52         7.00         0.10        20.68        18.15 
TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y TCGA-SO-A8JP 
        9.14         1.38        16.31         9.63        17.23         3.52 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       36.79        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 TCGA-XE-A8H4 
       41.52        24.26         3.65         5.06         0.82        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO3 TCGA-XE-AAO4 
       40.01        34.22        65.98         0.46        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
        7.89        16.87        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
        8.32        20.12         6.90        57.90        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 
       21.96         0.56         5.29        58.88        40.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.16              0.10 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           212.65            229.22 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            37.18             37.99 
[1] "0.2 - 212.7 (37.2)" "0.1 - 229.2 (38.0)"
[1] "hr="     "8.7e+07"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED         4        4        1        1         1         0
  3P GAIN WILD-TYPE      15       21       10        4         5         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P GAIN MUTATED           0         1          0          0          1
  3P GAIN WILD-TYPE         1         1          1          6          4
                   vv
clus                STAGE IS
  3P GAIN MUTATED          9
  3P GAIN WILD-TYPE       37
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  4                15
  STAGE IA                 4                21
  STAGE IB                 1                10
  STAGE II                 1                 4
  STAGE IIA                1                 5
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                1                 1
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               1                 4
  STAGE IS                 9                37
[1] 12  2
[1] 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
  3P GAIN MUTATED   12  9  2
  3P GAIN WILD-TYPE 63 42  4
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              12                63
  T2               9                42
  T3               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  3P GAIN MUTATED   10     2
  3P GAIN WILD-TYPE 36    11
D5V5, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0                 10                36
  N1+N2               2                11
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   18  2
  3P GAIN WILD-TYPE 96  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     18    2
  3P GAIN WILD-TYPE   96    2
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              18                96
  1               2                 2
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         0    21
  3P GAIN WILD-TYPE     4                         6    97
D5V7, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  21                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3 18
  3P GAIN WILD-TYPE  8 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   18
  3P GAIN WILD-TYPE    8   93
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              18                93
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   30  1
  3Q GAIN WILD-TYPE 99  3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               31               102 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                 3 
$`3Q GAIN MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFI TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG8 TCGA-2G-AAGA 
       59.70        14.14        40.70        36.89        63.22        68.22 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGW 
       79.76        67.96        92.09       108.16        59.64        61.45 
TCGA-2G-AAGY TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-4K-AAAL TCGA-SB-A6J6 
       80.94       122.50       212.65        95.67         4.83        13.58 
TCGA-VF-A8A8 TCGA-W4-A7U3 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       37.18         4.90         0.16         0.82        28.14         6.87 
TCGA-XE-AANV TCGA-XE-AAOC TCGA-XY-A8S2 TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94I 
       53.03         8.88        12.92        21.96         0.56         7.96 
TCGA-ZM-AA0N 
       10.85 

$`3Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        38.30       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      191.31        36.99        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       16.50        36.13        40.01        52.37        71.24        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGJ TCGA-2G-AAGN 
       61.71        63.32        72.85        68.38        75.09       106.39 
TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX 
      115.00       120.62        59.28       124.57       128.94       170.33 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
        6.08       161.72       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JW 
        2.73         0.13         3.52         7.00         0.10        20.68 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X 
       18.15         9.14         1.38        16.31         9.63        10.26 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC 
       17.23         3.52        36.79        37.68        24.99        35.61 
TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       33.07        23.90        41.52        24.26         3.65         5.06 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO3 
       18.38        40.01        34.22        65.98         0.46        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
       12.07         7.89        16.87        67.66        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
        0.43         8.32        20.12         6.90        57.90        54.35 
TCGA-YU-A90S TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
       31.92         5.29        58.88        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.16              0.10 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           212.65            229.22 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            37.18             37.99 
[1] "0.2 - 212.7 (37.2)" "0.1 - 229.2 (38.0)"
[1] "hr=" "1.8"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         4        5        4        1         1         0
  3Q GAIN WILD-TYPE      15       20        7        4         5         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q GAIN MUTATED           0         2          0          0          2
  3Q GAIN WILD-TYPE         1         0          1          6          3
                   vv
clus                STAGE IS
  3Q GAIN MUTATED         10
  3Q GAIN WILD-TYPE       36
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  4                15
  STAGE IA                 5                20
  STAGE IB                 4                 7
  STAGE II                 1                 4
  STAGE IIA                1                 5
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                2                 0
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               2                 3
  STAGE IS                10                36
[1] 12  2
[1] 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
  3Q GAIN MUTATED   14 13  4
  3Q GAIN WILD-TYPE 61 38  2
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              14                61
  T2              13                38
  T3               4                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  3Q GAIN MUTATED   14     2
  3Q GAIN WILD-TYPE 32    11
D6V5, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0                 14                32
  N1+N2               2                11
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   24  2
  3Q GAIN WILD-TYPE 90  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     24    2
  3Q GAIN WILD-TYPE   90    2
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              24                90
  1               2                 2
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         1    28
  3Q GAIN WILD-TYPE     4                         5    90
D6V7, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  28                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    2 25
  3Q GAIN WILD-TYPE  9 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2   25
  3Q GAIN WILD-TYPE    9   86
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              25                86
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     3   0
  4P GAIN WILD-TYPE 126   4
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3               130 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                0                 4 
$`4P GAIN MUTATED`
TCGA-2G-AAG6 TCGA-2G-AAGW TCGA-XE-AAOL 
       72.20        61.45         0.43 

$`4P GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       40.01        52.37        71.24        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
       59.28       124.57       128.94       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23         3.52 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       37.18        36.79        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       23.90        41.52         4.90        24.26         3.65         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        0.16         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
        7.89        16.87         8.88        67.66        41.69        50.96 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
        8.32        12.92        20.12         6.90        57.90        54.35 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       31.92        21.96         0.56         5.29        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       40.96         8.15        37.02        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.43              0.10 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            72.20            229.22 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            61.45             37.43 
[1] "0.4 - 72.2 (61.5)"  "0.1 - 229.2 (37.4)"
[1] "hr="     "9200000"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         1        0        0        0         0         0
  4P GAIN WILD-TYPE      18       25       11        5         6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P GAIN MUTATED           0         0          0          0          0
  4P GAIN WILD-TYPE         1         2          1          6          5
                   vv
clus                STAGE IS
  4P GAIN MUTATED          2
  4P GAIN WILD-TYPE       44
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  1                18
  STAGE IA                 0                25
  STAGE IB                 0                11
  STAGE II                 0                 5
  STAGE IIA                0                 6
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               0                 5
  STAGE IS                 2                44
[1] 12  2
[1] 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
  4P GAIN MUTATED    3  0  0
  4P GAIN WILD-TYPE 72 51  6
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               3                72
  T2               0                51
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  4P GAIN MUTATED    2     0
  4P GAIN WILD-TYPE 44    13
D7V5, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                57 
       TCGA-2G-AAEW        TCGA-2G-AAEX        TCGA-2G-AAF1        TCGA-2G-AAF4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-2G-AAF6        TCGA-2G-AAF8        TCGA-2G-AAFE        TCGA-2G-AAFG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-2G-AAFH        TCGA-2G-AAFI        TCGA-2G-AAFJ        TCGA-2G-AAFL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-2G-AAFM        TCGA-2G-AAFN        TCGA-2G-AAFO        TCGA-2G-AAFV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-2G-AAFY        TCGA-2G-AAG0        TCGA-2G-AAG5        TCGA-2G-AAG7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-2G-AAG8        TCGA-2G-AAG9        TCGA-2G-AAGA        TCGA-2G-AAGC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-2G-AAGE        TCGA-2G-AAGF        TCGA-2G-AAGG        TCGA-2G-AAGI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-2G-AAGJ        TCGA-2G-AAGK        TCGA-2G-AAGM        TCGA-2G-AAGN 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-2G-AAGO        TCGA-2G-AAGP        TCGA-2G-AAGS        TCGA-2G-AAGX 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-2G-AAGY        TCGA-2G-AAGZ        TCGA-2G-AAH2        TCGA-2G-AAHG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-2G-AAHL        TCGA-2G-AAHN        TCGA-2G-AAHP        TCGA-2G-AAHT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-2G-AAKG        TCGA-2G-AAL5        TCGA-2G-AAL7        TCGA-4K-AA1G 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-4K-AA1H        TCGA-4K-AA1I        TCGA-4K-AAAL        TCGA-SO-A8JP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-VF-A8A8        TCGA-VF-A8A9        TCGA-VF-A8AA        TCGA-VF-A8AB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-X3-A8G4 
"4P GAIN WILD-TYPE" 
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     3   0
  4P GAIN WILD-TYPE 111   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3    0
  4P GAIN WILD-TYPE  111    4
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               3               111
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       0                         1     2
  4P GAIN WILD-TYPE     4                         5   116
D7V7, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   2               116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   3
  4P GAIN WILD-TYPE  11 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    3
  4P GAIN WILD-TYPE   11  108
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO               3               108
[1] 2 2
[1] FALSE

Clustering(8) Variable = 5P GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED     6   0
  5P GAIN WILD-TYPE 123   4
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                6               127 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                0                 4 
$`5P GAIN MUTATED`
TCGA-2G-AAFM TCGA-2G-AAG0 TCGA-2G-AAKH TCGA-SN-A84Y TCGA-VF-A8A9 TCGA-W4-A7U4 
        9.57        40.01       161.72        17.23        36.79        24.26 

$`5P GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 
       14.86        16.50        40.70        36.13        36.89        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      122.50       212.65        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA 
       16.31         9.63        10.26         3.52        37.18        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 
       24.99        35.61        33.07        23.90        41.52         4.90 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             9.57              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           161.72            229.22 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           30.525            38.300 
[1] "9.6 - 161.7 (30.5)" "0.1 - 229.2 (38.3)"
[1] "hr="     "2.6e+07"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         0        1        0        1         1         0
  5P GAIN WILD-TYPE      19       24       11        4         5         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P GAIN MUTATED           0         0          0          0          0
  5P GAIN WILD-TYPE         1         2          1          6          5
                   vv
clus                STAGE IS
  5P GAIN MUTATED          2
  5P GAIN WILD-TYPE       44
D8V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  0                19
  STAGE IA                 1                24
  STAGE IB                 0                11
  STAGE II                 1                 4
  STAGE IIA                1                 5
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               0                 5
  STAGE IS                 2                44
[1] 12  2
[1] 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
  5P GAIN MUTATED    2  4  0
  5P GAIN WILD-TYPE 73 47  6
D8V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               2                73
  T2               4                47
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  5P GAIN MUTATED    2     1
  5P GAIN WILD-TYPE 44    12
D8V5, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0                  2                44
  N1+N2               1                12
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     6   0
  5P GAIN WILD-TYPE 108   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      6    0
  5P GAIN WILD-TYPE  108    4
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0               6               108
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       0                         0     6
  5P GAIN WILD-TYPE     4                         6   112
D8V7, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   6               112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1   5
  5P GAIN WILD-TYPE  10 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1    5
  5P GAIN WILD-TYPE   10  106
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO               5               106
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5Q GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED     3   0
  5Q GAIN WILD-TYPE 126   4
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3               130 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                 4 
$`5Q GAIN MUTATED`
TCGA-2G-AAFM TCGA-SN-A84Y TCGA-W4-A7U4 
        9.57        17.23        24.26 

$`5Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
        6.08       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      184.41       131.21        70.59         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
        7.00         0.10         4.83        20.68        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SO-A8JP 
       13.58         1.38        16.31         9.63        10.26         3.52 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       37.18        36.79        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       23.90        41.52         4.90         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
       16.87         8.88        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
        8.32        12.92        20.12         6.90        57.90        54.35 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       31.92        21.96         0.56         5.29        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       40.96         8.15        37.02        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             9.57              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            24.26            229.22 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           17.230            38.825 
[1] "9.6 - 24.3 (17.2)"  "0.1 - 229.2 (38.8)"
[1] "hr="     "9200000"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         0        0        0        0         1         0
  5Q GAIN WILD-TYPE      19       25       11        5         5         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q GAIN MUTATED           0         0          0          0          0
  5Q GAIN WILD-TYPE         1         2          1          6          5
                   vv
clus                STAGE IS
  5Q GAIN MUTATED          1
  5Q GAIN WILD-TYPE       45
D9V3, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2               126 
       TCGA-2G-AAEW        TCGA-2G-AAEX        TCGA-2G-AAF1        TCGA-2G-AAF4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAF6        TCGA-2G-AAF8        TCGA-2G-AAFE        TCGA-2G-AAFG 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAFH        TCGA-2G-AAFI        TCGA-2G-AAFJ        TCGA-2G-AAFL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAFN        TCGA-2G-AAFO        TCGA-2G-AAFV        TCGA-2G-AAFY 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAFZ        TCGA-2G-AAG0        TCGA-2G-AAG3        TCGA-2G-AAG5 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAG6        TCGA-2G-AAG7        TCGA-2G-AAG8        TCGA-2G-AAG9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAGA        TCGA-2G-AAGC        TCGA-2G-AAGE        TCGA-2G-AAGF 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAGG        TCGA-2G-AAGI        TCGA-2G-AAGJ        TCGA-2G-AAGK 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAGM        TCGA-2G-AAGN        TCGA-2G-AAGO        TCGA-2G-AAGP 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAGS        TCGA-2G-AAGT        TCGA-2G-AAGV        TCGA-2G-AAGW 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAGX        TCGA-2G-AAGY        TCGA-2G-AAGZ        TCGA-2G-AAH0 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAH2        TCGA-2G-AAH3        TCGA-2G-AAH4        TCGA-2G-AAH8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAHA        TCGA-2G-AAHC        TCGA-2G-AAHG        TCGA-2G-AAHL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAHN        TCGA-2G-AAHP        TCGA-2G-AAHT        TCGA-2G-AAKD 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAKG        TCGA-2G-AAKH        TCGA-2G-AAKL        TCGA-2G-AAKM 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAL5        TCGA-2G-AAL7        TCGA-2G-AALP        TCGA-2X-A9D5 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2X-A9D6        TCGA-4K-AA1G        TCGA-4K-AA1H        TCGA-4K-AA1I 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-4K-AAAL        TCGA-S6-A8JW        TCGA-S6-A8JX        TCGA-S6-A8JY 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-SB-A6J6        TCGA-SN-A6IS        TCGA-SN-A84W        TCGA-SN-A84X 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-SO-A8JP        TCGA-VF-A8A8        TCGA-VF-A8A9        TCGA-VF-A8AA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-VF-A8AB        TCGA-VF-A8AC        TCGA-VF-A8AD        TCGA-VF-A8AE 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-WZ-A7V3        TCGA-WZ-A7V4        TCGA-WZ-A7V5        TCGA-X3-A8G4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-XE-A8H1        TCGA-XE-A8H4        TCGA-XE-A8H5        TCGA-XE-AANI 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-XE-AANJ        TCGA-XE-AANR        TCGA-XE-AANV        TCGA-XE-AAO3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-XE-AAO4        TCGA-XE-AAO6        TCGA-XE-AAOB        TCGA-XE-AAOC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-XE-AAOD        TCGA-XE-AAOF        TCGA-XE-AAOJ        TCGA-XE-AAOL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-XY-A89B        TCGA-XY-A8S2        TCGA-XY-A8S3        TCGA-XY-A9T9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-YU-A90P        TCGA-YU-A90Q        TCGA-YU-A90S        TCGA-YU-A90W 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-YU-A90Y        TCGA-YU-A912        TCGA-YU-A94D        TCGA-YU-A94I 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-YU-AA4L        TCGA-YU-AA61        TCGA-ZM-AA05        TCGA-ZM-AA06 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ZM-AA0B        TCGA-ZM-AA0D        TCGA-ZM-AA0E        TCGA-ZM-AA0F 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ZM-AA0H        TCGA-ZM-AA0N 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
                   vv
clus                T1 T2 T3
  5Q GAIN MUTATED    0  3  0
  5Q GAIN WILD-TYPE 75 48  6
D9V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               0                75
  T2               3                48
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  5Q GAIN MUTATED    0     1
  5Q GAIN WILD-TYPE 46    12
D9V5, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1                58 
       TCGA-2G-AAEW        TCGA-2G-AAEX        TCGA-2G-AAF1        TCGA-2G-AAF4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAF6        TCGA-2G-AAF8        TCGA-2G-AAFE        TCGA-2G-AAFG 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAFH        TCGA-2G-AAFI        TCGA-2G-AAFJ        TCGA-2G-AAFL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAFN        TCGA-2G-AAFO        TCGA-2G-AAFV        TCGA-2G-AAFY 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAG0        TCGA-2G-AAG5        TCGA-2G-AAG6        TCGA-2G-AAG7 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAG8        TCGA-2G-AAG9        TCGA-2G-AAGA        TCGA-2G-AAGC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAGE        TCGA-2G-AAGF        TCGA-2G-AAGG        TCGA-2G-AAGI 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAGJ        TCGA-2G-AAGK        TCGA-2G-AAGM        TCGA-2G-AAGN 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAGO        TCGA-2G-AAGP        TCGA-2G-AAGS        TCGA-2G-AAGW 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAGX        TCGA-2G-AAGY        TCGA-2G-AAGZ        TCGA-2G-AAH2 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAHG        TCGA-2G-AAHL        TCGA-2G-AAHN        TCGA-2G-AAHP 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-2G-AAHT        TCGA-2G-AAKG        TCGA-2G-AAL5        TCGA-2G-AAL7 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-4K-AA1G        TCGA-4K-AA1H        TCGA-4K-AA1I        TCGA-4K-AAAL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-SO-A8JP        TCGA-VF-A8A8        TCGA-VF-A8A9        TCGA-VF-A8AA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-VF-A8AB        TCGA-X3-A8G4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D9V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     3   0
  5Q GAIN WILD-TYPE 111   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    0
  5Q GAIN WILD-TYPE  111    4
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               3               111
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         0     3
  5Q GAIN WILD-TYPE     4                         6   115
D9V7, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   3               115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1   2
  5Q GAIN WILD-TYPE  10 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1    2
  5Q GAIN WILD-TYPE   10  109
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO               2               109
[1] 2 2
[1] FALSE

Clustering(10) Variable = 6P GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    21   0
  6P GAIN WILD-TYPE 108   4
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               21               112 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                0                 4 
$`6P GAIN MUTATED`
TCGA-2G-AAF1 TCGA-2G-AAG3 TCGA-2G-AAG6 TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGP 
       38.30        52.37        72.20        67.96        92.09       120.62 
TCGA-2G-AAH2 TCGA-2G-AAHA TCGA-2G-AAHN TCGA-2G-AAKL TCGA-2X-A9D6 TCGA-SN-A84X 
       59.84        98.53        91.43        95.67         0.13        10.26 
TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-XE-AAOC TCGA-XY-A8S2 TCGA-YU-A94I 
       17.23        37.18        37.68         8.88        12.92         7.96 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0N 
       37.02        39.35        10.85 

$`6P GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG5 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       71.24        61.71        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN 
       68.38        79.76        75.09       108.16        59.64       106.39 
TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      115.00        59.28       124.57       128.94        61.45       170.33 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       80.94        60.16        60.26        59.90       125.69        61.84 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.74        59.80        59.80       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      212.65       161.72       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
        2.73         3.52         7.00         0.10         4.83        20.68 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       18.15         9.14        13.58         1.38        16.31         9.63 
TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
        3.52        36.79        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       41.52         4.90        24.26         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
       16.87        67.66        41.69        50.96         0.43         8.32 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       20.12         6.90        57.90        54.35        31.92        21.96 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA0B 
        0.56         5.29        58.88        40.96         8.15        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       17.39        16.41        11.34        46.88 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.13              0.10 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           120.62            229.22 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            38.30             36.94 
[1] "0.1 - 120.6 (38.3)" "0.1 - 229.2 (36.9)"
[1] "hr="     "8.7e+07"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         4        3        3        1         1         0
  6P GAIN WILD-TYPE      15       22        8        4         5         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P GAIN MUTATED           1         0          0          0          1
  6P GAIN WILD-TYPE         0         2          1          6          4
                   vv
clus                STAGE IS
  6P GAIN MUTATED          7
  6P GAIN WILD-TYPE       39
D10V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  4                15
  STAGE IA                 3                22
  STAGE IB                 3                 8
  STAGE II                 1                 4
  STAGE IIA                1                 5
  STAGE IIB                0                 1
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               1                 4
  STAGE IS                 7                39
[1] 12  2
[1] 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
  6P GAIN MUTATED   10 10  1
  6P GAIN WILD-TYPE 65 41  5
D10V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              10                65
  T2              10                41
  T3               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  6P GAIN MUTATED    7     2
  6P GAIN WILD-TYPE 39    11
D10V5, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0                  7                39
  N1+N2               2                11
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   19  1
  6P GAIN WILD-TYPE 95  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     19    1
  6P GAIN WILD-TYPE   95    3
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              19                95
  1               1                 3
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       1                         0    19
  6P GAIN WILD-TYPE     3                         6    99
D10V7, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  19                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    3 17
  6P GAIN WILD-TYPE  8 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3   17
  6P GAIN WILD-TYPE    8   94
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              17                94
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6Q GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    17   0
  6Q GAIN WILD-TYPE 112   4
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               17               116 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                0                 4 
$`6Q GAIN MUTATED`
TCGA-2G-AAF1 TCGA-2G-AAG6 TCGA-2G-AAGG TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGY 
       38.30        72.20        67.96       120.62       124.57        80.94 
TCGA-2G-AAH2 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2X-A9D6 TCGA-SN-A84X TCGA-SN-A84Y 
       59.84        61.84        98.53         0.13        10.26        17.23 
TCGA-VF-A8AA TCGA-XE-AAOC TCGA-XY-A8S2 TCGA-ZM-AA05 TCGA-ZM-AA06 
       37.68         8.88        12.92        37.02        39.35 

$`6Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       52.37        71.24        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       72.85        68.38        79.76        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW 
       59.64       106.39       115.00        59.28       128.94        61.45 
TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC 
      170.33        60.16        60.26        59.90       125.69        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
       70.59         2.73         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       20.68        18.15         9.14        13.58         1.38        16.31 
TCGA-SN-A84W TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AC 
        9.63         3.52        37.18        36.79        24.99        35.61 
TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 
       33.07        23.90        41.52         4.90        24.26         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
        5.06         0.16         0.82        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
       12.07         7.89        16.87        67.66        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
        0.43         8.32        20.12         6.90        57.90        54.35 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       31.92        21.96         0.56         5.29        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       40.96         8.15        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.13              0.10 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           124.57            229.22 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            39.35             36.94 
[1] "0.1 - 124.6 (39.4)" "0.1 - 229.2 (36.9)"
[1] "hr="     "8.3e+07"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         3        1        2        0         1         0
  6Q GAIN WILD-TYPE      16       24        9        5         5         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q GAIN MUTATED           1         0          0          0          2
  6Q GAIN WILD-TYPE         0         2          1          6          3
                   vv
clus                STAGE IS
  6Q GAIN MUTATED          7
  6Q GAIN WILD-TYPE       39
D11V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  3                16
  STAGE IA                 1                24
  STAGE IB                 2                 9
  STAGE II                 0                 5
  STAGE IIA                1                 5
  STAGE IIB                0                 1
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               2                 3
  STAGE IS                 7                39
[1] 12  2
[1] 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
  6Q GAIN MUTATED    7  9  1
  6Q GAIN WILD-TYPE 68 42  5
D11V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               7                68
  T2               9                42
  T3               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  6Q GAIN MUTATED    5     2
  6Q GAIN WILD-TYPE 41    11
D11V5, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0                  5                41
  N1+N2               2                11
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   16  1
  6Q GAIN WILD-TYPE 98  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     16    1
  6Q GAIN WILD-TYPE   98    3
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              16                98
  1               1                 3
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       1                         0    16
  6Q GAIN WILD-TYPE     3                         6   102
D11V7, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  16               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    3 14
  6Q GAIN WILD-TYPE  8 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3   14
  6Q GAIN WILD-TYPE    8   97
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              14                97
[1] 2 2
[1] FALSE

Clustering(12) Variable = 7P GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   107   3
  7P GAIN WILD-TYPE  22   1
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              110                23 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                3                 1 
$`7P GAIN MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        36.99        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       72.20        61.71        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV 
       59.64       106.39       115.00       120.62       124.57       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
       61.45       170.33        80.94        60.26        59.84        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN 
      125.69        61.84        98.53        59.74        59.80        91.43 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
        6.08       122.50       161.72        95.67       229.22       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AAAL TCGA-S6-A8JW 
       70.59         2.73         0.13         3.52         4.83        20.68 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X 
       18.15         9.14        13.58         1.38        16.31        10.26 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AC 
       17.23         3.52        37.18        36.79        37.68        35.61 
TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       33.07        23.90        41.52        24.26         3.65         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.16         0.82        28.14        18.38        40.01        34.22 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOL 
        0.46        53.03        93.93        12.07         7.89         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
        8.32        12.92        20.12         6.90        57.90        54.35 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L 
       31.92        21.96         0.56         5.29         7.96        40.96 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

$`7P GAIN WILD-TYPE`
TCGA-2G-AAFI TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAGS TCGA-2G-AAGZ TCGA-2G-AAHG 
       14.14        52.37        71.24        59.28        60.16        59.80 
TCGA-2G-AAHP TCGA-2G-AAKG TCGA-2G-AAL5 TCGA-4K-AA1H TCGA-4K-AA1I TCGA-SN-A84W 
      176.15       212.65       184.41         7.00         0.10         9.63 
TCGA-VF-A8AB TCGA-W4-A7U3 TCGA-XE-A8H1 TCGA-XE-AANJ TCGA-XE-AAOB TCGA-XE-AAOC 
       24.99         4.90         6.87        65.98        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-YU-A94D TCGA-YU-AA61 
       67.66        41.69        50.96        58.88         8.15 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.13              0.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           229.22            212.65 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            37.10             50.96 
[1] "0.1 - 229.2 (37.1)" "0.1 - 212.7 (51.0)"
[1] "hr=" "2.5"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED        16       20        9        5         6         1
  7P GAIN WILD-TYPE       3        5        2        0         0         0
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P GAIN MUTATED           1         2          0          4          5
  7P GAIN WILD-TYPE         0         0          1          2          0
                   vv
clus                STAGE IS
  7P GAIN MUTATED         37
  7P GAIN WILD-TYPE        9
D12V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 16                 3
  STAGE IA                20                 5
  STAGE IB                 9                 2
  STAGE II                 5                 0
  STAGE IIA                6                 0
  STAGE IIB                1                 0
  STAGE IIC                1                 0
  STAGE III                2                 0
  STAGE IIIA               0                 1
  STAGE IIIB               4                 2
  STAGE IIIC               5                 0
  STAGE IS                37                 9
[1] 12  2
[1] 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
  7P GAIN MUTATED   62 42  5
  7P GAIN WILD-TYPE 13  9  1
D12V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              62                13
  T2              42                 9
  T3               5                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  7P GAIN MUTATED   37    11
  7P GAIN WILD-TYPE  9     2
D12V5, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0                 37                 9
  N1+N2              11                 2
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   95  3
  7P GAIN WILD-TYPE 19  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     95    3
  7P GAIN WILD-TYPE   19    1
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              95                19
  1               3                 1
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       3                         5    98
  7P GAIN WILD-TYPE     1                         1    20
D12V7, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   3                 1
  BLACK OR AFRICAN AMERICAN               5                 1
  WHITE                                  98                20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    6 96
  7P GAIN WILD-TYPE  5 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6   96
  7P GAIN WILD-TYPE    5   15
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 5
  NOT HISPANIC OR LATINO              96                15
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7Q GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   93  3
  7Q GAIN WILD-TYPE 36  1
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               96                37 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                 1 
$`7Q GAIN MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAFH 
       20.32        38.30        59.70       102.35       154.59        36.99 
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       14.14        14.56        17.16         9.57        14.86        16.50 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 
       40.70        36.13        36.89        40.01        72.20        61.71 
TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       63.22        63.32        68.22        72.85        68.38        79.76 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN 
       67.96        92.09        75.09       108.16        59.64       106.39 
TCGA-2G-AAGO TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAH0 
      115.00       124.57       128.94        61.45        80.94        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKH 
       59.80        91.43       176.15         6.08       122.50       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
       95.67       229.22       131.21        70.59         2.73         0.13 
TCGA-4K-AA1G TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        3.52         4.83        20.68        18.15         9.14        13.58 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AA TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U2 
       17.23         3.52        37.68        35.61        33.07        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H4 TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       18.38         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Q 
        0.43         8.32        12.92        20.12        57.90        54.35 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 
       31.92        21.96         0.56         7.96        40.96        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       39.35        17.39        16.41        11.34        46.88        10.85 

$`7Q GAIN WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAGP 
       30.35       122.40       191.31        52.37        71.24       120.62 
TCGA-2G-AAGS TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAHG TCGA-2G-AAKG TCGA-2G-AAL5 
       59.28       170.33        60.16        59.80       212.65       184.41 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X 
        7.00         0.10         1.38        16.31         9.63        10.26 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AE TCGA-W4-A7U3 TCGA-XE-A8H1 
       37.18        36.79        24.99        23.90         4.90         6.87 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       40.01        34.22        65.98        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A9T9 TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA61 
       41.69        50.96         6.90         5.29        58.88         8.15 
TCGA-ZM-AA0B 
       27.55 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.13              0.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           229.22            212.65 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           38.825            36.790 
[1] "0.1 - 229.2 (38.8)" "0.1 - 212.7 (36.8)"
[1] "hr=" "1.3"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED        16       14       10        5         5         1
  7Q GAIN WILD-TYPE       3       11        1        0         1         0
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q GAIN MUTATED           1         2          0          4          4
  7Q GAIN WILD-TYPE         0         0          1          2          1
                   vv
clus                STAGE IS
  7Q GAIN MUTATED         31
  7Q GAIN WILD-TYPE       15
D13V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 16                 3
  STAGE IA                14                11
  STAGE IB                10                 1
  STAGE II                 5                 0
  STAGE IIA                5                 1
  STAGE IIB                1                 0
  STAGE IIC                1                 0
  STAGE III                2                 0
  STAGE IIIA               0                 1
  STAGE IIIB               4                 2
  STAGE IIIC               4                 1
  STAGE IS                31                15
[1] 12  2
[1] 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
  7Q GAIN MUTATED   48 42  5
  7Q GAIN WILD-TYPE 27  9  1
D13V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              48                27
  T2              42                 9
  T3               5                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  7Q GAIN MUTATED   33    10
  7Q GAIN WILD-TYPE 13     3
D13V5, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0                 33                13
  N1+N2              10                 3
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   82  3
  7Q GAIN WILD-TYPE 32  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     82    3
  7Q GAIN WILD-TYPE   32    1
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              82                32
  1               3                 1
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       3                         4    86
  7Q GAIN WILD-TYPE     1                         2    32
D13V7, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   3                 1
  BLACK OR AFRICAN AMERICAN               4                 2
  WHITE                                  86                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    3 86
  7Q GAIN WILD-TYPE  8 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3   86
  7Q GAIN WILD-TYPE    8   25
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              86                25
[1] 2 2
[1] FALSE

Clustering(14) Variable = 8P GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   97  4
  8P GAIN WILD-TYPE 32  0
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              101                32 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                 0 
$`8P GAIN MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFM TCGA-2G-AAFO 
      154.59       191.31        36.99        14.14         9.57        16.50 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAG9 
       36.13        36.89        52.37        72.20        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGN 
       68.22        72.85        79.76        92.09        59.64       106.39 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      120.62        59.28       128.94        61.45       170.33        80.94 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       60.26        59.84        59.90        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        59.80        91.43       176.15       122.50       212.65 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I 
       95.67       229.22       131.21         0.13         3.52         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
        4.83        20.68        18.15        13.58         1.38        16.31 
TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA 
       10.26        17.23         3.52        37.18        36.79        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 
       24.99        35.61        23.90        41.52        24.26         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        5.06         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       16.87        41.69        50.96         0.43         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y 
       20.12         6.90        57.90        54.35        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        5.29        58.88         8.15        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

$`8P GAIN WILD-TYPE`
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFN TCGA-2G-AAFV TCGA-2G-AAG0 TCGA-2G-AAG5 
       14.56        17.16        14.86        40.70        40.01        71.24 
TCGA-2G-AAG7 TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGO 
       61.71        68.38        67.96        75.09       108.16       115.00 
TCGA-2G-AAGT TCGA-2G-AAGZ TCGA-2G-AAH4 TCGA-2G-AAHT TCGA-2G-AAKH TCGA-2G-AAL5 
      124.57        60.16       125.69         6.08       161.72       184.41 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1H TCGA-S6-A8JY TCGA-SN-A84W TCGA-VF-A8AD 
       70.59         2.73         7.00         9.14         9.63        33.07 
TCGA-W4-A7U3 TCGA-WZ-A7V5 TCGA-XE-AANI TCGA-XE-AAOC TCGA-XE-AAOD TCGA-YU-A90S 
        4.90         0.16        34.22         8.88        67.66        31.92 
TCGA-YU-A94I TCGA-YU-AA4L 
        7.96        40.96 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.10              0.16 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           229.22            184.41 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           37.180            40.355 
[1] "0.1 - 229.2 (37.2)" "0.2 - 184.4 (40.4)"
[1] "hr="     "2.7e+08"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED        15       20        8        3         6         1
  8P GAIN WILD-TYPE       4        5        3        2         0         0
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P GAIN MUTATED           1         2          0          4          3
  8P GAIN WILD-TYPE         0         0          1          2          2
                   vv
clus                STAGE IS
  8P GAIN MUTATED         34
  8P GAIN WILD-TYPE       12
D14V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 15                 4
  STAGE IA                20                 5
  STAGE IB                 8                 3
  STAGE II                 3                 2
  STAGE IIA                6                 0
  STAGE IIB                1                 0
  STAGE IIC                1                 0
  STAGE III                2                 0
  STAGE IIIA               0                 1
  STAGE IIIB               4                 2
  STAGE IIIC               3                 2
  STAGE IS                34                12
[1] 12  2
[1] 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
  8P GAIN MUTATED   57 38  5
  8P GAIN WILD-TYPE 18 13  1
D14V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              57                18
  T2              38                13
  T3               5                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  8P GAIN MUTATED   33    10
  8P GAIN WILD-TYPE 13     3
D14V5, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0                 33                13
  N1+N2              10                 3
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   90  1
  8P GAIN WILD-TYPE 24  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     90    1
  8P GAIN WILD-TYPE   24    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              90                24
  1               1                 3
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       3                         4    90
  8P GAIN WILD-TYPE     1                         2    28
D14V7, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   3                 1
  BLACK OR AFRICAN AMERICAN               4                 2
  WHITE                                  90                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    9 85
  8P GAIN WILD-TYPE  2 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9   85
  8P GAIN WILD-TYPE    2   26
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                 2
  NOT HISPANIC OR LATINO              85                26
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8Q GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   99  4
  8Q GAIN WILD-TYPE 30  0
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              103                30 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                4                 0 
$`8Q GAIN MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      154.59       191.31        14.14         9.57        14.86        16.50 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 
       36.13        36.89        52.37        71.24        72.20        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGI TCGA-2G-AAGM 
       63.32        68.22        72.85        79.76        92.09        59.64 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
      106.39       115.00       120.62        59.28       124.57       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
       61.45       170.33        80.94        60.26        59.84        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       61.84        98.53        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM 
      176.15         6.08       122.50       212.65        95.67       229.22 
TCGA-2G-AAL7 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL 
      131.21         2.73         0.13         3.52         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X 
       20.68        18.15        13.58         1.38        16.31        10.26 
TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC 
       17.23        37.18        36.79        37.68        24.99        35.61 
TCGA-VF-A8AE TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       23.90        24.26         3.65         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANR TCGA-XE-AANV 
       28.14         6.87        18.38        40.01         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XE-AAOL 
       93.93        12.07         7.89        16.87        41.69         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
        8.32        12.92        20.12         6.90        57.90        54.35 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA05 
       21.96         0.56         5.29        58.88         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

$`8Q GAIN WILD-TYPE`
TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAG0 TCGA-2G-AAG7 
       36.99        14.56        17.16        40.70        40.01        61.71 
TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGZ TCGA-2G-AAH4 
       68.38        67.96        75.09       108.16        60.16       125.69 
TCGA-2G-AAKH TCGA-2G-AAL5 TCGA-2G-AALP TCGA-4K-AA1H TCGA-S6-A8JY TCGA-SN-A84W 
      161.72       184.41        70.59         7.00         9.14         9.63 
TCGA-SO-A8JP TCGA-VF-A8AD TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-XE-AANI TCGA-XE-AANJ 
        3.52        33.07        41.52         4.90        34.22        65.98 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-YU-A90S TCGA-YU-A94I TCGA-YU-AA4L 
        8.88        67.66        50.96        31.92         7.96        40.96 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.10              3.52 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           229.22            184.41 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            37.02             40.83 
[1] "0.1 - 229.2 (37.0)" "3.5 - 184.4 (40.8)"
[1] "hr="     "2.8e+08"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED        16       20        8        3         6         0
  8Q GAIN WILD-TYPE       3        5        3        2         0         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q GAIN MUTATED           1         2          0          5          3
  8Q GAIN WILD-TYPE         0         0          1          1          2
                   vv
clus                STAGE IS
  8Q GAIN MUTATED         36
  8Q GAIN WILD-TYPE       10
D15V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 16                 3
  STAGE IA                20                 5
  STAGE IB                 8                 3
  STAGE II                 3                 2
  STAGE IIA                6                 0
  STAGE IIB                0                 1
  STAGE IIC                1                 0
  STAGE III                2                 0
  STAGE IIIA               0                 1
  STAGE IIIB               5                 1
  STAGE IIIC               3                 2
  STAGE IS                36                10
[1] 12  2
[1] 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
  8Q GAIN MUTATED   55 42  5
  8Q GAIN WILD-TYPE 20  9  1
D15V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              55                20
  T2              42                 9
  T3               5                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  8Q GAIN MUTATED   35    10
  8Q GAIN WILD-TYPE 11     3
D15V5, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0                 35                11
  N1+N2              10                 3
[1] 2 2
[1] FALSE
D15V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   92  1
  8Q GAIN WILD-TYPE 22  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     92    1
  8Q GAIN WILD-TYPE   22    3
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              92                22
  1               1                 3
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       3                         4    92
  8Q GAIN WILD-TYPE     1                         2    26
D15V7, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   3                 1
  BLACK OR AFRICAN AMERICAN               4                 2
  WHITE                                  92                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    7 89
  8Q GAIN WILD-TYPE  4 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      7   89
  8Q GAIN WILD-TYPE    4   22
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 4
  NOT HISPANIC OR LATINO              89                22
[1] 2 2
[1] FALSE

Clustering(16) Variable = 9P GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    14   0
  9P GAIN WILD-TYPE 115   4
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               119 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                 4 
$`9P GAIN MUTATED`
TCGA-2G-AAGT TCGA-2G-AAH2 TCGA-2G-AAKL TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8AA 
      124.57        59.84        95.67        10.26        17.23        37.68 
TCGA-VF-A8AD TCGA-WZ-A7V3 TCGA-XE-AAOC TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90W 
       33.07         3.65         8.88        12.92        20.12        21.96 
TCGA-YU-AA61 TCGA-ZM-AA05 
        8.15        37.02 

$`9P GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       40.01        52.37        71.24        72.20        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       63.32        68.22        72.85        68.38        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       92.09        75.09       108.16        59.64       106.39       115.00 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      120.62        59.28       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.16        60.26        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      122.50       212.65       161.72       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AB 
       16.31         9.63         3.52        37.18        36.79        24.99 
TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V4 
       35.61        23.90        41.52         4.90        24.26         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        0.16         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
        7.89        16.87        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90Y 
        8.32         6.90        57.90        54.35        31.92         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA06 TCGA-ZM-AA0B 
        5.29        58.88         7.96        40.96        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             3.65              0.10 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           124.57            229.22 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            21.04             40.01 
[1] "3.6 - 124.6 (21.0)" "0.1 - 229.2 (40.0)"
[1] "hr="     "7.7e+07"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         3        2        1        1         0         0
  9P GAIN WILD-TYPE      16       23       10        4         6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P GAIN MUTATED           1         0          0          0          0
  9P GAIN WILD-TYPE         0         2          1          6          5
                   vv
clus                STAGE IS
  9P GAIN MUTATED          6
  9P GAIN WILD-TYPE       40
D16V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  3                16
  STAGE IA                 2                23
  STAGE IB                 1                10
  STAGE II                 1                 4
  STAGE IIA                0                 6
  STAGE IIB                0                 1
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               0                 5
  STAGE IS                 6                40
[1] 12  2
[1] 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
  9P GAIN MUTATED    6  8  0
  9P GAIN WILD-TYPE 69 43  6
D16V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               6                69
  T2               8                43
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  9P GAIN MUTATED    2     0
  9P GAIN WILD-TYPE 44    13
D16V5, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                57 
       TCGA-2G-AAEW        TCGA-2G-AAEX        TCGA-2G-AAF1        TCGA-2G-AAF4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2G-AAF6        TCGA-2G-AAF8        TCGA-2G-AAFE        TCGA-2G-AAFG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2G-AAFH        TCGA-2G-AAFI        TCGA-2G-AAFJ        TCGA-2G-AAFL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2G-AAFM        TCGA-2G-AAFN        TCGA-2G-AAFO        TCGA-2G-AAFV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2G-AAFY        TCGA-2G-AAG0        TCGA-2G-AAG5        TCGA-2G-AAG6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2G-AAG7        TCGA-2G-AAG8        TCGA-2G-AAG9        TCGA-2G-AAGA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2G-AAGC        TCGA-2G-AAGE        TCGA-2G-AAGF        TCGA-2G-AAGG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2G-AAGI        TCGA-2G-AAGJ        TCGA-2G-AAGK        TCGA-2G-AAGM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2G-AAGN        TCGA-2G-AAGO        TCGA-2G-AAGP        TCGA-2G-AAGS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2G-AAGW        TCGA-2G-AAGX        TCGA-2G-AAGY        TCGA-2G-AAGZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2G-AAHG        TCGA-2G-AAHL        TCGA-2G-AAHN        TCGA-2G-AAHP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2G-AAHT        TCGA-2G-AAKG        TCGA-2G-AAL5        TCGA-2G-AAL7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-4K-AA1G        TCGA-4K-AA1H        TCGA-4K-AA1I        TCGA-4K-AAAL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-SO-A8JP        TCGA-VF-A8A8        TCGA-VF-A8A9        TCGA-VF-A8AB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-X3-A8G4 
"9P GAIN WILD-TYPE" 
D16V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    11   0
  9P GAIN WILD-TYPE 103   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     11    0
  9P GAIN WILD-TYPE  103    4
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              11               103
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         0    14
  9P GAIN WILD-TYPE     4                         6   104
D16V7, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  14               104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     3   9
  9P GAIN WILD-TYPE   8 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    9
  9P GAIN WILD-TYPE    8  102
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO               9               102
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9Q GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    15   0
  9Q GAIN WILD-TYPE 114   4
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               15               118 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                 4 
$`9Q GAIN MUTATED`
TCGA-2G-AAEX TCGA-2G-AAFV TCGA-2G-AAGJ TCGA-2G-AAGO TCGA-2G-AAGZ TCGA-2G-AAKL 
       30.35        40.70        75.09       115.00        60.16        95.67 
TCGA-VF-A8AA TCGA-VF-A8AD TCGA-W4-A7U2 TCGA-WZ-A7V3 TCGA-XE-AANJ TCGA-XE-AAO3 
       37.68        33.07        41.52         3.65        65.98        93.93 
TCGA-XE-AAO6 TCGA-YU-AA61 TCGA-ZM-AA05 
        7.89         8.15        37.02 

$`9Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        38.30        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       14.86        16.50        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK 
       72.85        68.38        79.76        67.96        92.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
       59.64       106.39       120.62        59.28       124.57       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
       61.45       170.33        80.94        60.26        59.84        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL 
      125.69        61.84        98.53        59.74        59.80        59.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
       91.43       176.15         6.08       122.50       212.65       161.72 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      229.22       184.41       131.21        70.59         2.73         0.13 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
        3.52         7.00         0.10         4.83        20.68        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X 
        9.14        13.58         1.38        16.31         9.63        10.26 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AC 
       17.23         3.52        37.18        36.79        24.99        35.61 
TCGA-VF-A8AE TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       23.90         4.90        24.26         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANR 
       28.14         6.87        18.38        40.01        34.22         0.46 
TCGA-XE-AANV TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF 
       53.03        12.07        16.87         8.88        67.66        41.69 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       50.96         0.43         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       58.88         7.96        40.96        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             3.65              0.10 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           115.00            229.22 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           40.700            37.085 
[1] "3.6 - 115.0 (40.7)" "0.1 - 229.2 (37.1)"
[1] "hr="     "8.2e+07"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         3        2        1        1         0         0
  9Q GAIN WILD-TYPE      16       23       10        4         6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q GAIN MUTATED           1         0          1          0          0
  9Q GAIN WILD-TYPE         0         2          0          6          5
                   vv
clus                STAGE IS
  9Q GAIN MUTATED          5
  9Q GAIN WILD-TYPE       41
D17V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  3                16
  STAGE IA                 2                23
  STAGE IB                 1                10
  STAGE II                 1                 4
  STAGE IIA                0                 6
  STAGE IIB                0                 1
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIA               1                 0
  STAGE IIIB               0                 6
  STAGE IIIC               0                 5
  STAGE IS                 5                41
[1] 12  2
[1] 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
  9Q GAIN MUTATED    8  7  0
  9Q GAIN WILD-TYPE 67 44  6
D17V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               8                67
  T2               7                44
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  9Q GAIN MUTATED    5     1
  9Q GAIN WILD-TYPE 41    12
D17V5, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0                  5                41
  N1+N2               1                12
[1] 2 2
[1] FALSE
D17V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    11   1
  9Q GAIN WILD-TYPE 103   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     11    1
  9Q GAIN WILD-TYPE  103    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              11               103
  1               1                 3
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       1                         1    13
  9Q GAIN WILD-TYPE     3                         5   105
D17V7, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  13               105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    1 13
  9Q GAIN WILD-TYPE 10 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   13
  9Q GAIN WILD-TYPE   10   98
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              13                98
[1] 2 2
[1] FALSE

Clustering(18) Variable = 10P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     6   0
  10P GAIN WILD-TYPE 123   4
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                127 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  4 
$`10P GAIN MUTATED`
TCGA-2G-AAG3 TCGA-2G-AAGM TCGA-WZ-A8D5 TCGA-XE-AAOL TCGA-YU-A94I TCGA-ZM-AA0N 
       52.37        59.64         0.82         0.43         7.96        10.85 

$`10P GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       40.01        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
       75.09       108.16       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23         3.52 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       37.18        36.79        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       23.90        41.52         4.90        24.26         3.65         5.06 
TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.16        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B 
       16.87         8.88        67.66        41.69        50.96         8.32 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       12.92        20.12         6.90        57.90        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 
       21.96         0.56         5.29        58.88        40.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H 
       46.88 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.43               0.10 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             59.64             229.22 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             9.405             38.300 
[1] "0.4 - 59.6 (9.4)"   "0.1 - 229.2 (38.3)"
[1] "hr="     "2.5e+07"
D18V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED         1        1        1        0         0         0
  10P GAIN WILD-TYPE      18       24       10        5         6         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  10P GAIN MUTATED           0         0          0          0          0
  10P GAIN WILD-TYPE         1         2          1          6          5
                    vv
clus                 STAGE IS
  10P GAIN MUTATED          2
  10P GAIN WILD-TYPE       44
D18V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   1                 18
  STAGE IA                  1                 24
  STAGE IB                  1                 10
  STAGE II                  0                  5
  STAGE IIA                 0                  6
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                0                  6
  STAGE IIIC                0                  5
  STAGE IS                  2                 44
[1] 12  2
[1] 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
  10P GAIN MUTATED    2  3  1
  10P GAIN WILD-TYPE 73 48  5
D18V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                2                 73
  T2                3                 48
  T3                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  10P GAIN MUTATED    1     0
  10P GAIN WILD-TYPE 45    13
D18V5, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 58 
        TCGA-2G-AAEW         TCGA-2G-AAEX         TCGA-2G-AAF1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAF4         TCGA-2G-AAF6         TCGA-2G-AAF8 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAFE         TCGA-2G-AAFG         TCGA-2G-AAFH 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAFI         TCGA-2G-AAFJ         TCGA-2G-AAFL 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAFM         TCGA-2G-AAFN         TCGA-2G-AAFO 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAFV         TCGA-2G-AAFY         TCGA-2G-AAG0 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAG5         TCGA-2G-AAG6         TCGA-2G-AAG7 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAG8         TCGA-2G-AAG9         TCGA-2G-AAGA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAGC         TCGA-2G-AAGE         TCGA-2G-AAGF 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAGG         TCGA-2G-AAGI         TCGA-2G-AAGJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAGK         TCGA-2G-AAGN         TCGA-2G-AAGO 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAGP         TCGA-2G-AAGS         TCGA-2G-AAGW 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAGX         TCGA-2G-AAGY         TCGA-2G-AAGZ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAH2         TCGA-2G-AAHG         TCGA-2G-AAHL 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAHN         TCGA-2G-AAHP         TCGA-2G-AAHT 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2G-AAKG         TCGA-2G-AAL5         TCGA-2G-AAL7 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-4K-AA1G         TCGA-4K-AA1H         TCGA-4K-AA1I 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-4K-AAAL         TCGA-SO-A8JP         TCGA-VF-A8A8 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-VF-A8A9         TCGA-VF-A8AA         TCGA-VF-A8AB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-X3-A8G4 
"10P GAIN WILD-TYPE" 
D18V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     5   0
  10P GAIN WILD-TYPE 109   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5    0
  10P GAIN WILD-TYPE  109    4
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                5                109
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         1     4
  10P GAIN WILD-TYPE     4                         5   114
D18V7, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                    4                114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0   5
  10P GAIN WILD-TYPE  11 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0    5
  10P GAIN WILD-TYPE   11  106
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO                5                106
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     8   0
  10Q GAIN WILD-TYPE 121   4
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                125 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 0                  4 
$`10Q GAIN MUTATED`
TCGA-2G-AAF8 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAGM TCGA-WZ-A8D5 TCGA-XE-A8H1 
      122.40        52.37        71.24        59.64         0.82         6.87 
TCGA-YU-A94I TCGA-ZM-AA0N 
        7.96        10.85 

$`10Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE 
       20.32        30.35        38.30        59.70       102.35       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       72.20        61.71        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
      106.39       115.00       120.62        59.28       124.57       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
       61.45       170.33        80.94        60.16        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
        2.73         0.13         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       20.68        18.15         9.14        13.58         1.38        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 
        9.63        10.26        17.23         3.52        37.18        36.79 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 
        4.90        24.26         3.65         5.06         0.16        28.14 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
        5.29        58.88        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       27.55        17.39        16.41        11.34        46.88 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.82               0.10 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            122.40             229.22 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             31.61              37.68 
[1] "0.8 - 122.4 (31.6)" "0.1 - 229.2 (37.7)"
[1] "hr="     "2.6e+07"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         0        2        1        0         0         0
  10Q GAIN WILD-TYPE      19       23       10        5         6         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  10Q GAIN MUTATED           0         0          0          0          0
  10Q GAIN WILD-TYPE         1         2          1          6          5
                    vv
clus                 STAGE IS
  10Q GAIN MUTATED          4
  10Q GAIN WILD-TYPE       42
D19V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                 19
  STAGE IA                  2                 23
  STAGE IB                  1                 10
  STAGE II                  0                  5
  STAGE IIA                 0                  6
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                0                  6
  STAGE IIIC                0                  5
  STAGE IS                  4                 42
[1] 12  2
[1] 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
  10Q GAIN MUTATED    3  4  1
  10Q GAIN WILD-TYPE 72 47  5
D19V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                3                 72
  T2                4                 47
  T3                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  10Q GAIN MUTATED    3     0
  10Q GAIN WILD-TYPE 43    13
D19V5, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                   3                 43
  N1+N2                0                 13
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     7   0
  10Q GAIN WILD-TYPE 107   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      7    0
  10Q GAIN WILD-TYPE  107    4
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                7                107
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0     7
  10Q GAIN WILD-TYPE     4                         6   111
D19V7, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    7                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   6
  10Q GAIN WILD-TYPE  10 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    6
  10Q GAIN WILD-TYPE   10  105
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO                6                105
[1] 2 2
[1] FALSE

Clustering(20) Variable = 11P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     9   0
  11P GAIN WILD-TYPE 120   4
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                124 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                  4 
$`11P GAIN MUTATED`
TCGA-2G-AAG8 TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAKH TCGA-2G-AAKL TCGA-4K-AAAL 
       63.22       120.62       124.57       161.72        95.67         4.83 
TCGA-X3-A8G4 TCGA-YU-A94I TCGA-ZM-AA0B 
       28.14         7.96        27.55 

$`11P GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 
       40.01        52.37        71.24        72.20        61.71        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS 
       75.09       108.16        59.64       106.39       115.00        59.28 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
      212.65       229.22       184.41       131.21        70.59         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JW TCGA-S6-A8JX 
        0.13         3.52         7.00         0.10        20.68        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X 
        9.14        13.58         1.38        16.31         9.63        10.26 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
       17.23         3.52        37.18        36.79        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 
       35.61        33.07        23.90        41.52         4.90        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-A8H4 
        3.65         5.06         0.16         0.82         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF 
       12.07         7.89        16.87         8.88        67.66        41.69 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       50.96         0.43         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0D 
       58.88        40.96         8.15        37.02        39.35        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              4.83               0.10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            161.72             229.22 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             63.22              37.43 
[1] "4.8 - 161.7 (63.2)" "0.1 - 229.2 (37.4)"
[1] "hr="     "7.4e+07"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         0        2        1        2         1         0
  11P GAIN WILD-TYPE      19       23       10        3         5         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  11P GAIN MUTATED           0         0          0          0          0
  11P GAIN WILD-TYPE         1         2          1          6          5
                    vv
clus                 STAGE IS
  11P GAIN MUTATED          3
  11P GAIN WILD-TYPE       43
D20V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   0                 19
  STAGE IA                  2                 23
  STAGE IB                  1                 10
  STAGE II                  2                  3
  STAGE IIA                 1                  5
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                0                  6
  STAGE IIIC                0                  5
  STAGE IS                  3                 43
[1] 12  2
[1] 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
  11P GAIN MUTATED    4  5  0
  11P GAIN WILD-TYPE 71 46  6
D20V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                4                 71
  T2                5                 46
  T3                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  11P GAIN MUTATED    3     1
  11P GAIN WILD-TYPE 43    12
D20V5, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                   3                 43
  N1+N2                1                 12
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     8   0
  11P GAIN WILD-TYPE 106   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      8    0
  11P GAIN WILD-TYPE  106    4
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                8                106
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         0     8
  11P GAIN WILD-TYPE     4                         6   110
D20V7, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    8                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0   8
  11P GAIN WILD-TYPE  11 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    8
  11P GAIN WILD-TYPE   11  103
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO                8                103
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     4   0
  11Q GAIN WILD-TYPE 125   4
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                129 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                  4 
$`11Q GAIN MUTATED`
TCGA-2G-AAGT TCGA-2G-AAKH TCGA-2G-AAKL TCGA-YU-A94I 
      124.57       161.72        95.67         7.96 

$`11Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       40.01        52.37        71.24        72.20        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       63.32        68.22        72.85        68.38        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       92.09        75.09       108.16        59.64       106.39       115.00 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      120.62        59.28       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
        6.08       122.50       212.65       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23         3.52        37.18 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       36.79        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       41.52         4.90        24.26         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
       16.87         8.88        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
        8.32        12.92        20.12         6.90        57.90        54.35 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L 
       31.92        21.96         0.56         5.29        58.88        40.96 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
        8.15        37.02        39.35        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       11.34        46.88        10.85 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              7.96               0.10 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            161.72             229.22 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            110.12              37.18 
[1] "8.0 - 161.7 (110.1)" "0.1 - 229.2 (37.2)" 
[1] "hr="     "2.5e+07"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         0        1        0        2         0         0
  11Q GAIN WILD-TYPE      19       24       11        3         6         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  11Q GAIN MUTATED           0         0          0          0          0
  11Q GAIN WILD-TYPE         1         2          1          6          5
                    vv
clus                 STAGE IS
  11Q GAIN MUTATED          1
  11Q GAIN WILD-TYPE       45
D21V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   0                 19
  STAGE IA                  1                 24
  STAGE IB                  0                 11
  STAGE II                  2                  3
  STAGE IIA                 0                  6
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                0                  6
  STAGE IIIC                0                  5
  STAGE IS                  1                 45
[1] 12  2
[1] 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
  11Q GAIN MUTATED    2  2  0
  11Q GAIN WILD-TYPE 73 49  6
D21V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                2                 73
  T2                2                 49
  T3                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  11Q GAIN MUTATED    0     0
  11Q GAIN WILD-TYPE 46    13
D21V5, multiclass
D21V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3   0
  11Q GAIN WILD-TYPE 111   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    0
  11Q GAIN WILD-TYPE  111    4
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                3                111
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         0     3
  11Q GAIN WILD-TYPE     4                         6   115
D21V7, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0   3
  11Q GAIN WILD-TYPE  11 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    3
  11Q GAIN WILD-TYPE   11  108
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO                3                108
[1] 2 2
[1] FALSE

Clustering(22) Variable = 12P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED   125   4
  12P GAIN WILD-TYPE   4   0
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               129                  4 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                  0 
$`12P GAIN MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       40.01        52.37        71.24        72.20        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       63.32        68.22        72.85        68.38        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       92.09        75.09       108.16        59.64       106.39       115.00 
TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      120.62       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
        6.08       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      184.41       131.21        70.59         2.73         0.13         3.52 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23         3.52 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       37.18        36.79        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       23.90        41.52         4.90        24.26         3.65         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        0.16         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
        7.89        16.87         8.88        67.66        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
        0.43         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       54.35        21.96         0.56         5.29        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0E 
       40.96         8.15        37.02        39.35        27.55        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       11.34        46.88        10.85 

$`12P GAIN WILD-TYPE`
TCGA-2G-AAGS TCGA-4K-AA1H TCGA-YU-A90S TCGA-ZM-AA0D 
       59.28         7.00        31.92        17.39 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               0.1                7.0 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            229.22              59.28 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            38.300             24.655 
[1] "0.1 - 229.2 (38.3)" "7.0 - 59.3 (24.7)" 
[1] "hr="     "2.5e+07"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED        19       22       11        5         6         1
  12P GAIN WILD-TYPE       0        3        0        0         0         0
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  12P GAIN MUTATED           1         2          1          5          5
  12P GAIN WILD-TYPE         0         0          0          1          0
                    vv
clus                 STAGE IS
  12P GAIN MUTATED         46
  12P GAIN WILD-TYPE        0
D22V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  19                  0
  STAGE IA                 22                  3
  STAGE IB                 11                  0
  STAGE II                  5                  0
  STAGE IIA                 6                  0
  STAGE IIB                 1                  0
  STAGE IIC                 1                  0
  STAGE III                 2                  0
  STAGE IIIA                1                  0
  STAGE IIIB                5                  1
  STAGE IIIC                5                  0
  STAGE IS                 46                  0
[1] 12  2
[1] 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
  12P GAIN MUTATED   72 50  6
  12P GAIN WILD-TYPE  3  1  0
D22V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               72                  3
  T2               50                  1
  T3                6                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  12P GAIN MUTATED   45    12
  12P GAIN WILD-TYPE  1     1
D22V5, multiclass
[1] "Remove cluster labels:" "12P GAIN WILD-TYPE"    
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                57                  2 
      TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1       TCGA-2G-AAF4 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
      TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFE       TCGA-2G-AAFG 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
      TCGA-2G-AAFH       TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
      TCGA-2G-AAFM       TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
      TCGA-2G-AAFY       TCGA-2G-AAG0       TCGA-2G-AAG5       TCGA-2G-AAG6 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
      TCGA-2G-AAG7       TCGA-2G-AAG8       TCGA-2G-AAG9       TCGA-2G-AAGA 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
      TCGA-2G-AAGC       TCGA-2G-AAGE       TCGA-2G-AAGF       TCGA-2G-AAGG 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
      TCGA-2G-AAGI       TCGA-2G-AAGJ       TCGA-2G-AAGK       TCGA-2G-AAGM 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
      TCGA-2G-AAGN       TCGA-2G-AAGO       TCGA-2G-AAGP       TCGA-2G-AAGW 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
      TCGA-2G-AAGX       TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH2 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
      TCGA-2G-AAHG       TCGA-2G-AAHL       TCGA-2G-AAHN       TCGA-2G-AAHP 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
      TCGA-2G-AAHT       TCGA-2G-AAKG       TCGA-2G-AAL5       TCGA-2G-AAL7 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
      TCGA-4K-AA1G       TCGA-4K-AA1I       TCGA-4K-AAAL       TCGA-SO-A8JP 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
      TCGA-VF-A8A8       TCGA-VF-A8A9       TCGA-VF-A8AA       TCGA-VF-A8AB 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
      TCGA-X3-A8G4 
"12P GAIN MUTATED" 
D22V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   111   4
  12P GAIN WILD-TYPE   3   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    111    4
  12P GAIN WILD-TYPE    3    0
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0              111                  3
  1                4                  0
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       4                         6   114
  12P GAIN WILD-TYPE     0                         0     4
D22V7, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    4                  0
  BLACK OR AFRICAN AMERICAN                6                  0
  WHITE                                  114                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    11 108
  12P GAIN WILD-TYPE   0   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     11  108
  12P GAIN WILD-TYPE    0    3
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                   11                  0
  NOT HISPANIC OR LATINO              108                  3
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   88  2
  12Q GAIN WILD-TYPE 41  2
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                90                 43 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                  2 
$`12Q GAIN MUTATED`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAFH 
       30.35        38.30        59.70       122.40       154.59        36.99 
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       14.14        17.16        14.86        16.50        40.70        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAG9 
       36.89        40.01        71.24        72.20        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       68.22        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGW TCGA-2G-AAGY 
      108.16        59.64       106.39       120.62        61.45        80.94 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       59.74        91.43       176.15       161.72        95.67       229.22 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I 
      131.21        70.59         2.73         0.13         3.52         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A6IS 
        4.83        20.68        18.15         9.14        13.58        16.31 
TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA 
       10.26        17.23         3.52        37.18        36.79        37.68 
TCGA-VF-A8AB TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.99        33.07        23.90        41.52         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
        6.87        40.01        65.98        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A8S2 
        7.89         8.88        67.66        50.96         0.43        12.92 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I 
       57.90        54.35        21.96         0.56         5.29         7.96 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       37.02        39.35        27.55        11.34        46.88        10.85 

$`12Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF6 TCGA-2G-AAFG TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAG3 
       20.32       102.35       191.31        14.56         9.57        52.37 
TCGA-2G-AAG7 TCGA-2G-AAGC TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
       61.71        72.85       115.00        59.28       124.57       128.94 
TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHT TCGA-2G-AAKD 
      170.33        60.16        59.80        59.80         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAL5 TCGA-4K-AA1H TCGA-SB-A76C TCGA-SN-A84W TCGA-VF-A8AC 
      212.65       184.41         7.00         1.38         9.63        35.61 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-XE-A8H4 
        4.90        24.26         3.65         5.06         0.16        18.38 
TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XY-A89B TCGA-XY-A8S3 
       34.22         0.46        16.87        41.69         8.32        20.12 
TCGA-XY-A9T9 TCGA-YU-A90S TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA0D 
        6.90        31.92        58.88        40.96         8.15        17.39 
TCGA-ZM-AA0E 
       16.41 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.10               0.16 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            229.22             212.65 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             39.68              31.92 
[1] "0.1 - 229.2 (39.7)" "0.2 - 212.7 (31.9)"
[1] "hr=" "4.7"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED        10       16       11        4         5         1
  12Q GAIN WILD-TYPE       9        9        0        1         1         0
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  12Q GAIN MUTATED           1         1          0          4          4
  12Q GAIN WILD-TYPE         0         1          1          2          1
                    vv
clus                 STAGE IS
  12Q GAIN MUTATED         31
  12Q GAIN WILD-TYPE       15
D23V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  10                  9
  STAGE IA                 16                  9
  STAGE IB                 11                  0
  STAGE II                  4                  1
  STAGE IIA                 5                  1
  STAGE IIB                 1                  0
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIA                0                  1
  STAGE IIIB                4                  2
  STAGE IIIC                4                  1
  STAGE IS                 31                 15
[1] 12  2
[1] 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
  12Q GAIN MUTATED   48 37  5
  12Q GAIN WILD-TYPE 27 14  1
D23V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               48                 27
  T2               37                 14
  T3                5                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  12Q GAIN MUTATED   32    10
  12Q GAIN WILD-TYPE 14     3
D23V5, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                  32                 14
  N1+N2               10                  3
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   80  3
  12Q GAIN WILD-TYPE 34  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     80    3
  12Q GAIN WILD-TYPE   34    1
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               80                 34
  1                3                  1
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       2                         5    79
  12Q GAIN WILD-TYPE     2                         1    39
D23V7, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    2                  2
  BLACK OR AFRICAN AMERICAN                5                  1
  WHITE                                   79                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    9 75
  12Q GAIN WILD-TYPE  2 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      9   75
  12Q GAIN WILD-TYPE    2   36
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    9                  2
  NOT HISPANIC OR LATINO               75                 36
[1] 2 2
[1] FALSE

Clustering(24) Variable = 14Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED   43  2
  14Q GAIN WILD-TYPE 86  2
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                45                 88 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                  2 
$`14Q GAIN MUTATED`
TCGA-2G-AAEX TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFZ 
       30.35       191.31        36.99        14.14        14.56        36.89 
TCGA-2G-AAG3 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGI 
       52.37        72.20        63.22        68.22        72.85        92.09 
TCGA-2G-AAGM TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.64        60.26        59.84        59.90        98.53        59.74 
TCGA-2G-AAKL TCGA-2G-AAL7 TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL 
       95.67       131.21         2.73         3.52         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-VF-A8AA TCGA-WZ-A7V3 TCGA-WZ-A7V5 
       20.68        18.15        13.58        37.68         3.65         0.16 
TCGA-X3-A8G4 TCGA-XE-AANV TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOJ 
       28.14        53.03         7.89        16.87         8.88        50.96 
TCGA-XE-AAOL TCGA-XY-A8S3 TCGA-YU-A90Y TCGA-YU-A94I TCGA-ZM-AA05 TCGA-ZM-AA06 
        0.43        20.12         0.56         7.96        37.02        39.35 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0N 
       17.39        16.41        10.85 

$`14Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        38.30        59.70       102.35       122.40       154.59 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       17.16         9.57        14.86        16.50        40.70        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGE TCGA-2G-AAGF 
       40.01        71.24        61.71        63.32        68.38        79.76 
TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       67.96        75.09       108.16       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       60.16       125.69        61.84        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM 
      176.15         6.08       122.50       212.65       161.72       229.22 
TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-S6-A8JY TCGA-SB-A76C 
      184.41        70.59         0.13         7.00         9.14         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23         3.52        37.18 
TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       36.79        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V4 TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-A8H4 
        4.90        24.26         5.06         0.82         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO3 TCGA-XE-AAO4 
       40.01        34.22        65.98         0.46        93.93        12.07 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A9T9 TCGA-YU-A90P 
       67.66        41.69         8.32        12.92         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L 
       54.35        31.92        21.96         5.29        58.88        40.96 
TCGA-YU-AA61 TCGA-ZM-AA0B TCGA-ZM-AA0F TCGA-ZM-AA0H 
        8.15        27.55        11.34        46.88 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.10               0.13 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            191.31             229.22 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             30.35              40.83 
[1] "0.1 - 191.3 (30.4)" "0.1 - 229.2 (40.8)"
[1] "hr=" "4.5"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         7        7        7        1         1         1
  14Q GAIN WILD-TYPE      12       18        4        4         5         0
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  14Q GAIN MUTATED           1         1          0          0          1
  14Q GAIN WILD-TYPE         0         1          1          6          4
                    vv
clus                 STAGE IS
  14Q GAIN MUTATED         18
  14Q GAIN WILD-TYPE       28
D24V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   7                 12
  STAGE IA                  7                 18
  STAGE IB                  7                  4
  STAGE II                  1                  4
  STAGE IIA                 1                  5
  STAGE IIB                 1                  0
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIA                0                  1
  STAGE IIIB                0                  6
  STAGE IIIC                1                  4
  STAGE IS                 18                 28
[1] 12  2
[1] 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
  14Q GAIN MUTATED   25 18  2
  14Q GAIN WILD-TYPE 50 33  4
D24V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               25                 50
  T2               18                 33
  T3                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  14Q GAIN MUTATED   16     2
  14Q GAIN WILD-TYPE 30    11
D24V5, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                  16                 30
  N1+N2                2                 11
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   40  1
  14Q GAIN WILD-TYPE 74  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     40    1
  14Q GAIN WILD-TYPE   74    3
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               40                 74
  1                1                  3
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       1                         2    40
  14Q GAIN WILD-TYPE     3                         4    78
D24V7, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                   40                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    2 41
  14Q GAIN WILD-TYPE  9 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   41
  14Q GAIN WILD-TYPE    9   70
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               41                 70
[1] 2 2
[1] FALSE

Clustering(25) Variable = 15Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED   46  1
  15Q GAIN WILD-TYPE 83  3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                47                 86 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                  3 
$`15Q GAIN MUTATED`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAFE TCGA-2G-AAFH TCGA-2G-AAG3 TCGA-2G-AAGE 
       30.35        38.30       154.59        36.99        52.37        68.38 
TCGA-2G-AAGN TCGA-2G-AAGW TCGA-2G-AAH2 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
      106.39        61.45        59.84        61.84        98.53        59.74 
TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAL7 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
       91.43         6.08       131.21         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        0.10        20.68        18.15         9.14        13.58         1.38 
TCGA-SN-A84Y TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AE TCGA-W4-A7U4 TCGA-WZ-A7V5 
       17.23        36.79        37.68        23.90        24.26         0.16 
TCGA-XE-AANV TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOD TCGA-XE-AAOL TCGA-XY-A89B 
       53.03        12.07         7.89        67.66         0.43         8.32 
TCGA-XY-A8S2 TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-AA61 TCGA-ZM-AA06 
       12.92        54.35        21.96         0.56         8.15        39.35 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

$`15Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFI 
       20.32        59.70       102.35       122.40       191.31        14.14 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       14.56        17.16         9.57        14.86        16.50        40.70 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 
       36.13        36.89        40.01        71.24        72.20        61.71 
TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG 
       63.22        63.32        68.22        72.85        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGO TCGA-2G-AAGP 
       92.09        75.09       108.16        59.64       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
       59.28       124.57       128.94       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP 
       60.26        59.90       125.69        59.80        59.80       176.15 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AAAL TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X 
       70.59         2.73         4.83        16.31         9.63        10.26 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U2 
        3.52        37.18        24.99        35.61        33.07        41.52 
TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
        4.90         3.65         5.06         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO3 
       18.38        40.01        34.22        65.98         0.46        93.93 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A8S3 TCGA-XY-A9T9 
       16.87         8.88        41.69        50.96        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90S TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       57.90        31.92         5.29        58.88         7.96        40.96 
TCGA-ZM-AA05 TCGA-ZM-AA0B 
       37.02        27.55 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.10               0.46 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            154.59             229.22 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            21.960             46.325 
[1] "0.1 - 154.6 (22.0)" "0.5 - 229.2 (46.3)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED         6       12        7        0         1         1
  15Q GAIN WILD-TYPE      13       13        4        5         5         0
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  15Q GAIN MUTATED           0         0          0          1          2
  15Q GAIN WILD-TYPE         1         2          1          5          3
                    vv
clus                 STAGE IS
  15Q GAIN MUTATED         15
  15Q GAIN WILD-TYPE       31
D25V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   6                 13
  STAGE IA                 12                 13
  STAGE IB                  7                  4
  STAGE II                  0                  5
  STAGE IIA                 1                  5
  STAGE IIB                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                1                  5
  STAGE IIIC                2                  3
  STAGE IS                 15                 31
[1] 12  2
[1] 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
  15Q GAIN MUTATED   26 19  2
  15Q GAIN WILD-TYPE 49 32  4
D25V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               26                 49
  T2               19                 32
  T3                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  15Q GAIN MUTATED   13     3
  15Q GAIN WILD-TYPE 33    10
D25V5, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                  13                 33
  N1+N2                3                 10
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   42  0
  15Q GAIN WILD-TYPE 72  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     42    0
  15Q GAIN WILD-TYPE   72    4
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               42                 72
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       1                         2    42
  15Q GAIN WILD-TYPE     3                         4    76
D25V7, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                   42                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    2 41
  15Q GAIN WILD-TYPE  9 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2   41
  15Q GAIN WILD-TYPE    9   70
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               41                 70
[1] 2 2
[1] FALSE

Clustering(26) Variable = 16P GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    12   1
  16P GAIN WILD-TYPE 117   3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                13                120 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                  3 
$`16P GAIN MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAGG TCGA-2G-AAGM TCGA-2G-AAGP 
       59.70        71.24        72.20        67.96        59.64       120.62 
TCGA-2G-AAGT TCGA-4K-AA1G TCGA-SN-A84Y TCGA-XE-AAOC TCGA-YU-A90P TCGA-YU-A90Y 
      124.57         3.52        17.23         8.88        57.90         0.56 
TCGA-ZM-AA06 
       39.35 

$`16P GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        38.30       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       52.37        61.71        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN 
       68.38        79.76        92.09        75.09       108.16       106.39 
TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      115.00        59.28       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
        6.08       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H 
      184.41       131.21        70.59         2.73         0.13         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 
        1.38        16.31         9.63        10.26         3.52        37.18 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       36.79        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       41.52         4.90        24.26         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
       16.87        67.66        41.69        50.96         0.43         8.32 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       12.92        20.12         6.90        54.35        31.92        21.96 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.56               0.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            124.57             229.22 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            59.640             37.005 
[1] "0.6 - 124.6 (59.6)" "0.1 - 229.2 (37.0)"
[1] "hr=" "4.3"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED         1        2        1        0         1         0
  16P GAIN WILD-TYPE      18       23       10        5         5         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  16P GAIN MUTATED           0         0          0          0          2
  16P GAIN WILD-TYPE         1         2          1          6          3
                    vv
clus                 STAGE IS
  16P GAIN MUTATED          6
  16P GAIN WILD-TYPE       40
D26V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   1                 18
  STAGE IA                  2                 23
  STAGE IB                  1                 10
  STAGE II                  0                  5
  STAGE IIA                 1                  5
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                0                  6
  STAGE IIIC                2                  3
  STAGE IS                  6                 40
[1] 12  2
[1] 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
  16P GAIN MUTATED    5  6  2
  16P GAIN WILD-TYPE 70 45  4
D26V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                5                 70
  T2                6                 45
  T3                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  16P GAIN MUTATED    5     2
  16P GAIN WILD-TYPE 41    11
D26V5, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                   5                 41
  N1+N2                2                 11
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    10   1
  16P GAIN WILD-TYPE 104   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     10    1
  16P GAIN WILD-TYPE  104    3
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               10                104
  1                1                  3
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       0                         1    12
  16P GAIN WILD-TYPE     4                         5   106
D26V7, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   12                106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     2   9
  16P GAIN WILD-TYPE   9 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2    9
  16P GAIN WILD-TYPE    9  102
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO                9                102
[1] 2 2
[1] FALSE

Clustering(27) Variable = 16Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    12   1
  16Q GAIN WILD-TYPE 117   3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                120 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  3 
$`16Q GAIN MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGM 
       59.70        71.24        72.20        68.38        67.96        59.64 
TCGA-2G-AAGP TCGA-2G-AAGT TCGA-SN-A84Y TCGA-XE-AAOC TCGA-YU-A90P TCGA-YU-A90Y 
      120.62       124.57        17.23         8.88        57.90         0.56 
TCGA-ZM-AA06 
       39.35 

$`16Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        38.30       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       52.37        61.71        63.22        63.32        68.22        72.85 
TCGA-2G-AAGF TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO 
       79.76        92.09        75.09       108.16       106.39       115.00 
TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
       59.28       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 
        1.38        16.31         9.63        10.26         3.52        37.18 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       36.79        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       41.52         4.90        24.26         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
       16.87        67.66        41.69        50.96         0.43         8.32 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       12.92        20.12         6.90        54.35        31.92        21.96 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.56               0.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            124.57             229.22 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             59.70              36.94 
[1] "0.6 - 124.6 (59.7)" "0.1 - 229.2 (36.9)"
[1] "hr=" "4"  
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         1        2        1        0         1         0
  16Q GAIN WILD-TYPE      18       23       10        5         5         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  16Q GAIN MUTATED           0         0          0          0          2
  16Q GAIN WILD-TYPE         1         2          1          6          3
                    vv
clus                 STAGE IS
  16Q GAIN MUTATED          6
  16Q GAIN WILD-TYPE       40
D27V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   1                 18
  STAGE IA                  2                 23
  STAGE IB                  1                 10
  STAGE II                  0                  5
  STAGE IIA                 1                  5
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                0                  6
  STAGE IIIC                2                  3
  STAGE IS                  6                 40
[1] 12  2
[1] 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
  16Q GAIN MUTATED    6  5  2
  16Q GAIN WILD-TYPE 69 46  4
D27V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                6                 69
  T2                5                 46
  T3                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  16Q GAIN MUTATED    5     2
  16Q GAIN WILD-TYPE 41    11
D27V5, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                   5                 41
  N1+N2                2                 11
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    10   1
  16Q GAIN WILD-TYPE 104   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     10    1
  16Q GAIN WILD-TYPE  104    3
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               10                104
  1                1                  3
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       0                         1    12
  16Q GAIN WILD-TYPE     4                         5   106
D27V7, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   12                106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2   9
  16Q GAIN WILD-TYPE   9 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2    9
  16Q GAIN WILD-TYPE    9  102
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO                9                102
[1] 2 2
[1] FALSE

Clustering(28) Variable = 17P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED   30  2
  17P GAIN WILD-TYPE 99  2
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                32                101 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                  2 
$`17P GAIN MUTATED`
TCGA-2G-AAF8 TCGA-2G-AAFI TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG5 
      122.40        14.14        16.50        40.70        36.89        71.24 
TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       72.20        63.22        68.22        72.85        68.38        79.76 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS 
       67.96        92.09        59.64       106.39       120.62        59.28 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
       60.26        59.84       161.72        95.67       229.22       131.21 
TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AB TCGA-VF-A8AD TCGA-W4-A7U4 TCGA-XE-AAOC 
       17.23        37.18        24.99        33.07        24.26         8.88 
TCGA-XY-A8S2 TCGA-YU-A90Y 
       12.92         0.56 

$`17P GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE 
       20.32        30.35        38.30        59.70       102.35       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      191.31        36.99        14.56        17.16         9.57        14.86 
TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGJ 
       36.13        40.01        52.37        61.71        63.32        75.09 
TCGA-2G-AAGK TCGA-2G-AAGO TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      108.16       115.00       124.57       128.94        61.45       170.33 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       80.94        60.16        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      122.50       212.65       184.41        70.59         2.73         0.13 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
        3.52         7.00         0.10         4.83        20.68        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X 
        9.14        13.58         1.38        16.31         9.63        10.26 
TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 
        3.52        36.79        37.68        35.61        23.90        41.52 
TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
        4.90         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD 
       53.03        93.93        12.07         7.89        16.87        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S3 TCGA-XY-A9T9 
       41.69        50.96         0.43         8.32        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D 
       57.90        54.35        31.92        21.96         5.29        58.88 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        7.96        40.96         8.15        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.56               0.10 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            229.22             212.65 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             61.74              35.61 
[1] "0.6 - 229.2 (61.7)" "0.1 - 212.7 (35.6)"
[1] "hr=" "1.3"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         1        4        3        3         3         0
  17P GAIN WILD-TYPE      18       21        8        2         3         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  17P GAIN MUTATED           0         1          0          2          2
  17P GAIN WILD-TYPE         1         1          1          4          3
                    vv
clus                 STAGE IS
  17P GAIN MUTATED         12
  17P GAIN WILD-TYPE       34
D28V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   1                 18
  STAGE IA                  4                 21
  STAGE IB                  3                  8
  STAGE II                  3                  2
  STAGE IIA                 3                  3
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIA                0                  1
  STAGE IIIB                2                  4
  STAGE IIIC                2                  3
  STAGE IS                 12                 34
[1] 12  2
[1] 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
  17P GAIN MUTATED   15 14  3
  17P GAIN WILD-TYPE 60 37  3
D28V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               15                 60
  T2               14                 37
  T3                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  17P GAIN MUTATED   15     6
  17P GAIN WILD-TYPE 31     7
D28V5, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                  15                 31
  N1+N2                6                  7
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                  0  1
  17P GAIN MUTATED   29  2
  17P GAIN WILD-TYPE 85  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     29    2
  17P GAIN WILD-TYPE   85    2
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               29                 85
  1                2                  2
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       0                         2    30
  17P GAIN WILD-TYPE     4                         4    88
D28V7, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                   30                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    2 29
  17P GAIN WILD-TYPE  9 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2   29
  17P GAIN WILD-TYPE    9   82
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               29                 82
[1] 2 2
[1] FALSE

Clustering(29) Variable = 17Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   40  3
  17Q GAIN WILD-TYPE 89  1
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                43                 90 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                  1 
$`17Q GAIN MUTATED`
TCGA-2G-AAF8 TCGA-2G-AAFI TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 
      122.40        14.14        16.50        40.70        36.89        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       71.24        72.20        63.22        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGN 
       79.76        67.96        92.09        75.09        59.64       106.39 
TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH8 TCGA-2G-AAKH 
      115.00       120.62        60.26        59.84        61.84       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 
       95.67       229.22       131.21        10.26        17.23        37.18 
TCGA-VF-A8AB TCGA-VF-A8AD TCGA-W4-A7U4 TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-AAO6 
       24.99        33.07        24.26         0.16        28.14         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XY-A8S2 TCGA-YU-A90P TCGA-YU-A90Y TCGA-YU-AA61 
       16.87         8.88        12.92        57.90         0.56         8.15 
TCGA-ZM-AA0B 
       27.55 

$`17Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE 
       20.32        30.35        38.30        59.70       102.35       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      191.31        36.99        14.56        17.16         9.57        14.86 
TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGK TCGA-2G-AAGS 
       36.13        40.01        61.71        63.32       108.16        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL 
       59.90       125.69        98.53        59.74        59.80        59.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAL5 
       91.43       176.15         6.08       122.50       212.65       184.41 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AC 
       16.31         9.63         3.52        36.79        37.68        35.61 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 
       23.90        41.52         4.90         3.65         5.06         0.82 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
       53.03        93.93        12.07        67.66        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S 
        0.43         8.32        20.12         6.90        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 
       21.96         5.29        58.88         7.96        40.96        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       39.35        17.39        16.41        11.34        46.88        10.85 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.16               0.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            229.22             212.65 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             59.64              36.46 
[1] "0.2 - 229.2 (59.6)" "0.1 - 212.7 (36.5)"
[1] "hr=" "3.6"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         2        8        3        3         3         0
  17Q GAIN WILD-TYPE      17       17        8        2         3         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  17Q GAIN MUTATED           0         1          0          1          3
  17Q GAIN WILD-TYPE         1         1          1          5          2
                    vv
clus                 STAGE IS
  17Q GAIN MUTATED         18
  17Q GAIN WILD-TYPE       28
D29V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   2                 17
  STAGE IA                  8                 17
  STAGE IB                  3                  8
  STAGE II                  3                  2
  STAGE IIA                 3                  3
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIA                0                  1
  STAGE IIIB                1                  5
  STAGE IIIC                3                  2
  STAGE IS                 18                 28
[1] 12  2
[1] 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
  17Q GAIN MUTATED   21 19  3
  17Q GAIN WILD-TYPE 54 32  3
D29V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               21                 54
  T2               19                 32
  T3                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  17Q GAIN MUTATED   18     5
  17Q GAIN WILD-TYPE 28     8
D29V5, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                  18                 28
  N1+N2                5                  8
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   37  2
  17Q GAIN WILD-TYPE 77  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     37    2
  17Q GAIN WILD-TYPE   77    2
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               37                 77
  1                2                  2
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       0                         3    40
  17Q GAIN WILD-TYPE     4                         3    78
D29V7, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                3                  3
  WHITE                                   40                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    3 37
  17Q GAIN WILD-TYPE  8 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3   37
  17Q GAIN WILD-TYPE    8   74
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               37                 74
[1] 2 2
[1] FALSE

Clustering(30) Variable = 18P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     4   0
  18P GAIN WILD-TYPE 125   4
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                129 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                  4 
$`18P GAIN MUTATED`
TCGA-2G-AAFJ TCGA-2G-AAGP TCGA-4K-AA1G TCGA-SO-A8JP 
       14.56       120.62         3.52         3.52 

$`18P GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        36.99        14.14        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS 
       75.09       108.16        59.64       106.39       115.00        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I 
      131.21        70.59         2.73         0.13         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 
       16.31         9.63        10.26        17.23        37.18        36.79 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
        4.90        24.26         3.65         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ 
       28.14         6.87        18.38        40.01        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        53.03        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43         8.32 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       12.92        20.12         6.90        57.90        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       21.96         0.56         5.29        58.88         7.96        40.96 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
        8.15        37.02        39.35        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       11.34        46.88        10.85 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              3.52               0.10 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            120.62             229.22 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              9.04              38.30 
[1] "3.5 - 120.6 (9.0)"  "0.1 - 229.2 (38.3)"
[1] "hr="     "9200000"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         2        0        0        0         1         0
  18P GAIN WILD-TYPE      17       25       11        5         5         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  18P GAIN MUTATED           0         0          0          0          0
  18P GAIN WILD-TYPE         1         2          1          6          5
                    vv
clus                 STAGE IS
  18P GAIN MUTATED          1
  18P GAIN WILD-TYPE       45
D30V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   2                 17
  STAGE IA                  0                 25
  STAGE IB                  0                 11
  STAGE II                  0                  5
  STAGE IIA                 1                  5
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                0                  6
  STAGE IIIC                0                  5
  STAGE IS                  1                 45
[1] 12  2
[1] 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
  18P GAIN MUTATED    2  2  0
  18P GAIN WILD-TYPE 73 49  6
D30V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                2                 73
  T2                2                 49
  T3                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  18P GAIN MUTATED    3     1
  18P GAIN WILD-TYPE 43    12
D30V5, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                   3                 43
  N1+N2                1                 12
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4   0
  18P GAIN WILD-TYPE 110   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    0
  18P GAIN WILD-TYPE  110    4
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                4                110
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       1                         0     3
  18P GAIN WILD-TYPE     3                         6   115
D30V7, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0   4
  18P GAIN WILD-TYPE  11 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0    4
  18P GAIN WILD-TYPE   11  107
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO                4                107
[1] 2 2
[1] FALSE

Clustering(31) Variable = 19P GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   32  0
  19P GAIN WILD-TYPE 97  4
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                32                101 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                  4 
$`19P GAIN MUTATED`
TCGA-2G-AAEX TCGA-2G-AAFH TCGA-2G-AAGI TCGA-2G-AAGW TCGA-2G-AAH0 TCGA-2G-AAH8 
       30.35        36.99        92.09        61.45        60.26        61.84 
TCGA-2G-AAHA TCGA-2G-AAHP TCGA-4K-AAAL TCGA-S6-A8JW TCGA-SB-A6J6 TCGA-SN-A84X 
       98.53       176.15         4.83        20.68        13.58        10.26 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-WZ-A7V5 TCGA-XE-A8H5 TCGA-XE-AANV 
       37.18        36.79        37.68         0.16        40.01        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOL TCGA-XY-A9T9 
       93.93        12.07         7.89         8.88         0.43         6.90 
TCGA-YU-A90W TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       21.96         8.15        37.02        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0N 
       16.41        10.85 

$`19P GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        38.30        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      191.31        14.14        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK 
       72.85        68.38        79.76        67.96        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 
      128.94       170.33        80.94        60.16        59.84        59.90 
TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT 
      125.69        59.74        59.80        59.80        91.43         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
        0.10        18.15         9.14         1.38        16.31         9.63 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       17.23         3.52        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 
       41.52         4.90        24.26         3.65         5.06         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
       28.14         6.87        18.38        34.22        65.98         0.46 
TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 
       16.87        67.66        41.69        50.96         8.32        12.92 
TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90Y TCGA-YU-A912 
       20.12        57.90        54.35        31.92         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA0F TCGA-ZM-AA0H 
       58.88         7.96        40.96        11.34        46.88 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.16               0.10 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            176.15             229.22 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             28.95              41.69 
[1] "0.2 - 176.2 (29.0)" "0.1 - 229.2 (41.7)"
[1] "hr="     "2.7e+08"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         4       10        4        0         0         1
  19P GAIN WILD-TYPE      15       15        7        5         6         0
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  19P GAIN MUTATED           1         0          0          0          1
  19P GAIN WILD-TYPE         0         2          1          6          4
                    vv
clus                 STAGE IS
  19P GAIN MUTATED         11
  19P GAIN WILD-TYPE       35
D31V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   4                 15
  STAGE IA                 10                 15
  STAGE IB                  4                  7
  STAGE II                  0                  5
  STAGE IIA                 0                  6
  STAGE IIB                 1                  0
  STAGE IIC                 1                  0
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                0                  6
  STAGE IIIC                1                  4
  STAGE IS                 11                 35
[1] 12  2
[1] 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
  19P GAIN MUTATED   20 12  0
  19P GAIN WILD-TYPE 55 39  6
D31V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               20                 55
  T2               12                 39
  T3                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  19P GAIN MUTATED    8     1
  19P GAIN WILD-TYPE 38    12
D31V5, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                   8                 38
  N1+N2                1                 12
[1] 2 2
[1] FALSE
D31V6, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   29  0
  19P GAIN WILD-TYPE 85  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     29    0
  19P GAIN WILD-TYPE   85    4
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               29                 85
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       1                         1    28
  19P GAIN WILD-TYPE     3                         5    90
D31V7, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   28                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    4 26
  19P GAIN WILD-TYPE  7 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      4   26
  19P GAIN WILD-TYPE    7   85
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               26                 85
[1] 2 2
[1] FALSE

Clustering(32) Variable = 19Q GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    26   0
  19Q GAIN WILD-TYPE 103   4
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                26                107 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  4 
$`19Q GAIN MUTATED`
TCGA-2G-AAEX TCGA-2G-AAF8 TCGA-2G-AAFH TCGA-2G-AAH8 TCGA-4K-AAAL TCGA-S6-A8JW 
       30.35       122.40        36.99        61.84         4.83        20.68 
TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-WZ-A7V5 TCGA-XE-A8H5 
       10.26        37.18        36.79        37.68         0.16        40.01 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOL 
       53.03        93.93        12.07         7.89         8.88         0.43 
TCGA-XY-A9T9 TCGA-YU-A90W TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
        6.90        21.96         8.15        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0N 
       16.41        10.85 

$`19Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAFG 
       20.32        38.30        59.70       102.35       154.59       191.31 
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       14.14        14.56        17.16         9.57        14.86        16.50 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 
       40.70        36.13        36.89        40.01        52.37        71.24 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       72.20        61.71        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.84        59.90       125.69        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JX 
        2.73         0.13         3.52         7.00         0.10        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y 
        9.14        13.58         1.38        16.31         9.63        17.23 
TCGA-SO-A8JP TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
        3.52        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 TCGA-X3-A8G4 
        4.90        24.26         3.65         5.06         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAOB 
        6.87        18.38        34.22        65.98         0.46        16.87 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       67.66        41.69        50.96         8.32        12.92        20.12 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       57.90        54.35        31.92         0.56         5.29        58.88 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA0F TCGA-ZM-AA0H 
        7.96        40.96        37.02        11.34        46.88 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.16               0.10 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            122.40             229.22 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             21.32              46.88 
[1] "0.2 - 122.4 (21.3)" "0.1 - 229.2 (46.9)"
[1] "hr="     "8.9e+07"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         4       10        3        0         0         1
  19Q GAIN WILD-TYPE      15       15        8        5         6         0
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  19Q GAIN MUTATED           0         0          0          0          1
  19Q GAIN WILD-TYPE         1         2          1          6          4
                    vv
clus                 STAGE IS
  19Q GAIN MUTATED          7
  19Q GAIN WILD-TYPE       39
D32V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   4                 15
  STAGE IA                 10                 15
  STAGE IB                  3                  8
  STAGE II                  0                  5
  STAGE IIA                 0                  6
  STAGE IIB                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                0                  6
  STAGE IIIC                1                  4
  STAGE IS                  7                 39
[1] 12  2
[1] 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
  19Q GAIN MUTATED   18  8  0
  19Q GAIN WILD-TYPE 57 43  6
D32V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               18                 57
  T2                8                 43
  T3                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  19Q GAIN MUTATED    6     1
  19Q GAIN WILD-TYPE 40    12
D32V5, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                   6                 40
  N1+N2                1                 12
[1] 2 2
[1] FALSE
D32V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   23  0
  19Q GAIN WILD-TYPE 91  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     23    0
  19Q GAIN WILD-TYPE   91    4
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               23                 91
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       1                         1    22
  19Q GAIN WILD-TYPE     3                         5    96
D32V7, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   22                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    4 20
  19Q GAIN WILD-TYPE  7 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      4   20
  19Q GAIN WILD-TYPE    7   91
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               20                 91
[1] 2 2
[1] FALSE

Clustering(33) Variable = 20P GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    29   1
  20P GAIN WILD-TYPE 100   3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                30                103 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                  3 
$`20P GAIN MUTATED`
TCGA-2G-AAFI TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG8 TCGA-2G-AAGG TCGA-2G-AAGI 
       14.14        36.89        52.37        63.22        67.96        92.09 
TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH8 TCGA-2G-AAHA 
       59.64       124.57        60.26        59.84        61.84        98.53 
TCGA-2G-AAHP TCGA-2G-AAKL TCGA-2G-AAL7 TCGA-4K-AAAL TCGA-S6-A8JW TCGA-SB-A6J6 
      176.15        95.67       131.21         4.83        20.68        13.58 
TCGA-SN-A84X TCGA-SO-A8JP TCGA-W4-A7U4 TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-AAOC 
       10.26         3.52        24.26         0.16        28.14         8.88 
TCGA-YU-A90P TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94I TCGA-ZM-AA05 TCGA-ZM-AA06 
       57.90        21.96         0.56         7.96        37.02        39.35 

$`20P GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        36.99        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG5 
       14.86        16.50        40.70        36.13        40.01        71.24 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       72.20        61.71        63.32        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       79.76        75.09       108.16       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
       59.28       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       59.90       125.69        59.74        59.80        59.80        91.43 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL5 
        6.08       122.50       212.65       161.72       229.22       184.41 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y 
       18.15         9.14         1.38        16.31         9.63        17.23 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       37.18        36.79        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 
       23.90        41.52         4.90         3.65         5.06         0.82 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD 
       53.03        93.93        12.07         7.89        16.87        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L 
        6.90        54.35        31.92         5.29        58.88        40.96 
TCGA-YU-AA61 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
        8.15        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.16               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            176.15             229.22 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            38.185             37.680 
[1] "0.2 - 176.2 (38.2)" "0.1 - 229.2 (37.7)"
[1] "hr=" "1.7"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         2        5        4        1         0         0
  20P GAIN WILD-TYPE      17       20        7        4         6         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  20P GAIN MUTATED           1         1          0          0          3
  20P GAIN WILD-TYPE         0         1          1          6          2
                    vv
clus                 STAGE IS
  20P GAIN MUTATED         12
  20P GAIN WILD-TYPE       34
D33V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   2                 17
  STAGE IA                  5                 20
  STAGE IB                  4                  7
  STAGE II                  1                  4
  STAGE IIA                 0                  6
  STAGE IIB                 0                  1
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIA                0                  1
  STAGE IIIB                0                  6
  STAGE IIIC                3                  2
  STAGE IS                 12                 34
[1] 12  2
[1] 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
  20P GAIN MUTATED   10 17  3
  20P GAIN WILD-TYPE 65 34  3
D33V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               10                 65
  T2               17                 34
  T3                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  20P GAIN MUTATED   10     1
  20P GAIN WILD-TYPE 36    12
D33V5, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                  10                 36
  N1+N2                1                 12
[1] 2 2
[1] FALSE
D33V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   23  2
  20P GAIN WILD-TYPE 91  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     23    2
  20P GAIN WILD-TYPE   91    2
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               23                 91
  1                2                  2
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       0                         1    28
  20P GAIN WILD-TYPE     4                         5    90
D33V7, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   28                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    2 24
  20P GAIN WILD-TYPE  9 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2   24
  20P GAIN WILD-TYPE    9   87
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               24                 87
[1] 2 2
[1] FALSE

Clustering(34) Variable = 20Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   32  1
  20Q GAIN WILD-TYPE 97  3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                33                100 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                  3 
$`20Q GAIN MUTATED`
TCGA-2G-AAFI TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG8 TCGA-2G-AAGG 
       14.14        40.70        36.89        52.37        63.22        67.96 
TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAH0 TCGA-2G-AAH2 
       92.09        59.64       120.62       124.57        60.26        59.84 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHP TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAL7 
       61.84        98.53       176.15       161.72        95.67       131.21 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-SB-A6J6 TCGA-SO-A8JP TCGA-W4-A7U4 TCGA-WZ-A7V5 
        4.83        20.68        13.58         3.52        24.26         0.16 
TCGA-X3-A8G4 TCGA-XE-AAOC TCGA-YU-A90P TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94I 
       28.14         8.88        57.90        21.96         0.56         7.96 
TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA06 
       40.96        37.02        39.35 

$`20Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        36.99        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 
       14.86        16.50        36.13        40.01        71.24        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       61.71        63.32        68.22        72.85        68.38        79.76 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGV 
       75.09       108.16       106.39       115.00        59.28       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH3 TCGA-2G-AAH4 
       61.45       170.33        80.94        60.16        59.90       125.69 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD 
       59.74        59.80        59.80        91.43         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      212.65       229.22       184.41        70.59         2.73         0.13 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C 
        3.52         7.00         0.10        18.15         9.14         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 
       16.31         9.63        10.26        17.23        37.18        36.79 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-A8H4 
        4.90         3.65         5.06         0.82         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
       12.07         7.89        16.87        67.66        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q 
        0.43         8.32        12.92        20.12         6.90        54.35 
TCGA-YU-A90S TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       31.92         5.29        58.88         8.15        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.16               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            176.15             229.22 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             40.96              36.89 
[1] "0.2 - 176.2 (41.0)" "0.1 - 229.2 (36.9)"
[1] "hr=" "1.4"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         2        5        4        2         1         0
  20Q GAIN WILD-TYPE      17       20        7        3         5         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  20Q GAIN MUTATED           1         1          0          0          4
  20Q GAIN WILD-TYPE         0         1          1          6          1
                    vv
clus                 STAGE IS
  20Q GAIN MUTATED         12
  20Q GAIN WILD-TYPE       34
D34V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   2                 17
  STAGE IA                  5                 20
  STAGE IB                  4                  7
  STAGE II                  2                  3
  STAGE IIA                 1                  5
  STAGE IIB                 0                  1
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIA                0                  1
  STAGE IIIB                0                  6
  STAGE IIIC                4                  1
  STAGE IS                 12                 34
[1] 12  2
[1] 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
  20Q GAIN MUTATED   13 17  3
  20Q GAIN WILD-TYPE 62 34  3
D34V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               13                 62
  T2               17                 34
  T3                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  20Q GAIN MUTATED   11     2
  20Q GAIN WILD-TYPE 35    11
D34V5, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                  11                 35
  N1+N2                2                 11
[1] 2 2
[1] FALSE
D34V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   25  2
  20Q GAIN WILD-TYPE 89  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     25    2
  20Q GAIN WILD-TYPE   89    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               25                 89
  1                2                  2
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       0                         2    30
  20Q GAIN WILD-TYPE     4                         4    88
D34V7, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                   30                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    1 27
  20Q GAIN WILD-TYPE 10 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      1   27
  20Q GAIN WILD-TYPE   10   84
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               27                 84
[1] 2 2
[1] FALSE

Clustering(35) Variable = 21Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED   110   2
  21Q GAIN WILD-TYPE  19   2
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               112                 21 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                  2 
$`21Q GAIN MUTATED`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       30.35        38.30        59.70       102.35       122.40       154.59 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFO 
       36.99        14.14        14.56        17.16         9.57        16.50 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       36.13        36.89        40.01        52.37        71.24        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       61.71        63.32        68.22        68.38        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP 
       92.09        75.09       108.16        59.64       106.39       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAH0 
       59.28       124.57       128.94        61.45       170.33        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKH TCGA-2G-AAKL 
       59.80        59.80        91.43         6.08       161.72        95.67 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      229.22       131.21        70.59         2.73         0.13         3.52 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23         3.52 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 
       37.18        36.79        37.68        35.61        23.90        41.52 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
        4.90        24.26         3.65         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
       28.14        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A912 
       20.12         6.90        57.90        54.35        21.96         5.29 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0D 
        7.96        40.96         8.15        37.02        39.35        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

$`21Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAFG TCGA-2G-AAFN TCGA-2G-AAFV TCGA-2G-AAG8 TCGA-2G-AAGC 
       20.32       191.31        14.86        40.70        63.22        72.85 
TCGA-2G-AAGO TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKG 
      115.00        80.94        60.16       176.15       122.50       212.65 
TCGA-2G-AAL5 TCGA-4K-AA1H TCGA-VF-A8AB TCGA-VF-A8AD TCGA-XE-A8H1 TCGA-YU-A90S 
      184.41         7.00        24.99        33.07         6.87        31.92 
TCGA-YU-A90Y TCGA-YU-A94D TCGA-ZM-AA0B 
        0.56        58.88        27.55 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.10               0.56 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            229.22             212.65 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             37.10              58.88 
[1] "0.1 - 229.2 (37.1)" "0.6 - 212.7 (58.9)"
[1] "hr=" "9.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED        17       21        9        5         6         1
  21Q GAIN WILD-TYPE       2        4        2        0         0         0
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  21Q GAIN MUTATED           1         1          0          4          4
  21Q GAIN WILD-TYPE         0         1          1          2          1
                    vv
clus                 STAGE IS
  21Q GAIN MUTATED         38
  21Q GAIN WILD-TYPE        8
D35V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  17                  2
  STAGE IA                 21                  4
  STAGE IB                  9                  2
  STAGE II                  5                  0
  STAGE IIA                 6                  0
  STAGE IIB                 1                  0
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIA                0                  1
  STAGE IIIB                4                  2
  STAGE IIIC                4                  1
  STAGE IS                 38                  8
[1] 12  2
[1] 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
  21Q GAIN MUTATED   65 42  4
  21Q GAIN WILD-TYPE 10  9  2
D35V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               65                 10
  T2               42                  9
  T3                4                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  21Q GAIN MUTATED   34    11
  21Q GAIN WILD-TYPE 12     2
D35V5, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                  34                 12
  N1+N2               11                  2
[1] 2 2
[1] FALSE
D35V6, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   97  3
  21Q GAIN WILD-TYPE 17  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     97    3
  21Q GAIN WILD-TYPE   17    1
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               97                 17
  1                3                  1
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       4                         4   100
  21Q GAIN WILD-TYPE     0                         2    18
D35V7, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    4                  0
  BLACK OR AFRICAN AMERICAN                4                  2
  WHITE                                  100                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   10 94
  21Q GAIN WILD-TYPE  1 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10   94
  21Q GAIN WILD-TYPE    1   17
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   10                  1
  NOT HISPANIC OR LATINO               94                 17
[1] 2 2
[1] FALSE

Clustering(36) Variable = 22Q GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   34  0
  22Q GAIN WILD-TYPE 95  4
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                34                 99 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                  4 
$`22Q GAIN MUTATED`
TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAG3 
       30.35        59.70       102.35       191.31        36.99        52.37 
TCGA-2G-AAGK TCGA-2G-AAH2 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHN TCGA-2G-AAKH 
      108.16        59.84        98.53        59.74        91.43       161.72 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.13         3.52        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-W4-A7U2 TCGA-WZ-A8D5 TCGA-XE-A8H4 
        1.38         3.52        36.79        41.52         0.82        18.38 
TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANV TCGA-XE-AAO6 TCGA-XE-AAOL TCGA-XY-A9T9 
       40.01        65.98        53.03         7.89         0.43         6.90 
TCGA-YU-A90P TCGA-YU-A90W TCGA-ZM-AA06 TCGA-ZM-AA0N 
       57.90        21.96        39.35        10.85 

$`22Q GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAFI TCGA-2G-AAFJ 
       20.32        38.30       122.40       154.59        14.14        14.56 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       17.16         9.57        14.86        16.50        40.70        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.89        40.01        71.24        72.20        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       63.32        68.22        72.85        68.38        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       92.09        75.09        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHG 
       60.16        60.26        59.90       125.69        61.84        59.80 
TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL 
       59.80       176.15         6.08       122.50       212.65        95.67 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1H 
      229.22       184.41       131.21        70.59         2.73         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y 
        0.10         4.83        16.31         9.63        10.26        17.23 
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       37.18        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 
        4.90        24.26         3.65         5.06         0.16        28.14 
TCGA-XE-A8H1 TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB 
        6.87        34.22         0.46        93.93        12.07        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 
        8.88        67.66        41.69        50.96         8.32        12.92 
TCGA-XY-A8S3 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       20.12        54.35        31.92         0.56         5.29        58.88 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D 
        7.96        40.96         8.15        37.02        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       16.41        11.34        46.88 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.13               0.10 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            191.31             229.22 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             36.89              38.30 
[1] "0.1 - 191.3 (36.9)" "0.1 - 229.2 (38.3)"
[1] "hr="     "2.8e+08"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         5        6        5        1         0         1
  22Q GAIN WILD-TYPE      14       19        6        4         6         0
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  22Q GAIN MUTATED           0         0          0          0          0
  22Q GAIN WILD-TYPE         1         2          1          6          5
                    vv
clus                 STAGE IS
  22Q GAIN MUTATED         13
  22Q GAIN WILD-TYPE       33
D36V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   5                 14
  STAGE IA                  6                 19
  STAGE IB                  5                  6
  STAGE II                  1                  4
  STAGE IIA                 0                  6
  STAGE IIB                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                0                  6
  STAGE IIIC                0                  5
  STAGE IS                 13                 33
[1] 12  2
[1] 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
  22Q GAIN MUTATED   23  9  1
  22Q GAIN WILD-TYPE 52 42  5
D36V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               23                 52
  T2                9                 42
  T3                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  22Q GAIN MUTATED   10     1
  22Q GAIN WILD-TYPE 36    12
D36V5, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                  10                 36
  N1+N2                1                 12
[1] 2 2
[1] FALSE
D36V6, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED   31  0
  22Q GAIN WILD-TYPE 83  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     31    0
  22Q GAIN WILD-TYPE   83    4
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               31                 83
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       0                         1    31
  22Q GAIN WILD-TYPE     4                         5    87
D36V7, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   31                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    2 30
  22Q GAIN WILD-TYPE  9 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2   30
  22Q GAIN WILD-TYPE    9   81
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               30                 81
[1] 2 2
[1] FALSE

Clustering(37) Variable = XP GAIN MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    18   0
  XP GAIN WILD-TYPE 111   4
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               18               115 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                0                 4 
$`XP GAIN MUTATED`
TCGA-2G-AAFI TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAGI TCGA-2G-AAGK 
       14.14        40.70        36.89        52.37        92.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAHA TCGA-2G-AAKL 
       59.64       124.57        61.45        80.94        98.53        95.67 
TCGA-2G-AALP TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-XE-AAOC TCGA-XE-AAOL 
       70.59        10.26        37.18        37.68         8.88         0.43 

$`XP GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        36.99        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 
       14.86        16.50        36.13        40.01        71.24        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       61.71        63.22        63.32        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       79.76        67.96        75.09       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
       59.28       128.94       170.33        60.16        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL 
       59.90       125.69        61.84        59.74        59.80        59.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
       91.43       176.15         6.08       122.50       212.65       161.72 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      229.22       184.41       131.21         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
        7.00         0.10         4.83        20.68        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y TCGA-SO-A8JP 
       13.58         1.38        16.31         9.63        17.23         3.52 
TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       36.79        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
        4.90        24.26         3.65         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ 
       28.14         6.87        18.38        40.01        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        53.03        93.93        12.07         7.89        16.87 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       67.66        41.69        50.96         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.43              0.10 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           124.57            229.22 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           56.005            36.790 
[1] "0.4 - 124.6 (56.0)" "0.1 - 229.2 (36.8)"
[1] "hr="     "8.5e+07"
D37V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED         2        2        2        1         0         0
  XP GAIN WILD-TYPE      17       23        9        4         6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XP GAIN MUTATED           0         1          0          1          0
  XP GAIN WILD-TYPE         1         1          1          5          5
                   vv
clus                STAGE IS
  XP GAIN MUTATED          9
  XP GAIN WILD-TYPE       37
D37V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                  2                17
  STAGE IA                 2                23
  STAGE IB                 2                 9
  STAGE II                 1                 4
  STAGE IIA                0                 6
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                1                 1
  STAGE IIIA               0                 1
  STAGE IIIB               1                 5
  STAGE IIIC               0                 5
  STAGE IS                 9                37
[1] 12  2
[1] 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
  XP GAIN MUTATED    9  8  1
  XP GAIN WILD-TYPE 66 43  5
D37V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               9                66
  T2               8                43
  T3               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  XP GAIN MUTATED    9     0
  XP GAIN WILD-TYPE 37    13
D37V5, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  N0                  9                37
  N1+N2               0                13
[1] 2 2
[1] FALSE
D37V6, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   16  2
  XP GAIN WILD-TYPE 98  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     16    2
  XP GAIN WILD-TYPE   98    2
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              16                98
  1               2                 2
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       0                         1    17
  XP GAIN WILD-TYPE     4                         5   101
D37V7, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  17               101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    2 16
  XP GAIN WILD-TYPE  9 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2   16
  XP GAIN WILD-TYPE    9   95
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              16                95
[1] 2 2
[1] FALSE

Clustering(38) Variable = XQ GAIN MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    18   0
  XQ GAIN WILD-TYPE 111   4
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               18               115 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                 4 
$`XQ GAIN MUTATED`
TCGA-2G-AAFI TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAGI 
       14.14        40.70        36.89        52.37        71.24        92.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGO TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAHA 
      108.16        59.64       115.00       124.57        61.45        98.53 
TCGA-2G-AAKL TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-XE-AAOC TCGA-XE-AAOL 
       95.67        10.26        37.18        37.68         8.88         0.43 

$`XQ GAIN WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        36.99        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 
       14.86        16.50        36.13        40.01        72.20        61.71 
TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       63.22        63.32        68.22        72.85        68.38        79.76 
TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV 
       67.96        75.09       106.39       120.62        59.28       128.94 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
      170.33        80.94        60.16        60.26        59.84        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
      125.69        61.84        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM 
      176.15         6.08       122.50       212.65       161.72       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      184.41       131.21        70.59         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
        7.00         0.10         4.83        20.68        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y TCGA-SO-A8JP 
       13.58         1.38        16.31         9.63        17.23         3.52 
TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       36.79        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
        4.90        24.26         3.65         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ 
       28.14         6.87        18.38        40.01        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        53.03        93.93        12.07         7.89        16.87 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       67.66        41.69        50.96         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.43              0.10 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           124.57            229.22 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           56.005            36.790 
[1] "0.4 - 124.6 (56.0)" "0.1 - 229.2 (36.8)"
[1] "hr="     "8.5e+07"
D38V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         2        2        2        1         0         0
  XQ GAIN WILD-TYPE      17       23        9        4         6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ GAIN MUTATED           0         1          0          0          0
  XQ GAIN WILD-TYPE         1         1          1          6          5
                   vv
clus                STAGE IS
  XQ GAIN MUTATED         10
  XQ GAIN WILD-TYPE       36
D38V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  2                17
  STAGE IA                 2                23
  STAGE IB                 2                 9
  STAGE II                 1                 4
  STAGE IIA                0                 6
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                1                 1
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               0                 5
  STAGE IS                10                36
[1] 12  2
[1] 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
  XQ GAIN MUTATED    8  9  1
  XQ GAIN WILD-TYPE 67 42  5
D38V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               8                67
  T2               9                42
  T3               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  XQ GAIN MUTATED   10     0
  XQ GAIN WILD-TYPE 36    13
D38V5, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0                 10                36
  N1+N2               0                13
[1] 2 2
[1] FALSE
D38V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   17  1
  XQ GAIN WILD-TYPE 97  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     17    1
  XQ GAIN WILD-TYPE   97    3
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              17                97
  1               1                 3
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         1    17
  XQ GAIN WILD-TYPE     4                         5   101
D38V7, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  17               101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2 16
  XQ GAIN WILD-TYPE  9 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2   16
  XQ GAIN WILD-TYPE    9   95
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              16                95
[1] 2 2
[1] FALSE

Clustering(39) Variable = 1P LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    15   2
  1P LOSS WILD-TYPE 114   2
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               17               116 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                 2 
$`1P LOSS MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF4 TCGA-2G-AAFE TCGA-2G-AAG6 TCGA-2G-AAGJ TCGA-2G-AAH0 
       20.32        59.70       154.59        72.20        75.09        60.26 
TCGA-2G-AAH2 TCGA-2G-AAHP TCGA-2X-A9D5 TCGA-SB-A76C TCGA-SN-A84W TCGA-SO-A8JP 
       59.84       176.15         2.73         1.38         9.63         3.52 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-XE-AANI TCGA-YU-A90Y TCGA-YU-A94I 
       23.90        41.52        34.22         0.56         7.96 

$`1P LOSS WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH 
       30.35        38.30       102.35       122.40       191.31        36.99 
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       14.14        14.56        17.16         9.57        14.86        16.50 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 
       40.70        36.13        36.89        40.01        52.37        71.24 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       61.71        63.22        63.32        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN 
       79.76        67.96        92.09       108.16        59.64       106.39 
TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW 
      115.00       120.62        59.28       124.57       128.94        61.45 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      170.33        80.94        60.16        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT 
       98.53        59.74        59.80        59.80        91.43         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
      131.21        70.59         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A6IS 
        4.83        20.68        18.15         9.14        13.58        16.31 
TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
       10.26        17.23        37.18        36.79        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       35.61        33.07         4.90        24.26         3.65         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        0.16         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
       16.87         8.88        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
        8.32        12.92        20.12         6.90        57.90        54.35 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 
       31.92        21.96         5.29        58.88        40.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.56              0.10 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           176.15            229.22 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            34.22             37.99 
[1] "0.6 - 176.2 (34.2)" "0.1 - 229.2 (38.0)"
[1] "hr=" "14" 
D39V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         3        3        0        0         1         0
  1P LOSS WILD-TYPE      16       22       11        5         5         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P LOSS MUTATED           0         0          0          0          1
  1P LOSS WILD-TYPE         1         2          1          6          4
                   vv
clus                STAGE IS
  1P LOSS MUTATED          7
  1P LOSS WILD-TYPE       39
D39V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  3                16
  STAGE IA                 3                22
  STAGE IB                 0                11
  STAGE II                 0                 5
  STAGE IIA                1                 5
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               1                 4
  STAGE IS                 7                39
[1] 12  2
[1] 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
  1P LOSS MUTATED   12  4  1
  1P LOSS WILD-TYPE 63 47  5
D39V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              12                63
  T2               4                47
  T3               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  1P LOSS MUTATED    7     1
  1P LOSS WILD-TYPE 39    12
D39V5, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0                  7                39
  N1+N2               1                12
[1] 2 2
[1] FALSE
D39V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    14   0
  1P LOSS WILD-TYPE 100   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     14    0
  1P LOSS WILD-TYPE  100    4
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              14               100
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       0                         2    14
  1P LOSS WILD-TYPE     4                         4   104
D39V7, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               2                 4
  WHITE                                  14               104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1 14
  1P LOSS WILD-TYPE 10 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   14
  1P LOSS WILD-TYPE   10   97
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              14                97
[1] 2 2
[1] FALSE

Clustering(40) Variable = 1Q LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED     7   1
  1Q LOSS WILD-TYPE 122   3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8               125 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                 3 
$`1Q LOSS MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAG6 TCGA-2G-AAGJ TCGA-2G-AAH2 TCGA-2G-AAHP TCGA-XE-AANI 
       59.70        72.20        75.09        59.84       176.15        34.22 
TCGA-YU-A90Y TCGA-YU-A94I 
        0.56         7.96 

$`1Q LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        38.30       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       52.37        71.24        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK 
       72.85        68.38        79.76        67.96        92.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
       59.80        91.43         6.08       122.50       212.65       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
       95.67       229.22       184.41       131.21        70.59         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
        0.13         3.52         7.00         0.10         4.83        20.68 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       18.15         9.14        13.58         1.38        16.31         9.63 
TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA 
       10.26        17.23         3.52        37.18        36.79        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 
       24.99        35.61        33.07        23.90        41.52         4.90 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
        6.87        18.38        40.01        65.98         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 
        6.90        57.90        54.35        31.92        21.96         5.29 
TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
       58.88        40.96         8.15        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.56              0.10 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           176.15            229.22 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            59.77             37.18 
[1] "0.6 - 176.2 (59.8)" "0.1 - 229.2 (37.2)"
[1] "hr=" "7.1"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         1        2        0        0         0         0
  1Q LOSS WILD-TYPE      18       23       11        5         6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q LOSS MUTATED           0         0          0          0          1
  1Q LOSS WILD-TYPE         1         2          1          6          4
                   vv
clus                STAGE IS
  1Q LOSS MUTATED          4
  1Q LOSS WILD-TYPE       42
D40V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  1                18
  STAGE IA                 2                23
  STAGE IB                 0                11
  STAGE II                 0                 5
  STAGE IIA                0                 6
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               1                 4
  STAGE IS                 4                42
[1] 12  2
[1] 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
  1Q LOSS MUTATED    6  1  1
  1Q LOSS WILD-TYPE 69 50  5
D40V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               6                69
  T2               1                50
  T3               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  1Q LOSS MUTATED    5     0
  1Q LOSS WILD-TYPE 41    13
D40V5, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0                  5                41
  N1+N2               0                13
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     6   0
  1Q LOSS WILD-TYPE 108   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      6    0
  1Q LOSS WILD-TYPE  108    4
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               6               108
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         2     5
  1Q LOSS WILD-TYPE     4                         4   113
D40V7, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               2                 4
  WHITE                                   5               113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   6
  1Q LOSS WILD-TYPE  11 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    6
  1Q LOSS WILD-TYPE   11  105
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO               6               105
[1] 2 2
[1] FALSE

Clustering(41) Variable = 2P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     5   0
  2P LOSS WILD-TYPE 124   4
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5               128 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                 4 
$`2P LOSS MUTATED`
TCGA-2G-AAFH TCGA-2G-AAH2 TCGA-SN-A84Y TCGA-WZ-A8D5 TCGA-ZM-AA0D 
       36.99        59.84        17.23         0.82        17.39 

$`2P LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.16        60.26        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 
        1.38        16.31         9.63        10.26         3.52        37.18 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       36.79        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       41.52         4.90        24.26         3.65         5.06         0.16 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ 
       28.14         6.87        18.38        40.01        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        53.03        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43         8.32 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       12.92        20.12         6.90        57.90        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       21.96         0.56         5.29        58.88         7.96        40.96 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0E TCGA-ZM-AA0F 
        8.15        37.02        39.35        27.55        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.82              0.10 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            59.84            229.22 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           17.390            38.825 
[1] "0.8 - 59.8 (17.4)"  "0.1 - 229.2 (38.8)"
[1] "hr="     "2.6e+07"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         0        1        0        0         0         1
  2P LOSS WILD-TYPE      19       24       11        5         6         0
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P LOSS MUTATED           0         0          0          0          0
  2P LOSS WILD-TYPE         1         2          1          6          5
                   vv
clus                STAGE IS
  2P LOSS MUTATED          2
  2P LOSS WILD-TYPE       44
D41V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                19
  STAGE IA                 1                24
  STAGE IB                 0                11
  STAGE II                 0                 5
  STAGE IIA                0                 6
  STAGE IIB                1                 0
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               0                 5
  STAGE IS                 2                44
[1] 12  2
[1] 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
  2P LOSS MUTATED    3  1  1
  2P LOSS WILD-TYPE 72 50  5
D41V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               3                72
  T2               1                50
  T3               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  2P LOSS MUTATED    1     1
  2P LOSS WILD-TYPE 45    12
D41V5, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                57 
       TCGA-2G-AAEW        TCGA-2G-AAEX        TCGA-2G-AAF1        TCGA-2G-AAF4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2G-AAF6        TCGA-2G-AAF8        TCGA-2G-AAFE        TCGA-2G-AAFG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2G-AAFI        TCGA-2G-AAFJ        TCGA-2G-AAFL        TCGA-2G-AAFM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2G-AAFN        TCGA-2G-AAFO        TCGA-2G-AAFV        TCGA-2G-AAFY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2G-AAG0        TCGA-2G-AAG5        TCGA-2G-AAG6        TCGA-2G-AAG7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2G-AAG8        TCGA-2G-AAG9        TCGA-2G-AAGA        TCGA-2G-AAGC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2G-AAGE        TCGA-2G-AAGF        TCGA-2G-AAGG        TCGA-2G-AAGI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2G-AAGJ        TCGA-2G-AAGK        TCGA-2G-AAGM        TCGA-2G-AAGN 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2G-AAGO        TCGA-2G-AAGP        TCGA-2G-AAGS        TCGA-2G-AAGW 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2G-AAGX        TCGA-2G-AAGY        TCGA-2G-AAGZ        TCGA-2G-AAHG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2G-AAHL        TCGA-2G-AAHN        TCGA-2G-AAHP        TCGA-2G-AAHT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2G-AAKG        TCGA-2G-AAL5        TCGA-2G-AAL7        TCGA-4K-AA1G 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-4K-AA1H        TCGA-4K-AA1I        TCGA-4K-AAAL        TCGA-SO-A8JP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-VF-A8A8        TCGA-VF-A8A9        TCGA-VF-A8AA        TCGA-VF-A8AB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-X3-A8G4 
"2P LOSS WILD-TYPE" 
D41V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     5   0
  2P LOSS WILD-TYPE 109   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    0
  2P LOSS WILD-TYPE  109    4
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               5               109
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         0     5
  2P LOSS WILD-TYPE     4                         6   113
D41V7, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   5               113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1   4
  2P LOSS WILD-TYPE  10 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1    4
  2P LOSS WILD-TYPE   10  107
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO               4               107
[1] 2 2
[1] FALSE

Clustering(42) Variable = 2Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED     6   0
  2Q LOSS WILD-TYPE 123   4
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6               127 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                0                 4 
$`2Q LOSS MUTATED`
TCGA-2G-AAFH TCGA-2G-AAGS TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-SN-A84Y TCGA-ZM-AA0D 
       36.99        59.28        59.84       125.69        17.23        17.39 

$`2Q LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       60.26        59.90        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
        2.73         0.13         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       20.68        18.15         9.14        13.58         1.38        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA 
        9.63        10.26         3.52        37.18        36.79        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 
       24.99        35.61        33.07        23.90        41.52         4.90 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       20.12         6.90        57.90        54.35        31.92        21.96 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56         5.29        58.88         7.96        40.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        39.35        27.55        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            17.23              0.10 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           125.69            229.22 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           48.135            37.680 
[1] "17.2 - 125.7 (48.1)" "0.1 - 229.2 (37.7)" 
[1] "hr="     "2.6e+07"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         0        1        0        1         0         1
  2Q LOSS WILD-TYPE      19       24       11        4         6         0
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q LOSS MUTATED           0         0          0          1          0
  2Q LOSS WILD-TYPE         1         2          1          5          5
                   vv
clus                STAGE IS
  2Q LOSS MUTATED          2
  2Q LOSS WILD-TYPE       44
D42V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  0                19
  STAGE IA                 1                24
  STAGE IB                 0                11
  STAGE II                 1                 4
  STAGE IIA                0                 6
  STAGE IIB                1                 0
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               1                 5
  STAGE IIIC               0                 5
  STAGE IS                 2                44
[1] 12  2
[1] 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
  2Q LOSS MUTATED    5  1  0
  2Q LOSS WILD-TYPE 70 50  6
D42V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               5                70
  T2               1                50
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  2Q LOSS MUTATED    1     2
  2Q LOSS WILD-TYPE 45    11
D42V5, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0                  1                45
  N1+N2               2                11
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     6   0
  2Q LOSS WILD-TYPE 108   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      6    0
  2Q LOSS WILD-TYPE  108    4
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               6               108
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0     6
  2Q LOSS WILD-TYPE     4                         6   112
D42V7, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   6               112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1   5
  2Q LOSS WILD-TYPE  10 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    5
  2Q LOSS WILD-TYPE   10  106
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO               5               106
[1] 2 2
[1] FALSE

Clustering(43) Variable = 3P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    29   1
  3P LOSS WILD-TYPE 100   3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               30               103 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                 3 
$`3P LOSS MUTATED`
TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGE TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO 
       63.22        63.32        68.38        75.09       106.39       115.00 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       59.84        59.90        59.74        59.80        59.80        91.43 
TCGA-2G-AAKD TCGA-2G-AAKL TCGA-2G-AAL7 TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A9 
      122.50        95.67       131.21        17.23         3.52        36.79 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-XE-AANR TCGA-XE-AAO4 
       35.61        33.07         3.65         5.06         0.46        12.07 
TCGA-XY-A89B TCGA-YU-A90P TCGA-YU-A90Y TCGA-YU-A912 TCGA-ZM-AA06 TCGA-ZM-AA0H 
        8.32        57.90         0.56         5.29        39.35        46.88 

$`3P LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAGA 
       40.01        52.37        71.24        72.20        61.71        68.22 
TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM 
       72.85        79.76        67.96        92.09       108.16        59.64 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      120.62        59.28       124.57       128.94        61.45       170.33 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       80.94        60.16        60.26       125.69        61.84        98.53 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL5 
      176.15         6.08       212.65       161.72       229.22       184.41 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB 
       16.31         9.63        10.26        37.18        37.68        24.99 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       23.90        41.52         4.90        24.26         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ 
       28.14         6.87        18.38        40.01        34.22        65.98 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       53.03        93.93         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       41.69        50.96         0.43        12.92        20.12         6.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       54.35        31.92        21.96        58.88         7.96        40.96 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
        8.15        37.02        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0N 
       10.85 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.46              0.10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           131.21            229.22 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            58.82             36.99 
[1] "0.5 - 131.2 (58.8)" "0.1 - 229.2 (37.0)"
[1] "hr=" "1.6"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         8        6        3        1         0         0
  3P LOSS WILD-TYPE      11       19        8        4         6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P LOSS MUTATED           0         1          0          2          2
  3P LOSS WILD-TYPE         1         1          1          4          3
                   vv
clus                STAGE IS
  3P LOSS MUTATED          7
  3P LOSS WILD-TYPE       39
D43V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  8                11
  STAGE IA                 6                19
  STAGE IB                 3                 8
  STAGE II                 1                 4
  STAGE IIA                0                 6
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                1                 1
  STAGE IIIA               0                 1
  STAGE IIIB               2                 4
  STAGE IIIC               2                 3
  STAGE IS                 7                39
[1] 12  2
[1] 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
  3P LOSS MUTATED   15 13  2
  3P LOSS WILD-TYPE 60 38  4
D43V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              15                60
  T2              13                38
  T3               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  3P LOSS MUTATED   11     2
  3P LOSS WILD-TYPE 35    11
D43V5, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0                 11                35
  N1+N2               2                11
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   25  0
  3P LOSS WILD-TYPE 89  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     25    0
  3P LOSS WILD-TYPE   89    4
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              25                89
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       0                         3    27
  3P LOSS WILD-TYPE     4                         3    91
D43V7, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               3                 3
  WHITE                                  27                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    3 24
  3P LOSS WILD-TYPE  8 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3   24
  3P LOSS WILD-TYPE    8   87
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              24                87
[1] 2 2
[1] FALSE

Clustering(44) Variable = 3Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    22   0
  3Q LOSS WILD-TYPE 107   4
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               22               111 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                 4 
$`3Q LOSS MUTATED`
TCGA-2G-AAFJ TCGA-2G-AAG9 TCGA-2G-AAGE TCGA-2G-AAGJ TCGA-2G-AAGO TCGA-2G-AAH2 
       14.56        63.32        68.38        75.09       115.00        59.84 
TCGA-2G-AAH3 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAL7 
       59.90        59.74        59.80        59.80        91.43       131.21 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AC TCGA-WZ-A7V4 TCGA-XE-AAO4 
       17.23         3.52        36.79        35.61         5.06        12.07 
TCGA-XY-A89B TCGA-YU-A90P TCGA-YU-A912 TCGA-ZM-AA06 
        8.32        57.90         5.29        39.35 

$`3Q LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        36.99        14.14        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA 
       52.37        71.24        72.20        61.71        63.22        68.22 
TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM 
       72.85        79.76        67.96        92.09       108.16        59.64 
TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW 
      106.39       120.62        59.28       124.57       128.94        61.45 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH4 TCGA-2G-AAH8 
      170.33        80.94        60.16        60.26       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
       98.53       176.15         6.08       122.50       212.65       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
       95.67       229.22       184.41        70.59         2.73         0.13 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
        3.52         7.00         0.10         4.83        20.68        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X 
        9.14        13.58         1.38        16.31         9.63        10.26 
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.18        37.68        24.99        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
        4.90        24.26         3.65         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       53.03        93.93         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       41.69        50.96         0.43        12.92        20.12         6.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-A94I 
       54.35        31.92        21.96         0.56        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
       40.96         8.15        37.02        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       11.34        46.88        10.85 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             3.52              0.10 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           131.21            229.22 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            58.82             37.02 
[1] "3.5 - 131.2 (58.8)" "0.1 - 229.2 (37.0)"
[1] "hr="     "8.9e+07"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         7        6        1        0         0         0
  3Q LOSS WILD-TYPE      12       19       10        5         6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q LOSS MUTATED           0         0          0          1          1
  3Q LOSS WILD-TYPE         1         2          1          5          4
                   vv
clus                STAGE IS
  3Q LOSS MUTATED          6
  3Q LOSS WILD-TYPE       40
D44V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  7                12
  STAGE IA                 6                19
  STAGE IB                 1                10
  STAGE II                 0                 5
  STAGE IIA                0                 6
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               1                 5
  STAGE IIIC               1                 4
  STAGE IS                 6                40
[1] 12  2
[1] 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
  3Q LOSS MUTATED   15  7  0
  3Q LOSS WILD-TYPE 60 44  6
D44V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              15                60
  T2               7                44
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  3Q LOSS MUTATED   11     1
  3Q LOSS WILD-TYPE 35    12
D44V5, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0                 11                35
  N1+N2               1                12
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   19  0
  3Q LOSS WILD-TYPE 95  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     19    0
  3Q LOSS WILD-TYPE   95    4
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              19                95
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         2    19
  3Q LOSS WILD-TYPE     3                         4    99
D44V7, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               2                 4
  WHITE                                  19                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2 18
  3Q LOSS WILD-TYPE  9 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2   18
  3Q LOSS WILD-TYPE    9   93
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              18                93
[1] 2 2
[1] FALSE

Clustering(45) Variable = 4P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   79  4
  4P LOSS WILD-TYPE 50  0
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               83                50 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                 0 
$`4P LOSS MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFY 
      191.31        36.99        14.56        17.16         9.57        36.13 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       61.71        63.32        68.22        68.38        79.76        67.96 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGV 
       75.09       108.16        59.64       106.39       120.62       128.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKG 
       59.74        59.80        59.80       176.15         6.08       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-4K-AA1G TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SN-A6IS TCGA-SN-A84Y TCGA-SO-A8JP 
        3.52        20.68        18.15        16.31        17.23         3.52 
TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       36.79        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 
        4.90        24.26         3.65         5.06         0.16        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
        6.87        18.38        65.98         0.46        53.03        93.93 
TCGA-XE-AAOB TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       16.87        50.96         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA61 TCGA-ZM-AA05 
       57.90         0.56         5.29         7.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0N 
       39.35        17.39        16.41        11.34        10.85 

$`4P LOSS WILD-TYPE`
TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ 
       38.30        14.14        14.86        16.50        40.70        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAGC 
       40.01        52.37        71.24        72.20        63.22        72.85 
TCGA-2G-AAGI TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX 
       92.09       115.00        59.28       124.57        61.45       170.33 
TCGA-2G-AAGY TCGA-2G-AAHA TCGA-2G-AAHN TCGA-2G-AAKD TCGA-2X-A9D5 TCGA-2X-A9D6 
       80.94        98.53        91.43       122.50         2.73         0.13 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        7.00         0.10         4.83         9.14        13.58         1.38 
TCGA-SN-A84W TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-WZ-A8D5 TCGA-XE-A8H5 
        9.63        10.26        37.18        37.68         0.82        40.01 
TCGA-XE-AANI TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF 
       34.22        12.07         7.89         8.88        67.66        41.69 
TCGA-XE-AAOL TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-AA4L 
        0.43        54.35        31.92        21.96        58.88        40.96 
TCGA-ZM-AA0B TCGA-ZM-AA0H 
       27.55        46.88 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.16              0.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           229.22            170.33 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            37.02             37.99 
[1] "0.2 - 229.2 (37.0)" "0.1 - 170.3 (38.0)"
[1] "hr="     "3.8e+08"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED        14       13        6        5         5         1
  4P LOSS WILD-TYPE       5       12        5        0         1         0
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P LOSS MUTATED           1         0          1          3          4
  4P LOSS WILD-TYPE         0         2          0          3          1
                   vv
clus                STAGE IS
  4P LOSS MUTATED         27
  4P LOSS WILD-TYPE       19
D45V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 14                 5
  STAGE IA                13                12
  STAGE IB                 6                 5
  STAGE II                 5                 0
  STAGE IIA                5                 1
  STAGE IIB                1                 0
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIA               1                 0
  STAGE IIIB               3                 3
  STAGE IIIC               4                 1
  STAGE IS                27                19
[1] 12  2
[1] 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
  4P LOSS MUTATED   44 36  2
  4P LOSS WILD-TYPE 31 15  4
D45V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              44                31
  T2              36                15
  T3               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  4P LOSS MUTATED   27    10
  4P LOSS WILD-TYPE 19     3
D45V5, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0                 27                19
  N1+N2              10                 3
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   70  3
  4P LOSS WILD-TYPE 44  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     70    3
  4P LOSS WILD-TYPE   44    1
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              70                44
  1               3                 1
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       2                         4    75
  4P LOSS WILD-TYPE     2                         2    43
D45V7, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   2                 2
  BLACK OR AFRICAN AMERICAN               4                 2
  WHITE                                  75                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    6 71
  4P LOSS WILD-TYPE  5 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6   71
  4P LOSS WILD-TYPE    5   40
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                 5
  NOT HISPANIC OR LATINO              71                40
[1] 2 2
[1] FALSE

Clustering(46) Variable = 4Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   94  4
  4Q LOSS WILD-TYPE 35  0
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               98                35 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                 0 
$`4Q LOSS MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      191.31        36.99        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 
       16.50        36.13        40.01        72.20        61.71        63.32 
TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.22        68.38        79.76        67.96        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV 
       59.64       106.39       115.00       120.62        59.28       128.94 
TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
       61.45        60.16        60.26        59.84        59.90       125.69 
TCGA-2G-AAH8 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT 
       61.84        59.74        59.80        59.80       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AAAL TCGA-S6-A8JW 
      131.21        70.59         2.73         3.52         4.83        20.68 
TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y 
       18.15        13.58         1.38        16.31         9.63        17.23 
TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
        3.52        36.79        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       41.52         4.90        24.26         3.65         5.06         0.16 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ 
       28.14         6.87        18.38        40.01        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOJ 
        0.46        53.03        93.93        12.07        16.87        50.96 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Y 
        8.32        12.92        20.12         6.90        57.90         0.56 
TCGA-YU-A94I TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
        7.96         8.15        39.35        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0N 
       11.34        10.85 

$`4Q LOSS WILD-TYPE`
TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 
       38.30        14.14        40.70        36.89        52.37        71.24 
TCGA-2G-AAG8 TCGA-2G-AAGC TCGA-2G-AAGI TCGA-2G-AAGT TCGA-2G-AAGX TCGA-2G-AAGY 
       63.22        72.85        92.09       124.57       170.33        80.94 
TCGA-2G-AAHA TCGA-2G-AAHN TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JY 
       98.53        91.43         0.13         7.00         0.10         9.14 
TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-WZ-A8D5 TCGA-XE-AAO6 TCGA-XE-AAOC 
       10.26        37.18        37.68         0.82         7.89         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       67.66        41.69         0.43        54.35        31.92        21.96 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA0H 
        5.29        58.88        40.96        37.02        46.88 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.16              0.10 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           229.22            170.33 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            36.89             38.30 
[1] "0.2 - 229.2 (36.9)" "0.1 - 170.3 (38.3)"
[1] "hr="     "2.9e+08"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED        15       16        6        5         6         1
  4Q LOSS WILD-TYPE       4        9        5        0         0         0
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q LOSS MUTATED           0         1          1          5          3
  4Q LOSS WILD-TYPE         1         1          0          1          2
                   vv
clus                STAGE IS
  4Q LOSS MUTATED         35
  4Q LOSS WILD-TYPE       11
D46V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 15                 4
  STAGE IA                16                 9
  STAGE IB                 6                 5
  STAGE II                 5                 0
  STAGE IIA                6                 0
  STAGE IIB                1                 0
  STAGE IIC                0                 1
  STAGE III                1                 1
  STAGE IIIA               1                 0
  STAGE IIIB               5                 1
  STAGE IIIC               3                 2
  STAGE IS                35                11
[1] 12  2
[1] 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
  4Q LOSS MUTATED   54 41  2
  4Q LOSS WILD-TYPE 21 10  4
D46V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              54                21
  T2              41                10
  T3               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  4Q LOSS MUTATED   32    13
  4Q LOSS WILD-TYPE 14     0
D46V5, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0                 32                14
  N1+N2              13                 0
[1] 2 2
[1] FALSE
D46V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   86  3
  4Q LOSS WILD-TYPE 28  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     86    3
  4Q LOSS WILD-TYPE   28    1
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              86                28
  1               3                 1
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       2                         3    90
  4Q LOSS WILD-TYPE     2                         3    28
D46V7, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   2                 2
  BLACK OR AFRICAN AMERICAN               3                 3
  WHITE                                  90                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    9 84
  4Q LOSS WILD-TYPE  2 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9   84
  4Q LOSS WILD-TYPE    2   27
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   9                 2
  NOT HISPANIC OR LATINO              84                27
[1] 2 2
[1] FALSE

Clustering(47) Variable = 5P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED   89  3
  5P LOSS WILD-TYPE 40  1
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               92                41 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                 1 
$`5P LOSS MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG3 
      191.31        36.99        14.56        16.50        36.13        52.37 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       72.20        61.71        63.32        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGX 
       79.76        75.09       108.16       120.62       128.94       170.33 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC 
       80.94        60.16        59.84        59.90       125.69        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 
      212.65        95.67       229.22       184.41        70.59         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX TCGA-S6-A8JY 
        0.13         3.52         0.10         4.83        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SO-A8JP TCGA-VF-A8AB 
       13.58         1.38        16.31         9.63         3.52        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A7V4 
       35.61        33.07        23.90        41.52         4.90         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        0.16         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
       34.22        65.98        93.93        12.07         7.89        16.87 
TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       67.66        50.96         0.43         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L 
        6.90        57.90        54.35         5.29         7.96        40.96 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
        8.15        37.02        39.35        27.55        17.39        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

$`5P LOSS WILD-TYPE`
TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFV 
       38.30        14.14        17.16         9.57        14.86        40.70 
TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGG TCGA-2G-AAGI 
       36.89        40.01        71.24        63.22        67.96        92.09 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW 
       59.64       106.39       115.00        59.28       124.57        61.45 
TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAKH TCGA-2G-AAL7 TCGA-4K-AA1H 
       60.26        61.84        98.53       161.72       131.21         7.00 
TCGA-S6-A8JW TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA 
       20.68        10.26        17.23        37.18        36.79        37.68 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAOC TCGA-XE-AAOF 
       24.26         3.65         0.46        53.03         8.88        41.69 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-ZM-AA0E 
       31.92        21.96         0.56        58.88        16.41 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.10              0.46 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           229.22            161.72 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           37.005            38.300 
[1] "0.1 - 229.2 (37.0)" "0.5 - 161.7 (38.3)"
[1] "hr=" "1"  
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED        16       17        6        4         5         1
  5P LOSS WILD-TYPE       3        8        5        1         1         0
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P LOSS MUTATED           1         1          1          2          2
  5P LOSS WILD-TYPE         0         1          0          4          3
                   vv
clus                STAGE IS
  5P LOSS MUTATED         32
  5P LOSS WILD-TYPE       14
D47V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 16                 3
  STAGE IA                17                 8
  STAGE IB                 6                 5
  STAGE II                 4                 1
  STAGE IIA                5                 1
  STAGE IIB                1                 0
  STAGE IIC                1                 0
  STAGE III                1                 1
  STAGE IIIA               1                 0
  STAGE IIIB               2                 4
  STAGE IIIC               2                 3
  STAGE IS                32                14
[1] 12  2
[1] 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
  5P LOSS MUTATED   58 31  2
  5P LOSS WILD-TYPE 17 20  4
D47V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              58                17
  T2              31                20
  T3               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  5P LOSS MUTATED   30     8
  5P LOSS WILD-TYPE 16     5
D47V5, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0                 30                16
  N1+N2               8                 5
[1] 2 2
[1] FALSE
D47V6, binary
                   cls
clus                 0  1
  5P LOSS MUTATED   80  2
  5P LOSS WILD-TYPE 34  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     80    2
  5P LOSS WILD-TYPE   34    2
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              80                34
  1               2                 2
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       2                         5    82
  5P LOSS WILD-TYPE     2                         1    36
D47V7, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   2                 2
  BLACK OR AFRICAN AMERICAN               5                 1
  WHITE                                  82                36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    7 78
  5P LOSS WILD-TYPE  4 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      7   78
  5P LOSS WILD-TYPE    4   33
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                 4
  NOT HISPANIC OR LATINO              78                33
[1] 2 2
[1] FALSE

Clustering(48) Variable = 5Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   87  3
  5Q LOSS WILD-TYPE 42  1
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               90                43 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                 1 
$`5Q LOSS MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG3 
      191.31        36.99        14.56        16.50        36.13        52.37 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK 
       72.20        61.71        68.38        79.76        75.09       108.16 
TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 
      120.62       128.94       170.33        80.94        60.16        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       59.90       125.69        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      176.15         6.08       212.65        95.67       229.22       184.41 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL 
       70.59         2.73         0.13         3.52         0.10         4.83 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       18.15         9.14        13.58         1.38        16.31         9.63 
TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
        3.52        36.79        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       41.52         4.90         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AAO3 
        6.87        18.38        40.01        34.22        65.98        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL 
       12.07         7.89        16.87        67.66        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
        8.32        12.92        20.12         6.90        57.90        54.35 
TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
       21.96         5.29         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       39.35        27.55        17.39        11.34        46.88        10.85 

$`5Q LOSS WILD-TYPE`
TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFV 
       38.30        14.14        17.16         9.57        14.86        40.70 
TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       36.89        40.01        71.24        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       72.85        67.96        92.09        59.64       106.39       115.00 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA 
       59.28       124.57        61.45        60.26        61.84        98.53 
TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAL7 TCGA-4K-AA1H TCGA-S6-A8JW TCGA-SN-A84X 
      122.50       161.72       131.21         7.00        20.68        10.26 
TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-XE-AANR 
       17.23        37.18        37.68        24.26         3.65         0.46 
TCGA-XE-AANV TCGA-XE-AAOC TCGA-XE-AAOF TCGA-YU-A90S TCGA-YU-A90Y TCGA-YU-A94D 
       53.03         8.88        41.69        31.92         0.56        58.88 
TCGA-ZM-AA0E 
       16.41 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.10              0.46 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           229.22            161.72 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            35.87             41.69 
[1] "0.1 - 229.2 (35.9)" "0.5 - 161.7 (41.7)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED        16       19        6        4         4         1
  5Q LOSS WILD-TYPE       3        6        5        1         2         0
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q LOSS MUTATED           1         0          1          1          2
  5Q LOSS WILD-TYPE         0         2          0          5          3
                   vv
clus                STAGE IS
  5Q LOSS MUTATED         31
  5Q LOSS WILD-TYPE       15
D48V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 16                 3
  STAGE IA                19                 6
  STAGE IB                 6                 5
  STAGE II                 4                 1
  STAGE IIA                4                 2
  STAGE IIB                1                 0
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIA               1                 0
  STAGE IIIB               1                 5
  STAGE IIIC               2                 3
  STAGE IS                31                15
[1] 12  2
[1] 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
  5Q LOSS MUTATED   58 29  2
  5Q LOSS WILD-TYPE 17 22  4
D48V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              58                17
  T2              29                22
  T3               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  5Q LOSS MUTATED   30     6
  5Q LOSS WILD-TYPE 16     7
D48V5, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0                 30                16
  N1+N2               6                 7
[1] 2 2
[1] FALSE
D48V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   77  2
  5Q LOSS WILD-TYPE 37  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     77    2
  5Q LOSS WILD-TYPE   37    2
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              77                37
  1               2                 2
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       2                         5    80
  5Q LOSS WILD-TYPE     2                         1    38
D48V7, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   2                 2
  BLACK OR AFRICAN AMERICAN               5                 1
  WHITE                                  80                38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    7 75
  5Q LOSS WILD-TYPE  4 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7   75
  5Q LOSS WILD-TYPE    4   36
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                 4
  NOT HISPANIC OR LATINO              75                36
[1] 2 2
[1] FALSE

Clustering(49) Variable = 6P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    11   0
  6P LOSS WILD-TYPE 118   4
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               11               122 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                0                 4 
$`6P LOSS MUTATED`
TCGA-2G-AAGE TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAHG TCGA-4K-AA1G TCGA-SB-A6J6 
       68.38       108.16        59.64        59.80         3.52        13.58 
TCGA-W4-A7U4 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-YU-A90P TCGA-YU-AA4L 
       24.26        28.14         6.87        57.90        40.96 

$`6P LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       40.01        52.37        71.24        72.20        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       63.32        68.22        72.85        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       75.09       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
        2.73         0.13         7.00         0.10         4.83        20.68 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X 
       18.15         9.14         1.38        16.31         9.63        10.26 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
       17.23         3.52        37.18        36.79        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A7V3 
       35.61        33.07        23.90        41.52         4.90         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        5.06         0.16         0.82        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
       16.87         8.88        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S 
        8.32        12.92        20.12         6.90        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA61 
       21.96         0.56         5.29        58.88         7.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             3.52              0.10 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           108.16            229.22 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            40.96             37.43 
[1] "3.5 - 108.2 (41.0)" "0.1 - 229.2 (37.4)"
[1] "hr="     "7.6e+07"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED         1        2        0        0         0         0
  6P LOSS WILD-TYPE      18       23       11        5         6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P LOSS MUTATED           0         0          0          0          1
  6P LOSS WILD-TYPE         1         2          1          6          4
                   vv
clus                STAGE IS
  6P LOSS MUTATED          6
  6P LOSS WILD-TYPE       40
D49V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  1                18
  STAGE IA                 2                23
  STAGE IB                 0                11
  STAGE II                 0                 5
  STAGE IIA                0                 6
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               1                 4
  STAGE IS                 6                40
[1] 12  2
[1] 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
  6P LOSS MUTATED    6  5  0
  6P LOSS WILD-TYPE 69 46  6
D49V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               6                69
  T2               5                46
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  6P LOSS MUTATED    6     0
  6P LOSS WILD-TYPE 40    13
D49V5, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0                  6                40
  N1+N2               0                13
[1] 2 2
[1] FALSE
D49V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     9   0
  6P LOSS WILD-TYPE 105   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9    0
  6P LOSS WILD-TYPE  105    4
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0               9               105
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       0                         1    10
  6P LOSS WILD-TYPE     4                         5   108
D49V7, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  10               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1   8
  6P LOSS WILD-TYPE  10 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1    8
  6P LOSS WILD-TYPE   10  103
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO               8               103
[1] 2 2
[1] FALSE

Clustering(50) Variable = 6Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    14   0
  6Q LOSS WILD-TYPE 115   4
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14               119 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                0                 4 
$`6Q LOSS MUTATED`
TCGA-2G-AAGE TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGZ TCGA-2G-AAHG TCGA-2G-AAKL 
       68.38       108.16        59.64        60.16        59.80        95.67 
TCGA-4K-AA1G TCGA-SB-A6J6 TCGA-W4-A7U4 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-YU-A90P 
        3.52        13.58        24.26        28.14         6.87        57.90 
TCGA-YU-A94I TCGA-YU-AA4L 
        7.96        40.96 

$`6Q LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       40.01        52.37        71.24        72.20        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       63.32        68.22        72.85        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       75.09       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 
      128.94        61.45       170.33        80.94        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
       91.43       176.15         6.08       122.50       212.65       161.72 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      229.22       184.41       131.21        70.59         2.73         0.13 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
        7.00         0.10         4.83        20.68        18.15         9.14 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23         3.52 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       37.18        36.79        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       23.90        41.52         4.90         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        0.82        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
       20.12         6.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        5.29        58.88         8.15        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             3.52              0.10 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           108.16            229.22 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            49.43             37.18 
[1] "3.5 - 108.2 (49.4)" "0.1 - 229.2 (37.2)"
[1] "hr="     "7.9e+07"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         1        3        0        1         0         0
  6Q LOSS WILD-TYPE      18       22       11        4         6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q LOSS MUTATED           0         0          1          0          1
  6Q LOSS WILD-TYPE         1         2          0          6          4
                   vv
clus                STAGE IS
  6Q LOSS MUTATED          6
  6Q LOSS WILD-TYPE       40
D50V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  1                18
  STAGE IA                 3                22
  STAGE IB                 0                11
  STAGE II                 1                 4
  STAGE IIA                0                 6
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               1                 0
  STAGE IIIB               0                 6
  STAGE IIIC               1                 4
  STAGE IS                 6                40
[1] 12  2
[1] 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
  6Q LOSS MUTATED    7  7  0
  6Q LOSS WILD-TYPE 68 44  6
D50V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               7                68
  T2               7                44
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  6Q LOSS MUTATED    6     1
  6Q LOSS WILD-TYPE 40    12
D50V5, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0                  6                40
  N1+N2               1                12
[1] 2 2
[1] FALSE
D50V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    10   1
  6Q LOSS WILD-TYPE 104   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     10    1
  6Q LOSS WILD-TYPE  104    3
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              10               104
  1               1                 3
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       0                         1    12
  6Q LOSS WILD-TYPE     4                         5   106
D50V7, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  12               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1  10
  6Q LOSS WILD-TYPE  10 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1   10
  6Q LOSS WILD-TYPE   10  101
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              10               101
[1] 2 2
[1] FALSE

Clustering(51) Variable = 8P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    10   0
  8P LOSS WILD-TYPE 119   4
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10               123 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                 4 
$`8P LOSS MUTATED`
TCGA-2G-AAFN TCGA-2G-AAGG TCGA-2G-AAGT TCGA-2G-AAKH TCGA-2G-AAL5 TCGA-2G-AALP 
       14.86        67.96       124.57       161.72       184.41        70.59 
TCGA-VF-A8AD TCGA-WZ-A7V5 TCGA-YU-A94I TCGA-YU-AA4L 
       33.07         0.16         7.96        40.96 

$`8P LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
        9.57        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGI TCGA-2G-AAGJ 
       68.22        72.85        68.38        79.76        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2X-A9D5 TCGA-2X-A9D6 
      212.65        95.67       229.22       131.21         2.73         0.13 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
        3.52         7.00         0.10         4.83        20.68        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X 
        9.14        13.58         1.38        16.31         9.63        10.26 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
       17.23         3.52        37.18        36.79        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 
       35.61        23.90        41.52         4.90        24.26         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        5.06         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
        7.89        16.87         8.88        67.66        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
        0.43         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       54.35        31.92        21.96         0.56         5.29        58.88 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
        8.15        37.02        39.35        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       11.34        46.88        10.85 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.16              0.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           184.41            229.22 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            54.46             37.18 
[1] "0.2 - 184.4 (54.5)" "0.1 - 229.2 (37.2)"
[1] "hr="     "7.4e+07"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         2        1        1        1         0         0
  8P LOSS WILD-TYPE      17       24       10        4         6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P LOSS MUTATED           0         0          0          2          2
  8P LOSS WILD-TYPE         1         2          1          4          3
                   vv
clus                STAGE IS
  8P LOSS MUTATED          1
  8P LOSS WILD-TYPE       45
D51V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  2                17
  STAGE IA                 1                24
  STAGE IB                 1                10
  STAGE II                 1                 4
  STAGE IIA                0                 6
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               2                 4
  STAGE IIIC               2                 3
  STAGE IS                 1                45
[1] 12  2
[1] 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
  8P LOSS MUTATED    5  4  1
  8P LOSS WILD-TYPE 70 47  5
D51V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               5                70
  T2               4                47
  T3               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  8P LOSS MUTATED    1     2
  8P LOSS WILD-TYPE 45    11
D51V5, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0                  1                45
  N1+N2               2                11
[1] 2 2
[1] FALSE
D51V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     5   2
  8P LOSS WILD-TYPE 109   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5    2
  8P LOSS WILD-TYPE  109    2
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               5               109
  1               2                 2
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       0                         1     8
  8P LOSS WILD-TYPE     4                         5   110
D51V7, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   8               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     0   8
  8P LOSS WILD-TYPE  11 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0    8
  8P LOSS WILD-TYPE   11  103
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO               8               103
[1] 2 2
[1] FALSE

Clustering(52) Variable = 8Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     4   0
  8Q LOSS WILD-TYPE 125   4
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               129 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                 4 
$`8Q LOSS MUTATED`
TCGA-2G-AAGG TCGA-2G-AAL5 TCGA-YU-A94I TCGA-YU-AA4L 
       67.96       184.41         7.96        40.96 

$`8Q LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       40.01        52.37        71.24        72.20        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGI 
       63.32        68.22        72.85        68.38        79.76        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
        6.08       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23         3.52 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       37.18        36.79        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       23.90        41.52         4.90        24.26         3.65         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        0.16         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
        7.89        16.87         8.88        67.66        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
        0.43         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       54.35        31.92        21.96         0.56         5.29        58.88 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
        8.15        37.02        39.35        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       11.34        46.88        10.85 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             7.96              0.10 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           184.41            229.22 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            54.46             37.18 
[1] "8.0 - 184.4 (54.5)" "0.1 - 229.2 (37.2)"
[1] "hr="     "2.5e+07"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         1        1        0        0         0         0
  8Q LOSS WILD-TYPE      18       24       11        5         6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q LOSS MUTATED           0         0          0          0          2
  8Q LOSS WILD-TYPE         1         2          1          6          3
                   vv
clus                STAGE IS
  8Q LOSS MUTATED          0
  8Q LOSS WILD-TYPE       46
D52V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  1                18
  STAGE IA                 1                24
  STAGE IB                 0                11
  STAGE II                 0                 5
  STAGE IIA                0                 6
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               2                 3
  STAGE IS                 0                46
[1] 12  2
[1] 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
  8Q LOSS MUTATED    3  0  1
  8Q LOSS WILD-TYPE 72 51  5
D52V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               3                72
  T2               0                51
  T3               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  8Q LOSS MUTATED    1     1
  8Q LOSS WILD-TYPE 45    12
D52V5, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                57 
       TCGA-2G-AAEW        TCGA-2G-AAEX        TCGA-2G-AAF1        TCGA-2G-AAF4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2G-AAF6        TCGA-2G-AAF8        TCGA-2G-AAFE        TCGA-2G-AAFG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2G-AAFH        TCGA-2G-AAFI        TCGA-2G-AAFJ        TCGA-2G-AAFL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2G-AAFM        TCGA-2G-AAFN        TCGA-2G-AAFO        TCGA-2G-AAFV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2G-AAFY        TCGA-2G-AAG0        TCGA-2G-AAG5        TCGA-2G-AAG6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2G-AAG7        TCGA-2G-AAG8        TCGA-2G-AAG9        TCGA-2G-AAGA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2G-AAGC        TCGA-2G-AAGE        TCGA-2G-AAGF        TCGA-2G-AAGI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2G-AAGJ        TCGA-2G-AAGK        TCGA-2G-AAGM        TCGA-2G-AAGN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2G-AAGO        TCGA-2G-AAGP        TCGA-2G-AAGS        TCGA-2G-AAGW 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2G-AAGX        TCGA-2G-AAGY        TCGA-2G-AAGZ        TCGA-2G-AAH2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2G-AAHG        TCGA-2G-AAHL        TCGA-2G-AAHN        TCGA-2G-AAHP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2G-AAHT        TCGA-2G-AAKG        TCGA-2G-AAL7        TCGA-4K-AA1G 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-4K-AA1H        TCGA-4K-AA1I        TCGA-4K-AAAL        TCGA-SO-A8JP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-VF-A8A8        TCGA-VF-A8A9        TCGA-VF-A8AA        TCGA-VF-A8AB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-X3-A8G4 
"8Q LOSS WILD-TYPE" 
D52V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1   1
  8Q LOSS WILD-TYPE 113   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    1
  8Q LOSS WILD-TYPE  113    3
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               1               113
  1               1                 3
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         1     2
  8Q LOSS WILD-TYPE     4                         5   116
D52V7, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   2               116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0   2
  8Q LOSS WILD-TYPE  11 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    2
  8Q LOSS WILD-TYPE   11  109
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO               2               109
[1] 2 2
[1] FALSE

Clustering(53) Variable = 9P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   53  2
  9P LOSS WILD-TYPE 76  2
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               55                78 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                2                 2 
$`9P LOSS MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFJ 
       20.32       102.35       122.40       154.59       191.31        14.56 
TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE 
       40.01        72.20        61.71        63.32        72.85        68.38 
TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       67.96       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAHG TCGA-2G-AAHT 
       59.28       128.94        80.94        60.16        59.80         6.08 
TCGA-2G-AAKG TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-4K-AA1I 
      212.65       229.22       184.41       131.21        70.59         0.10 
TCGA-4K-AAAL TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A84W TCGA-SO-A8JP TCGA-VF-A8AB 
        4.83         9.14        13.58         9.63         3.52        24.99 
TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       41.52        24.26         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90P 
       18.38        40.01        41.69         0.43         6.90        57.90 
TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0E 
        5.29         7.96        40.96        39.35        27.55        16.41 
TCGA-ZM-AA0H 
       46.88 

$`9P LOSS WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL 
       30.35        38.30        59.70        36.99        14.14        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGF TCGA-2G-AAGI 
       52.37        71.24        63.22        68.22        79.76        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAH0 TCGA-2G-AAH2 
       75.09       124.57        61.45       170.33        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2X-A9D5 
       91.43       176.15       122.50       161.72        95.67         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A76C 
        0.13         3.52         7.00        20.68        18.15         1.38 
TCGA-SN-A6IS TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA 
       16.31        10.26        17.23        37.18        36.79        37.68 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       35.61        33.07        23.90         4.90         3.65         5.06 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XY-A89B 
        7.89        16.87         8.88        67.66        50.96         8.32 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
       12.92        20.12        54.35        31.92        21.96         0.56 
TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0N 
       58.88         8.15        37.02        17.39        11.34        10.85 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.10              0.13 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           229.22            176.15 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            41.69             36.46 
[1] "0.1 - 229.2 (41.7)" "0.1 - 176.2 (36.5)"
[1] "hr=" "1.5"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED         7       10        1        2         2         0
  9P LOSS WILD-TYPE      12       15       10        3         4         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P LOSS MUTATED           0         0          1          4          3
  9P LOSS WILD-TYPE         1         2          0          2          2
                   vv
clus                STAGE IS
  9P LOSS MUTATED         22
  9P LOSS WILD-TYPE       24
D53V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  7                12
  STAGE IA                10                15
  STAGE IB                 1                10
  STAGE II                 2                 3
  STAGE IIA                2                 4
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               1                 0
  STAGE IIIB               4                 2
  STAGE IIIC               3                 2
  STAGE IS                22                24
[1] 12  2
[1] 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
  9P LOSS MUTATED   33 18  3
  9P LOSS WILD-TYPE 42 33  3
D53V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              33                42
  T2              18                33
  T3               3                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  9P LOSS MUTATED   24     7
  9P LOSS WILD-TYPE 22     6
D53V5, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0                 24                22
  N1+N2               7                 6
[1] 2 2
[1] FALSE
D53V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   46  3
  9P LOSS WILD-TYPE 68  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     46    3
  9P LOSS WILD-TYPE   68    1
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              46                68
  1               3                 1
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       2                         4    47
  9P LOSS WILD-TYPE     2                         2    71
D53V7, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   2                 2
  BLACK OR AFRICAN AMERICAN               4                 2
  WHITE                                  47                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V8, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    3 48
  9P LOSS WILD-TYPE  8 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      3   48
  9P LOSS WILD-TYPE    8   63
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              48                63
[1] 2 2
[1] FALSE

Clustering(54) Variable = 9Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   48  2
  9Q LOSS WILD-TYPE 81  2
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               50                83 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                 2 
$`9Q LOSS MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAG0 TCGA-2G-AAG6 
       20.32       102.35       122.40       154.59        40.01        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGM 
       61.71        63.32        72.85        79.76        67.96        59.64 
TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY 
      106.39       120.62        59.28       128.94       170.33        80.94 
TCGA-2G-AAHG TCGA-2G-AAHT TCGA-2G-AAKG TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
       59.80         6.08       212.65       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A84W 
       70.59         0.10         4.83         9.14        13.58         9.63 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AB TCGA-W4-A7U4 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       17.23         3.52        24.99        24.26         5.06         0.16 
TCGA-X3-A8G4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A8S2 
       28.14        40.01        34.22        41.69         0.43        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A912 TCGA-YU-A94I TCGA-ZM-AA06 
       20.12         6.90        57.90         5.29         7.96        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0H 
       27.55        46.88 

$`9Q LOSS WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       30.35        38.30        59.70       191.31        36.99        14.14 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       14.56        17.16         9.57        14.86        16.50        40.70 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGA 
       36.13        36.89        52.37        71.24        63.22        68.22 
TCGA-2G-AAGE TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGO TCGA-2G-AAGT 
       68.38        92.09        75.09       108.16       115.00       124.57 
TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
       61.45        60.16        60.26        59.84        59.90       125.69 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       61.84        98.53        59.74        59.80        91.43       176.15 
TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      122.50       161.72        95.67         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X 
        7.00        20.68        18.15         1.38        16.31        10.26 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       37.18        36.79        37.68        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-A8H4 
       41.52         4.90         3.65         0.82         6.87        18.38 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XY-A89B TCGA-YU-A90Q 
       16.87         8.88        67.66        50.96         8.32        54.35 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 
       31.92        21.96         0.56        58.88        40.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0N 
       37.02        17.39        16.41        11.34        10.85 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.10              0.13 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           229.22            191.31 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            40.85             36.99 
[1] "0.1 - 229.2 (40.8)" "0.1 - 191.3 (37.0)"
[1] "hr=" "1.2"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         8        9        1        2         2         0
  9Q LOSS WILD-TYPE      11       16       10        3         4         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q LOSS MUTATED           0         0          0          4          2
  9Q LOSS WILD-TYPE         1         2          1          2          3
                   vv
clus                STAGE IS
  9Q LOSS MUTATED         21
  9Q LOSS WILD-TYPE       25
D54V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  8                11
  STAGE IA                 9                16
  STAGE IB                 1                10
  STAGE II                 2                 3
  STAGE IIA                2                 4
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               4                 2
  STAGE IIIC               2                 3
  STAGE IS                21                25
[1] 12  2
[1] 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
  9Q LOSS MUTATED   30 18  2
  9Q LOSS WILD-TYPE 45 33  4
D54V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              30                45
  T2              18                33
  T3               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  9Q LOSS MUTATED   21     6
  9Q LOSS WILD-TYPE 25     7
D54V5, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0                 21                25
  N1+N2               6                 7
[1] 2 2
[1] FALSE
D54V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   43  2
  9Q LOSS WILD-TYPE 71  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     43    2
  9Q LOSS WILD-TYPE   71    2
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              43                71
  1               2                 2
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       1                         3    44
  9Q LOSS WILD-TYPE     3                         3    74
D54V7, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               3                 3
  WHITE                                  44                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    3 44
  9Q LOSS WILD-TYPE  8 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3   44
  9Q LOSS WILD-TYPE    8   67
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              44                67
[1] 2 2
[1] FALSE

Clustering(55) Variable = 10P LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   64  3
  10P LOSS WILD-TYPE 65  1
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                67                 66 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                  1 
$`10P LOSS MUTATED`
TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
      102.35       154.59         9.57        14.86        16.50        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGC 
       40.01        72.20        61.71        63.22        63.32        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGP 
       68.38        79.76        67.96       108.16       106.39       120.62 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH3 TCGA-2G-AAH4 
      128.94        61.45        80.94        60.16        59.90       125.69 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
       59.74        59.80       176.15       122.50       212.65       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
       95.67       229.22       184.41       131.21        70.59         2.73 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C 
        3.52         7.00        20.68        18.15        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AC TCGA-W4-A7U2 
       16.31         9.63        17.23         3.52        35.61        41.52 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-A8H1 
        4.90        24.26         5.06         0.16        28.14         6.87 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XY-A8S2 TCGA-XY-A8S3 
       34.22        65.98        16.87        41.69        12.92        20.12 
TCGA-YU-A90P TCGA-YU-A90Y TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       57.90         0.56         8.15        39.35        27.55        17.39 
TCGA-ZM-AA0F 
       11.34 

$`10P LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        30.35        38.30        59.70       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAFZ 
       36.99        14.14        14.56        17.16        40.70        36.89 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAGA TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM 
       52.37        71.24        68.22        92.09        75.09        59.64 
TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGX TCGA-2G-AAH0 TCGA-2G-AAH2 
      115.00        59.28       124.57       170.33        60.26        59.84 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2X-A9D6 
       61.84        98.53        59.80        91.43         6.08         0.13 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JY TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8A9 
        0.10         4.83         9.14        10.26        37.18        36.79 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AD TCGA-VF-A8AE TCGA-WZ-A7V3 TCGA-WZ-A8D5 
       37.68        24.99        33.07        23.90         3.65         0.82 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       18.38        40.01         0.46        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        7.89         8.88        67.66        50.96         0.43         8.32 
TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D 
        6.90        54.35        31.92        21.96         5.29        58.88 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA0E TCGA-ZM-AA0H TCGA-ZM-AA0N 
        7.96        40.96        37.02        16.41        46.88        10.85 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.16               0.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            229.22             191.31 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            41.520             37.005 
[1] "0.2 - 229.2 (41.5)" "0.1 - 191.3 (37.0)"
[1] "hr=" "1.9"
D55V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         9        8        3        5         5         0
  10P LOSS WILD-TYPE      10       17        8        0         1         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  10P LOSS MUTATED           0         1          1          4          2
  10P LOSS WILD-TYPE         1         1          0          2          3
                    vv
clus                 STAGE IS
  10P LOSS MUTATED         25
  10P LOSS WILD-TYPE       21
D55V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   9                 10
  STAGE IA                  8                 17
  STAGE IB                  3                  8
  STAGE II                  5                  0
  STAGE IIA                 5                  1
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIA                1                  0
  STAGE IIIB                4                  2
  STAGE IIIC                2                  3
  STAGE IS                 25                 21
[1] 12  2
[1] 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
  10P LOSS MUTATED   35 30  2
  10P LOSS WILD-TYPE 40 21  4
D55V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               35                 40
  T2               30                 21
  T3                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  10P LOSS MUTATED   20    10
  10P LOSS WILD-TYPE 26     3
D55V5, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                  20                 26
  N1+N2               10                  3
[1] 2 2
[1] FALSE
D55V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   57  3
  10P LOSS WILD-TYPE 57  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     57    3
  10P LOSS WILD-TYPE   57    1
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               57                 57
  1                3                  1
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       1                         1    65
  10P LOSS WILD-TYPE     3                         5    53
D55V7, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   65                 53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V8, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    5 58
  10P LOSS WILD-TYPE  6 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      5   58
  10P LOSS WILD-TYPE    6   53
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  6
  NOT HISPANIC OR LATINO               58                 53
[1] 2 2
[1] FALSE

Clustering(56) Variable = 10Q LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   60  3
  10Q LOSS WILD-TYPE 69  1
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                63                 70 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 3                  1 
$`10Q LOSS MUTATED`
TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
      102.35       154.59         9.57        14.86        16.50        36.13 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE 
       72.20        61.71        63.22        63.32        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGV 
       79.76        67.96       108.16       106.39       120.62       128.94 
TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
       61.45        80.94        60.16        59.84        59.90       125.69 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
       59.74        59.80       176.15       122.50       212.65       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G 
       95.67       229.22       131.21        70.59         2.73         3.52 
TCGA-4K-AA1H TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SN-A84W TCGA-SN-A84Y TCGA-SO-A8JP 
        7.00        20.68        18.15         9.63        17.23         3.52 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V4 
       35.61        33.07        41.52         4.90        24.26         5.06 
TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A8S2 
        0.16        28.14        16.87        41.69         0.43        12.92 
TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-AA61 TCGA-ZM-AA06 
       20.12        57.90         0.56         5.29         8.15        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       27.55        17.39        11.34 

$`10Q LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        30.35        38.30        59.70       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAFZ 
       36.99        14.14        14.56        17.16        40.70        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAGA TCGA-2G-AAGI TCGA-2G-AAGJ 
       40.01        52.37        71.24        68.22        92.09        75.09 
TCGA-2G-AAGM TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGX TCGA-2G-AAH0 
       59.64       115.00        59.28       124.57       170.33        60.26 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAL5 
       61.84        98.53        59.80        91.43         6.08       184.41 
TCGA-2X-A9D6 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        0.13         0.10         4.83         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
       16.31        10.26        37.18        36.79        37.68        24.99 
TCGA-VF-A8AE TCGA-WZ-A7V3 TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
       23.90         3.65         0.82         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A9T9 
        7.89         8.88        67.66        50.96         8.32         6.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       54.35        31.92        21.96        58.88         7.96        40.96 
TCGA-ZM-AA05 TCGA-ZM-AA0E TCGA-ZM-AA0H TCGA-ZM-AA0N 
       37.02        16.41        46.88        10.85 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.16               0.10 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            229.22             191.31 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            41.690             37.005 
[1] "0.2 - 229.2 (41.7)" "0.1 - 191.3 (37.0)"
[1] "hr=" "2.1"
D56V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED         9        7        4        5         5         0
  10Q LOSS WILD-TYPE      10       18        7        0         1         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  10Q LOSS MUTATED           0         1          1          4          3
  10Q LOSS WILD-TYPE         1         1          0          2          2
                    vv
clus                 STAGE IS
  10Q LOSS MUTATED         21
  10Q LOSS WILD-TYPE       25
D56V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   9                 10
  STAGE IA                  7                 18
  STAGE IB                  4                  7
  STAGE II                  5                  0
  STAGE IIA                 5                  1
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIA                1                  0
  STAGE IIIB                4                  2
  STAGE IIIC                3                  2
  STAGE IS                 21                 25
[1] 12  2
[1] 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
  10Q LOSS MUTATED   33 28  2
  10Q LOSS WILD-TYPE 42 23  4
D56V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               33                 42
  T2               28                 23
  T3                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  10Q LOSS MUTATED   19    10
  10Q LOSS WILD-TYPE 27     3
D56V5, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                  19                 27
  N1+N2               10                  3
[1] 2 2
[1] FALSE
D56V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   52  3
  10Q LOSS WILD-TYPE 62  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     52    3
  10Q LOSS WILD-TYPE   62    1
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               52                 62
  1                3                  1
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       1                         3    59
  10Q LOSS WILD-TYPE     3                         3    59
D56V7, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                3                  3
  WHITE                                   59                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V8, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    2 56
  10Q LOSS WILD-TYPE  9 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2   56
  10Q LOSS WILD-TYPE    9   55
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               56                 55
[1] 2 2
[1] FALSE

Clustering(57) Variable = 11P LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   85  3
  11P LOSS WILD-TYPE 44  1
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                88                 45 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                  1 
$`11P LOSS MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAFG 
       20.32        59.70       102.35       122.40       154.59       191.31 
TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
       36.99        14.56         9.57        14.86        16.50        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE 
       40.01        72.20        61.71        63.32        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS 
       79.76        67.96       108.16       106.39       115.00        59.28 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 
      128.94        61.45       170.33        80.94        60.16        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       59.90       125.69        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKM TCGA-2G-AAL7 
      176.15         6.08       122.50       212.65       229.22       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW TCGA-S6-A8JX 
       70.59         2.73         3.52         7.00        20.68        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y 
        9.14        13.58         1.38        16.31         9.63        17.23 
TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 
       36.79        24.99        35.61        41.52        24.26         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ 
        5.06         0.16         6.87        18.38        40.01        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOD 
        0.46        53.03        93.93        12.07         7.89        67.66 
TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A9T9 TCGA-YU-A90P 
       41.69         0.43         8.32        12.92         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90Y TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0D 
       54.35         0.56         5.29        37.02        39.35        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

$`11P LOSS WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAFZ 
       30.35        38.30        14.14        17.16        40.70        36.89 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGI TCGA-2G-AAGJ 
       52.37        71.24        63.22        68.22        92.09        75.09 
TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA 
       59.64       120.62       124.57        60.26        61.84        98.53 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAL5 TCGA-2X-A9D6 TCGA-4K-AA1I TCGA-4K-AAAL 
      161.72        95.67       184.41         0.13         0.10         4.83 
TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AD TCGA-VF-A8AE 
       10.26         3.52        37.18        37.68        33.07        23.90 
TCGA-W4-A7U3 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-AANI TCGA-XE-AAOB TCGA-XE-AAOC 
        4.90         0.82        28.14        34.22        16.87         8.88 
TCGA-XE-AAOJ TCGA-XY-A8S3 TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-A94I 
       50.96        20.12        31.92        21.96        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA0B 
       40.96         8.15        27.55 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.16               0.10 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            229.22             184.41 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             40.01              36.89 
[1] "0.2 - 229.2 (40.0)" "0.1 - 184.4 (36.9)"
[1] "hr=" "1.1"
D57V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED        15       16        6        3         4         1
  11P LOSS WILD-TYPE       4        9        5        2         2         0
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  11P LOSS MUTATED           1         1          1          5          3
  11P LOSS WILD-TYPE         0         1          0          1          2
                    vv
clus                 STAGE IS
  11P LOSS MUTATED         29
  11P LOSS WILD-TYPE       17
D57V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  15                  4
  STAGE IA                 16                  9
  STAGE IB                  6                  5
  STAGE II                  3                  2
  STAGE IIA                 4                  2
  STAGE IIB                 1                  0
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIA                1                  0
  STAGE IIIB                5                  1
  STAGE IIIC                3                  2
  STAGE IS                 29                 17
[1] 12  2
[1] 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
  11P LOSS MUTATED   48 36  3
  11P LOSS WILD-TYPE 27 15  3
D57V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               48                 27
  T2               36                 15
  T3                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  11P LOSS MUTATED   29    11
  11P LOSS WILD-TYPE 17     2
D57V5, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                  29                 17
  N1+N2               11                  2
[1] 2 2
[1] FALSE
D57V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   77  3
  11P LOSS WILD-TYPE 37  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     77    3
  11P LOSS WILD-TYPE   37    1
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               77                 37
  1                3                  1
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       3                         4    78
  11P LOSS WILD-TYPE     1                         2    40
D57V7, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    3                  1
  BLACK OR AFRICAN AMERICAN                4                  2
  WHITE                                   78                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    8 76
  11P LOSS WILD-TYPE  3 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      8   76
  11P LOSS WILD-TYPE    3   35
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                  3
  NOT HISPANIC OR LATINO               76                 35
[1] 2 2
[1] FALSE

Clustering(58) Variable = 11Q LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED   100   4
  11Q LOSS WILD-TYPE  29   0
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               104                 29 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                  0 
$`11Q LOSS MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      191.31        36.99        14.56         9.57        14.86        16.50 
TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       36.13        40.01        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGK 
       68.22        72.85        68.38        79.76        67.96       108.16 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW 
      106.39       115.00       120.62        59.28       128.94        61.45 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
      170.33        80.94        60.16        60.26        59.84        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
      125.69        61.84        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKM TCGA-2G-AAL7 
      176.15         6.08       122.50       212.65       229.22       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AAAL TCGA-S6-A8JW 
       70.59         2.73         3.52         7.00         4.83        20.68 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       18.15         9.14        13.58         1.38        16.31         9.63 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 
       17.23         3.52        36.79        35.61        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD 
       53.03        93.93        12.07         7.89        16.87        67.66 
TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       41.69         0.43         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-AA61 
       57.90        54.35        21.96         0.56         5.29         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

$`11Q LOSS WILD-TYPE`
TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 
       38.30        14.14        17.16        40.70        36.89        52.37 
TCGA-2G-AAG5 TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAHA 
       71.24        92.09        75.09        59.64       124.57        98.53 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAL5 TCGA-2X-A9D6 TCGA-4K-AA1I TCGA-SN-A84X 
      161.72        95.67       184.41         0.13         0.10        10.26 
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AD TCGA-W4-A7U3 TCGA-XE-AAOC 
       37.18        37.68        24.99        33.07         4.90         8.88 
TCGA-XE-AAOJ TCGA-YU-A90S TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       50.96        31.92        58.88         7.96        40.96 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.16               0.10 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            229.22             184.41 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            37.005             38.300 
[1] "0.2 - 229.2 (37.0)" "0.1 - 184.4 (38.3)"
[1] "hr="     "2.7e+08"
D58V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED        16       18        7        3         6         1
  11Q LOSS WILD-TYPE       3        7        4        2         0         0
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  11Q LOSS MUTATED           1         1          1          5          4
  11Q LOSS WILD-TYPE         0         1          0          1          1
                    vv
clus                 STAGE IS
  11Q LOSS MUTATED         37
  11Q LOSS WILD-TYPE        9
D58V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  16                  3
  STAGE IA                 18                  7
  STAGE IB                  7                  4
  STAGE II                  3                  2
  STAGE IIA                 6                  0
  STAGE IIB                 1                  0
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIA                1                  0
  STAGE IIIB                5                  1
  STAGE IIIC                4                  1
  STAGE IS                 37                  9
[1] 12  2
[1] 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
  11Q LOSS MUTATED   57 42  4
  11Q LOSS WILD-TYPE 18  9  2
D58V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               57                 18
  T2               42                  9
  T3                4                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  11Q LOSS MUTATED   33    13
  11Q LOSS WILD-TYPE 13     0
D58V5, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                  33                 13
  N1+N2               13                  0
[1] 2 2
[1] FALSE
D58V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   91  3
  11Q LOSS WILD-TYPE 23  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     91    3
  11Q LOSS WILD-TYPE   23    1
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               91                 23
  1                3                  1
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       3                         3    95
  11Q LOSS WILD-TYPE     1                         3    23
D58V7, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    3                  1
  BLACK OR AFRICAN AMERICAN                3                  3
  WHITE                                   95                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    8 90
  11Q LOSS WILD-TYPE  3 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      8   90
  11Q LOSS WILD-TYPE    3   21
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                  3
  NOT HISPANIC OR LATINO               90                 21
[1] 2 2
[1] FALSE

Clustering(59) Variable = 13Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   99  4
  13Q LOSS WILD-TYPE 30  0
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               103                 30 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 4                  0 
$`13Q LOSS MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        36.99        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 
       14.86        36.13        40.01        72.20        61.71        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.22        72.85        79.76        67.96        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW 
       59.64       106.39       120.62        59.28       128.94        61.45 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH8 
      170.33        80.94        60.16        60.26        59.84        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
        6.08       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX 
      184.41        70.59         2.73         0.10         4.83        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y 
        9.14        13.58         1.38        16.31         9.63        17.23 
TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
        3.52        36.79        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       41.52         4.90         3.65         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ 
       28.14         6.87        18.38        40.01        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOF 
        0.46        93.93        12.07         7.89        16.87        41.69 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       50.96         0.43         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I 
       57.90        54.35        21.96         0.56         5.29         7.96 
TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
       40.96        37.02        39.35        27.55        17.39        16.41 
TCGA-ZM-AA0N 
       10.85 

$`13Q LOSS WILD-TYPE`
TCGA-2G-AAFI TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 
       14.14        16.50        40.70        36.89        52.37        71.24 
TCGA-2G-AAG8 TCGA-2G-AAGE TCGA-2G-AAGI TCGA-2G-AAGO TCGA-2G-AAGT TCGA-2G-AAH3 
       63.22        68.38        92.09       115.00       124.57        59.90 
TCGA-2G-AAH4 TCGA-2G-AAL7 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW 
      125.69       131.21         0.13         3.52         7.00        20.68 
TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-W4-A7U4 TCGA-XE-AANV TCGA-XE-AAOC 
       10.26        37.18        37.68        24.26        53.03         8.88 
TCGA-XE-AAOD TCGA-YU-A90S TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA0F TCGA-ZM-AA0H 
       67.66        31.92        58.88         8.15        11.34        46.88 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.10               0.13 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            229.22             131.21 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             37.02              39.19 
[1] "0.1 - 229.2 (37.0)" "0.1 - 131.2 (39.2)"
[1] "hr="     "2.7e+08"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED        16       20        7        4         5         1
  13Q LOSS WILD-TYPE       3        5        4        1         1         0
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  13Q LOSS MUTATED           1         1          1          5          5
  13Q LOSS WILD-TYPE         0         1          0          1          0
                    vv
clus                 STAGE IS
  13Q LOSS MUTATED         33
  13Q LOSS WILD-TYPE       13
D59V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  16                  3
  STAGE IA                 20                  5
  STAGE IB                  7                  4
  STAGE II                  4                  1
  STAGE IIA                 5                  1
  STAGE IIB                 1                  0
  STAGE IIC                 1                  0
  STAGE III                 1                  1
  STAGE IIIA                1                  0
  STAGE IIIB                5                  1
  STAGE IIIC                5                  0
  STAGE IS                 33                 13
[1] 12  2
[1] 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
  13Q LOSS MUTATED   61 38  3
  13Q LOSS WILD-TYPE 14 13  3
D59V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               61                 14
  T2               38                 13
  T3                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  13Q LOSS MUTATED   34    12
  13Q LOSS WILD-TYPE 12     1
D59V5, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                  34                 12
  N1+N2               12                  1
[1] 2 2
[1] FALSE
D59V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   88  3
  13Q LOSS WILD-TYPE 26  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     88    3
  13Q LOSS WILD-TYPE   26    1
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               88                 26
  1                3                  1
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       4                         6    90
  13Q LOSS WILD-TYPE     0                         0    28
D59V7, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    4                  0
  BLACK OR AFRICAN AMERICAN                6                  0
  WHITE                                   90                 28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V8, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    9 86
  13Q LOSS WILD-TYPE  2 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9   86
  13Q LOSS WILD-TYPE    2   25
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                  2
  NOT HISPANIC OR LATINO               86                 25
[1] 2 2
[1] FALSE

Clustering(60) Variable = 14Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    16   1
  14Q LOSS WILD-TYPE 113   3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                17                116 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 1                  3 
$`14Q LOSS MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAGE TCGA-2G-AAGG 
       59.70        14.86        36.13        40.01        68.38        67.96 
TCGA-2G-AAGP TCGA-2G-AAGW TCGA-2G-AAKM TCGA-S6-A8JY TCGA-SN-A84W TCGA-SN-A84Y 
      120.62        61.45       229.22         9.14         9.63        17.23 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-YU-A90P TCGA-YU-AA4L 
       41.52         4.90        24.26        57.90        40.96 

$`14Q LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        38.30       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       16.50        40.70        36.89        52.37        71.24        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF 
       61.71        63.22        63.32        68.22        72.85        79.76 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       92.09        75.09       108.16        59.64       106.39       115.00 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
       59.28       124.57       128.94       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAL5 TCGA-2G-AAL7 
      122.50       212.65       161.72        95.67       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
        4.83        20.68        18.15        13.58         1.38        16.31 
TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
       10.26         3.52        37.18        36.79        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       35.61        33.07        23.90         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
       16.87         8.88        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S 
        8.32        12.92        20.12         6.90        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA61 
       21.96         0.56         5.29        58.88         7.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               4.9                0.1 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            229.22             212.65 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             40.96              37.10 
[1] "4.9 - 229.2 (41.0)" "0.1 - 212.7 (37.1)"
[1] "hr="     "8.3e+07"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         1        1        0        1         2         0
  14Q LOSS WILD-TYPE      18       24       11        4         4         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  14Q LOSS MUTATED           0         0          0          1          2
  14Q LOSS WILD-TYPE         1         2          1          5          3
                    vv
clus                 STAGE IS
  14Q LOSS MUTATED          6
  14Q LOSS WILD-TYPE       40
D60V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   1                 18
  STAGE IA                  1                 24
  STAGE IB                  0                 11
  STAGE II                  1                  4
  STAGE IIA                 2                  4
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                1                  5
  STAGE IIIC                2                  3
  STAGE IS                  6                 40
[1] 12  2
[1] 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
  14Q LOSS MUTATED    8  8  1
  14Q LOSS WILD-TYPE 67 43  5
D60V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                8                 67
  T2                8                 43
  T3                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  14Q LOSS MUTATED    4     4
  14Q LOSS WILD-TYPE 42     9
D60V5, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                   4                 42
  N1+N2                4                  9
[1] 2 2
[1] FALSE
D60V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    12   1
  14Q LOSS WILD-TYPE 102   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     12    1
  14Q LOSS WILD-TYPE  102    3
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               12                102
  1                1                  3
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       0                         1    16
  14Q LOSS WILD-TYPE     4                         5   102
D60V7, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   16                102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    2 12
  14Q LOSS WILD-TYPE  9 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2   12
  14Q LOSS WILD-TYPE    9   99
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               12                 99
[1] 2 2
[1] FALSE

Clustering(61) Variable = 15Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    21   1
  15Q LOSS WILD-TYPE 108   3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                22                111 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                  3 
$`15Q LOSS MUTATED`
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAGF 
       17.16         9.57        40.01        72.20        63.22        79.76 
TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAKH 
       67.96        75.09        59.64       120.62        59.28       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AALP TCGA-VF-A8AD TCGA-WZ-A7V3 
       95.67       229.22       184.41        70.59        33.07         3.65 
TCGA-X3-A8G4 TCGA-XE-AAOJ TCGA-YU-A94I TCGA-YU-AA4L 
       28.14        50.96         7.96        40.96 

$`15Q LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFN 
      154.59       191.31        36.99        14.14        14.56        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 
       16.50        40.70        36.13        36.89        52.37        71.24 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGI 
       61.71        63.32        68.22        72.85        68.38        92.09 
TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW 
      108.16       106.39       115.00       124.57       128.94        61.45 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
      170.33        80.94        60.16        60.26        59.84        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL 
      125.69        61.84        98.53        59.74        59.80        59.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAL7 
       91.43       176.15         6.08       122.50       212.65       131.21 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
        2.73         0.13         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       20.68        18.15         9.14        13.58         1.38        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 
        9.63        10.26        17.23         3.52        37.18        36.79 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 
       37.68        24.99        35.61        23.90        41.52         4.90 
TCGA-W4-A7U4 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-A8H4 
       24.26         5.06         0.16         0.82         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF 
       12.07         7.89        16.87         8.88        67.66        41.69 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
        0.43         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       54.35        31.92        21.96         0.56         5.29        58.88 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
        8.15        37.02        39.35        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       11.34        46.88        10.85 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              3.65               0.10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            229.22             212.65 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             61.43              36.79 
[1] "3.6 - 229.2 (61.4)" "0.1 - 212.7 (36.8)"
[1] "hr="     "2.5e+08"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         2        2        3        3         2         0
  15Q LOSS WILD-TYPE      17       23        8        2         4         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  15Q LOSS MUTATED           0         0          0          2          2
  15Q LOSS WILD-TYPE         1         2          1          4          3
                    vv
clus                 STAGE IS
  15Q LOSS MUTATED          6
  15Q LOSS WILD-TYPE       40
D61V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   2                 17
  STAGE IA                  2                 23
  STAGE IB                  3                  8
  STAGE II                  3                  2
  STAGE IIA                 2                  4
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                2                  4
  STAGE IIIC                2                  3
  STAGE IS                  6                 40
[1] 12  2
[1] 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
  15Q LOSS MUTATED   11 10  1
  15Q LOSS WILD-TYPE 64 41  5
D61V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               11                 64
  T2               10                 41
  T3                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  15Q LOSS MUTATED    9     4
  15Q LOSS WILD-TYPE 37     9
D61V5, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                   9                 37
  N1+N2                4                  9
[1] 2 2
[1] FALSE
D61V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   17  2
  15Q LOSS WILD-TYPE 97  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     17    2
  15Q LOSS WILD-TYPE   97    2
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               17                 97
  1                2                  2
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       0                         2    19
  15Q LOSS WILD-TYPE     4                         4    99
D61V7, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                   19                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1 19
  15Q LOSS WILD-TYPE 10 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   19
  15Q LOSS WILD-TYPE   10   92
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               19                 92
[1] 2 2
[1] FALSE

Clustering(62) Variable = 16P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED   42  1
  16P LOSS WILD-TYPE 87  3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                43                 90 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                  3 
$`16P LOSS MUTATED`
TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      102.35       154.59       191.31        14.14        14.56        17.16 
TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG3 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGW 
       14.86        36.13        52.37        68.22        72.85        61.45 
TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
       60.26        59.90       122.50       212.65       161.72        95.67 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2X-A9D5 TCGA-SB-A6J6 TCGA-SB-A76C 
      229.22       184.41       131.21         2.73        13.58         1.38 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-WZ-A7V3 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       35.61        33.07         3.65         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO6 TCGA-XE-AAOJ TCGA-XY-A89B 
        6.87        65.98         0.46         7.89        50.96         8.32 
TCGA-XY-A8S2 TCGA-XY-A9T9 TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA0D 
       12.92         6.90         7.96        40.96         8.15        17.39 
TCGA-ZM-AA0N 
       10.85 

$`16P LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAFH 
       20.32        30.35        38.30        59.70       122.40        36.99 
TCGA-2G-AAFM TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 
        9.57        16.50        40.70        36.89        40.01        71.24 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGE TCGA-2G-AAGF 
       72.20        61.71        63.22        63.32        68.38        79.76 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN 
       67.96        92.09        75.09       108.16        59.64       106.39 
TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX 
      115.00       120.62        59.28       124.57       128.94       170.33 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       80.94        60.16        59.84       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
       70.59         0.13         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X 
       20.68        18.15         9.14        16.31         9.63        10.26 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
       17.23         3.52        37.18        36.79        37.68        24.99 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V4 TCGA-XE-A8H4 
       23.90        41.52         4.90        24.26         5.06        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB 
       40.01        34.22        53.03        93.93        12.07        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A8S3 TCGA-YU-A90P 
        8.88        67.66        41.69         0.43        20.12        57.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       54.35        31.92        21.96         0.56         5.29        58.88 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        39.35        27.55        16.41        11.34        46.88 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.16               0.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            229.22             176.15 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             33.07              39.68 
[1] "0.2 - 229.2 (33.1)" "0.1 - 176.2 (39.7)"
[1] "hr="     "3.1e+08"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED         9        6        4        3         3         0
  16P LOSS WILD-TYPE      10       19        7        2         3         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  16P LOSS MUTATED           0         1          0          1          1
  16P LOSS WILD-TYPE         1         1          1          5          4
                    vv
clus                 STAGE IS
  16P LOSS MUTATED         13
  16P LOSS WILD-TYPE       33
D62V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   9                 10
  STAGE IA                  6                 19
  STAGE IB                  4                  7
  STAGE II                  3                  2
  STAGE IIA                 3                  3
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIA                0                  1
  STAGE IIIB                1                  5
  STAGE IIIC                1                  4
  STAGE IS                 13                 33
[1] 12  2
[1] 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
  16P LOSS MUTATED   23 19  1
  16P LOSS WILD-TYPE 52 32  5
D62V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               23                 52
  T2               19                 32
  T3                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  16P LOSS MUTATED   11     4
  16P LOSS WILD-TYPE 35     9
D62V5, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                  11                 35
  N1+N2                4                  9
[1] 2 2
[1] FALSE
D62V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   38  0
  16P LOSS WILD-TYPE 76  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     38    0
  16P LOSS WILD-TYPE   76    4
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               38                 76
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                         1    40
  16P LOSS WILD-TYPE     3                         5    78
D62V7, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   40                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    4 36
  16P LOSS WILD-TYPE  7 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4   36
  16P LOSS WILD-TYPE    7   75
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               36                 75
[1] 2 2
[1] FALSE

Clustering(63) Variable = 16Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   45  1
  16Q LOSS WILD-TYPE 84  3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                46                 87 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                  3 
$`16Q LOSS MUTATED`
TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFJ 
      102.35       122.40       154.59       191.31        14.14        14.56 
TCGA-2G-AAFL TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG3 TCGA-2G-AAGA TCGA-2G-AAGC 
       17.16        14.86        36.13        52.37        68.22        72.85 
TCGA-2G-AAGW TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAHL TCGA-2G-AAHT TCGA-2G-AAKD 
       61.45        60.26        59.90        59.80         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-SB-A6J6 TCGA-VF-A8AC TCGA-VF-A8AD TCGA-WZ-A7V3 
        2.73         3.52        13.58        35.61        33.07         3.65 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-AANJ TCGA-XE-AANR 
        0.16         0.82        28.14         6.87        65.98         0.46 
TCGA-XE-AAO6 TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A9T9 TCGA-YU-A94I 
        7.89        50.96         8.32        12.92         6.90         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA0D TCGA-ZM-AA0N 
       40.96         8.15        17.39        10.85 

$`16Q LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAFH TCGA-2G-AAFM 
       20.32        30.35        38.30        59.70        36.99         9.57 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 
       16.50        40.70        36.89        40.01        71.24        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       61.71        63.22        63.32        68.38        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       92.09        75.09       108.16        59.64       106.39       115.00 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY 
      120.62        59.28       124.57       128.94       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       60.16        59.84       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1H 
       59.80        91.43       176.15        70.59         0.13         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C 
        0.10         4.83        20.68        18.15         9.14         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23         3.52        37.18 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 
       36.79        37.68        24.99        23.90        41.52         4.90 
TCGA-W4-A7U4 TCGA-WZ-A7V4 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANV 
       24.26         5.06        18.38        40.01        34.22        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF 
       93.93        12.07        16.87         8.88        67.66        41.69 
TCGA-XE-AAOL TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
        0.43        20.12        57.90        54.35        31.92        21.96 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        0.56         5.29        58.88        37.02        39.35        27.55 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       16.41        11.34        46.88 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.16               0.10 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            229.22             176.15 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             34.34              39.35 
[1] "0.2 - 229.2 (34.3)" "0.1 - 176.2 (39.4)"
[1] "hr="     "3.3e+08"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED        10        7        4        3         3         0
  16Q LOSS WILD-TYPE       9       18        7        2         3         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  16Q LOSS MUTATED           0         1          0          1          1
  16Q LOSS WILD-TYPE         1         1          1          5          4
                    vv
clus                 STAGE IS
  16Q LOSS MUTATED         15
  16Q LOSS WILD-TYPE       31
D63V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  10                  9
  STAGE IA                  7                 18
  STAGE IB                  4                  7
  STAGE II                  3                  2
  STAGE IIA                 3                  3
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIA                0                  1
  STAGE IIIB                1                  5
  STAGE IIIC                1                  4
  STAGE IS                 15                 31
[1] 12  2
[1] 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
  16Q LOSS MUTATED   23 22  1
  16Q LOSS WILD-TYPE 52 29  5
D63V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1               23                 52
  T2               22                 29
  T3                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  16Q LOSS MUTATED   15     4
  16Q LOSS WILD-TYPE 31     9
D63V5, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                  15                 31
  N1+N2                4                  9
[1] 2 2
[1] FALSE
D63V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   41  0
  16Q LOSS WILD-TYPE 73  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     41    0
  16Q LOSS WILD-TYPE   73    4
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               41                 73
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       1                         1    43
  16Q LOSS WILD-TYPE     3                         5    75
D63V7, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   43                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    4 39
  16Q LOSS WILD-TYPE  7 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4   39
  16Q LOSS WILD-TYPE    7   72
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               39                 72
[1] 2 2
[1] FALSE

Clustering(64) Variable = 17P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   33  1
  17P LOSS WILD-TYPE 96  3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                34                 99 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                  3 
$`17P LOSS MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFE TCGA-2G-AAFH TCGA-2G-AAG3 TCGA-2G-AAG9 TCGA-2G-AAGO 
       59.70       154.59        36.99        52.37        63.32       115.00 
TCGA-2G-AAGW TCGA-2G-AAH4 TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       61.45       125.69        59.80       176.15         6.08       122.50 
TCGA-2X-A9D5 TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A6IS TCGA-SO-A8JP 
        2.73        18.15         9.14        13.58        16.31         3.52 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H5 
       23.90        41.52         0.16         0.82        28.14        40.01 
TCGA-XE-AANJ TCGA-XE-AAOB TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A9T9 
       65.98        16.87        50.96         0.43         8.32         6.90 
TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-AA4L TCGA-ZM-AA06 
       21.96         5.29        40.96        39.35 

$`17P LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        30.35        38.30       102.35       122.40       191.31 
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       14.14        14.56        17.16         9.57        14.86        16.50 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 
       40.70        36.13        36.89        40.01        71.24        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       61.71        63.22        68.22        72.85        68.38        79.76 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN 
       67.96        92.09        75.09       108.16        59.64       106.39 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY 
      120.62        59.28       124.57       128.94       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.16        60.26        59.84        59.90        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHN TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
       59.74        59.80        91.43       212.65       161.72        95.67 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1G 
      229.22       184.41       131.21        70.59         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-SB-A76C TCGA-SN-A84W 
        7.00         0.10         4.83        20.68         1.38         9.63 
TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
       10.26        17.23        37.18        36.79        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       35.61        33.07         4.90        24.26         3.65         5.06 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
        6.87        18.38        34.22         0.46        53.03        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XY-A8S2 
       12.07         7.89         8.88        67.66        41.69        12.92 
TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90Y TCGA-YU-A94D 
       20.12        57.90        54.35        31.92         0.56        58.88 
TCGA-YU-A94I TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
        7.96         8.15        37.02        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       11.34        46.88        10.85 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.16               0.10 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            176.15             229.22 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            32.565             38.300 
[1] "0.2 - 176.2 (32.6)" "0.1 - 229.2 (38.3)"
[1] "hr=" "1.6"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         6        4        2        1         1         1
  17P LOSS WILD-TYPE      13       21        9        4         5         0
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  17P LOSS MUTATED           0         1          0          1          2
  17P LOSS WILD-TYPE         1         1          1          5          3
                    vv
clus                 STAGE IS
  17P LOSS MUTATED         13
  17P LOSS WILD-TYPE       33
D64V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   6                 13
  STAGE IA                  4                 21
  STAGE IB                  2                  9
  STAGE II                  1                  4
  STAGE IIA                 1                  5
  STAGE IIB                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIA                0                  1
  STAGE IIIB                1                  5
  STAGE IIIC                2                  3
  STAGE IS                 13                 33
[1] 12  2
[1] 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
  17P LOSS MUTATED   21 12  1
  17P LOSS WILD-TYPE 54 39  5
D64V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               21                 54
  T2               12                 39
  T3                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  17P LOSS MUTATED    8     3
  17P LOSS WILD-TYPE 38    10
D64V5, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                   8                 38
  N1+N2                3                 10
[1] 2 2
[1] FALSE
D64V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   29  0
  17P LOSS WILD-TYPE 85  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     29    0
  17P LOSS WILD-TYPE   85    4
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               29                 85
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       0                         3    30
  17P LOSS WILD-TYPE     4                         3    88
D64V7, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                3                  3
  WHITE                                   30                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    4 27
  17P LOSS WILD-TYPE  7 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4   27
  17P LOSS WILD-TYPE    7   84
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               27                 84
[1] 2 2
[1] FALSE

Clustering(65) Variable = 17Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    14   0
  17Q LOSS WILD-TYPE 115   4
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                14                119 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 0                  4 
$`17Q LOSS MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFE TCGA-2G-AAG9 TCGA-2G-AAGW TCGA-2G-AAHP TCGA-2G-AAHT 
       59.70       154.59        63.32        61.45       176.15         6.08 
TCGA-2G-AAKD TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-VF-A8AE TCGA-WZ-A8D5 TCGA-XE-AAOL 
      122.50        18.15        13.58        23.90         0.82         0.43 
TCGA-YU-A90W TCGA-ZM-AA06 
       21.96        39.35 

$`17Q LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        30.35        38.30       102.35       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       36.99        14.14        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC 
       71.24        72.20        61.71        63.22        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
      128.94       170.33        80.94        60.16        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       59.80        91.43       212.65       161.72        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      184.41       131.21        70.59         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JY TCGA-SB-A76C 
        7.00         0.10         4.83        20.68         9.14         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23         3.52        37.18 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U2 
       36.79        37.68        24.99        35.61        33.07        41.52 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 
        4.90        24.26         3.65         5.06         0.16        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       67.66        41.69        50.96         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90Y TCGA-YU-A912 
        6.90        57.90        54.35        31.92         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0B 
       58.88         7.96        40.96         8.15        37.02        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.43               0.10 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            176.15             229.22 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            31.625             37.680 
[1] "0.4 - 176.2 (31.6)" "0.1 - 229.2 (37.7)"
[1] "hr="     "7.8e+07"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         2        3        2        0         1         0
  17Q LOSS WILD-TYPE      17       22        9        5         5         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  17Q LOSS MUTATED           0         1          0          1          0
  17Q LOSS WILD-TYPE         1         1          1          5          5
                    vv
clus                 STAGE IS
  17Q LOSS MUTATED          3
  17Q LOSS WILD-TYPE       43
D65V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   2                 17
  STAGE IA                  3                 22
  STAGE IB                  2                  9
  STAGE II                  0                  5
  STAGE IIA                 1                  5
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIA                0                  1
  STAGE IIIB                1                  5
  STAGE IIIC                0                  5
  STAGE IS                  3                 43
[1] 12  2
[1] 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
  17Q LOSS MUTATED    6  7  1
  17Q LOSS WILD-TYPE 69 44  5
D65V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                6                 69
  T2                7                 44
  T3                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  17Q LOSS MUTATED    4     2
  17Q LOSS WILD-TYPE 42    11
D65V5, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                   4                 42
  N1+N2                2                 11
[1] 2 2
[1] FALSE
D65V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    13   0
  17Q LOSS WILD-TYPE 101   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     13    0
  17Q LOSS WILD-TYPE  101    4
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               13                101
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         1    13
  17Q LOSS WILD-TYPE     4                         5   105
D65V7, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   13                105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    0 13
  17Q LOSS WILD-TYPE 11 98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   13
  17Q LOSS WILD-TYPE   11   98
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               13                 98
[1] 2 2
[1] FALSE

Clustering(66) Variable = 18P LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   99  4
  18P LOSS WILD-TYPE 30  0
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               103                 30 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                  0 
$`18P LOSS MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        38.30        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      191.31        36.99        17.16         9.57        14.86        16.50 
TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        40.01        52.37        72.20        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       63.32        68.22        72.85        68.38        79.76        67.96 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS 
       75.09       108.16        59.64       106.39       115.00        59.28 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL 
       59.84        59.90       125.69        59.74        59.80        59.80 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM 
      176.15         6.08       122.50       212.65        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1I TCGA-4K-AAAL 
      184.41       131.21        70.59         2.73         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y 
       20.68        18.15         1.38        16.31         9.63        17.23 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U2 TCGA-W4-A7U3 
       37.68        24.99        35.61        33.07        41.52         4.90 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
       93.93        12.07        16.87        67.66        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
        0.43         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L 
       54.35        21.96         0.56         5.29         7.96        40.96 
TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
        8.15        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0N 
       10.85 

$`18P LOSS WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG5 
       30.35        14.14        14.56        40.70        36.89        71.24 
TCGA-2G-AAGI TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHN 
       92.09       120.62       124.57        61.84        98.53        91.43 
TCGA-2G-AAKH TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JY TCGA-SB-A6J6 
      161.72         0.13         3.52         7.00         9.14        13.58 
TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AE TCGA-XE-AANV 
       10.26         3.52        37.18        36.79        23.90        53.03 
TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-YU-A90S TCGA-YU-A94D TCGA-ZM-AA05 TCGA-ZM-AA0H 
        7.89         8.88        31.92        58.88        37.02        46.88 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.10               0.13 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            229.22             161.72 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             40.01              36.84 
[1] "0.1 - 229.2 (40.0)" "0.1 - 161.7 (36.8)"
[1] "hr="     "2.7e+08"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED        15       17        8        4         5         1
  18P LOSS WILD-TYPE       4        8        3        1         1         0
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  18P LOSS MUTATED           0         1          1          5          4
  18P LOSS WILD-TYPE         1         1          0          1          1
                    vv
clus                 STAGE IS
  18P LOSS MUTATED         37
  18P LOSS WILD-TYPE        9
D66V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  15                  4
  STAGE IA                 17                  8
  STAGE IB                  8                  3
  STAGE II                  4                  1
  STAGE IIA                 5                  1
  STAGE IIB                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIA                1                  0
  STAGE IIIB                5                  1
  STAGE IIIC                4                  1
  STAGE IS                 37                  9
[1] 12  2
[1] 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
  18P LOSS MUTATED   58 41  3
  18P LOSS WILD-TYPE 17 10  3
D66V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               58                 17
  T2               41                 10
  T3                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  18P LOSS MUTATED   34    12
  18P LOSS WILD-TYPE 12     1
D66V5, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                  34                 12
  N1+N2               12                  1
[1] 2 2
[1] FALSE
D66V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   87  3
  18P LOSS WILD-TYPE 27  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     87    3
  18P LOSS WILD-TYPE   27    1
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               87                 27
  1                3                  1
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       3                         6    91
  18P LOSS WILD-TYPE     1                         0    27
D66V7, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    3                  1
  BLACK OR AFRICAN AMERICAN                6                  0
  WHITE                                   91                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    9 85
  18P LOSS WILD-TYPE  2 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      9   85
  18P LOSS WILD-TYPE    2   26
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                  2
  NOT HISPANIC OR LATINO               85                 26
[1] 2 2
[1] FALSE

Clustering(67) Variable = 18Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   105   4
  18Q LOSS WILD-TYPE  24   0
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               109                 24 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                  0 
$`18Q LOSS MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        36.99        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG6 
       14.86        16.50        36.13        40.01        52.37        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       61.71        63.22        63.32        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN 
       79.76        67.96        75.09       108.16        59.64       106.39 
TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      115.00        59.28       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC 
       60.16        60.26        59.84        59.90       125.69        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        59.80       176.15         6.08       122.50       212.65 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
       95.67       229.22       184.41       131.21        70.59         2.73 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AA 
        1.38        16.31         9.63        17.23         3.52        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 
       24.99        35.61        33.07        41.52         4.90        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO3 
       18.38        40.01        34.22        65.98         0.46        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
       12.07         7.89        16.87        67.66        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
        0.43         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L 
       54.35        21.96         0.56         5.29         7.96        40.96 
TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
        8.15        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0N 
       10.85 

$`18Q LOSS WILD-TYPE`
TCGA-2G-AAFI TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAGI TCGA-2G-AAGP 
       14.14        40.70        36.89        71.24        92.09       120.62 
TCGA-2G-AAGT TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHN TCGA-2G-AAKH TCGA-2X-A9D6 
      124.57        61.84        98.53        91.43       161.72         0.13 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AE 
        3.52         7.00        10.26        37.18        36.79        23.90 
TCGA-XE-AANV TCGA-XE-AAOC TCGA-YU-A90S TCGA-YU-A94D TCGA-ZM-AA05 TCGA-ZM-AA0H 
       53.03         8.88        31.92        58.88        37.02        46.88 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.10               0.13 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            229.22             161.72 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             37.68              38.94 
[1] "0.1 - 229.2 (37.7)" "0.1 - 161.7 (38.9)"
[1] "hr="     "2.5e+08"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED        17       19        8        4         5         1
  18Q LOSS WILD-TYPE       2        6        3        1         1         0
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  18Q LOSS MUTATED           0         1          1          5          4
  18Q LOSS WILD-TYPE         1         1          0          1          1
                    vv
clus                 STAGE IS
  18Q LOSS MUTATED         39
  18Q LOSS WILD-TYPE        7
D67V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  17                  2
  STAGE IA                 19                  6
  STAGE IB                  8                  3
  STAGE II                  4                  1
  STAGE IIA                 5                  1
  STAGE IIB                 1                  0
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIA                1                  0
  STAGE IIIB                5                  1
  STAGE IIIC                4                  1
  STAGE IS                 39                  7
[1] 12  2
[1] 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
  18Q LOSS MUTATED   64 41  3
  18Q LOSS WILD-TYPE 11 10  3
D67V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               64                 11
  T2               41                 10
  T3                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  18Q LOSS MUTATED   37    12
  18Q LOSS WILD-TYPE  9     1
D67V5, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                  37                  9
  N1+N2               12                  1
[1] 2 2
[1] FALSE
D67V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   93  3
  18Q LOSS WILD-TYPE 21  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     93    3
  18Q LOSS WILD-TYPE   21    1
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               93                 21
  1                3                  1
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       4                         6    96
  18Q LOSS WILD-TYPE     0                         0    22
D67V7, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    4                  0
  BLACK OR AFRICAN AMERICAN                6                  0
  WHITE                                   96                 22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V8, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    9 91
  18Q LOSS WILD-TYPE  2 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      9   91
  18Q LOSS WILD-TYPE    2   20
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                  2
  NOT HISPANIC OR LATINO               91                 20
[1] 2 2
[1] FALSE

Clustering(68) Variable = 19P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED   38  2
  19P LOSS WILD-TYPE 91  2
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                40                 93 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                  2 
$`19P LOSS MUTATED`
TCGA-2G-AAF8 TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG0 
      122.40        14.56         9.57        14.86        36.13        40.01 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGG 
       72.20        61.71        63.22        68.22        68.38        67.96 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGV TCGA-2G-AAGY TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
      128.94        80.94       212.65       161.72        95.67       229.22 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-S6-A8JX TCGA-SN-A84Y TCGA-VF-A8AD TCGA-W4-A7U4 
      131.21        70.59        18.15        17.23        33.07        24.26 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-AANI TCGA-XE-AAOJ TCGA-XY-A8S2 TCGA-XY-A8S3 
       28.14         6.87        34.22        50.96        12.92        20.12 
TCGA-YU-A90P TCGA-YU-A90Y TCGA-YU-A94I TCGA-YU-AA4L 
       57.90         0.56         7.96        40.96 

$`19P LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE 
       20.32        30.35        38.30        59.70       102.35       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFO TCGA-2G-AAFV 
      191.31        36.99        14.14        17.16        16.50        40.70 
TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGF 
       36.89        52.37        71.24        63.32        72.85        79.76 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGZ 
       92.09        75.09       124.57        61.45       170.33        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAL5 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      122.50       184.41         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        0.10         4.83        20.68         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 
       16.31         9.63        10.26         3.52        37.18        36.79 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 
       37.68        24.99        35.61        23.90        41.52         4.90 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 
        3.65         5.06         0.16         0.82        18.38        40.01 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B 
       16.87         8.88        67.66        41.69         0.43         8.32 
TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D 
        6.90        54.35        31.92        21.96         5.29        58.88 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
        8.15        37.02        39.35        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       11.34        46.88        10.85 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.56               0.10 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            229.22             191.31 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             59.46              36.79 
[1] "0.6 - 229.2 (59.5)" "0.1 - 191.3 (36.8)"
[1] "hr=" "1"  
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         3        3        3        4         4         0
  19P LOSS WILD-TYPE      16       22        8        1         2         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  19P LOSS MUTATED           0         0          0          4          3
  19P LOSS WILD-TYPE         1         2          1          2          2
                    vv
clus                 STAGE IS
  19P LOSS MUTATED         15
  19P LOSS WILD-TYPE       31
D68V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   3                 16
  STAGE IA                  3                 22
  STAGE IB                  3                  8
  STAGE II                  4                  1
  STAGE IIA                 4                  2
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                4                  2
  STAGE IIIC                3                  2
  STAGE IS                 15                 31
[1] 12  2
[1] 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
  19P LOSS MUTATED   18 20  2
  19P LOSS WILD-TYPE 57 31  4
D68V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               18                 57
  T2               20                 31
  T3                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  19P LOSS MUTATED   14     8
  19P LOSS WILD-TYPE 32     5
D68V5, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                  14                 32
  N1+N2                8                  5
[1] 2 2
[1] FALSE
D68V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   34  2
  19P LOSS WILD-TYPE 80  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     34    2
  19P LOSS WILD-TYPE   80    2
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               34                 80
  1                2                  2
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       1                         2    36
  19P LOSS WILD-TYPE     3                         4    82
D68V7, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                   36                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V8, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    3 33
  19P LOSS WILD-TYPE  8 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3   33
  19P LOSS WILD-TYPE    8   78
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               33                 78
[1] 2 2
[1] FALSE

Clustering(69) Variable = 19Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED   40  2
  19Q LOSS WILD-TYPE 89  2
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                42                 91 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                  2 
$`19Q LOSS MUTATED`
TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG6 
       14.56         9.57        14.86        36.13        40.01        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGK 
       61.71        63.22        68.22        68.38        67.96       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV 
       59.64       106.39       115.00       120.62        59.28       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH4 TCGA-2G-AAKD TCGA-2G-AAKG 
       61.45       170.33        80.94       125.69       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-S6-A8JX 
      161.72        95.67       229.22       131.21        70.59        18.15 
TCGA-SN-A84Y TCGA-VF-A8AD TCGA-W4-A7U4 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-AANI 
       17.23        33.07        24.26        28.14         6.87        34.22 
TCGA-XE-AAOJ TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Y TCGA-YU-AA4L 
       50.96        12.92        20.12        57.90         0.56        40.96 

$`19Q LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFO 
      154.59       191.31        36.99        14.14        17.16        16.50 
TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG9 TCGA-2G-AAGC 
       40.70        36.89        52.37        71.24        63.32        72.85 
TCGA-2G-AAGF TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGT TCGA-2G-AAGZ TCGA-2G-AAH0 
       79.76        92.09        75.09       124.57        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.84        59.90        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAL5 TCGA-2X-A9D5 
       59.80        91.43       176.15         6.08       184.41         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
        0.13         3.52         7.00         0.10         4.83        20.68 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X 
        9.14        13.58         1.38        16.31         9.63        10.26 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC 
        3.52        37.18        36.79        37.68        24.99        35.61 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       23.90        41.52         4.90         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
        0.82        18.38        40.01        65.98         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S 
       41.69         0.43         8.32         6.90        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA61 TCGA-ZM-AA05 
       21.96         5.29        58.88         7.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.56               0.10 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            229.22             191.31 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             61.58              31.92 
[1] "0.6 - 229.2 (61.6)" "0.1 - 191.3 (31.9)"
[1] "hr=" "1.2"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         3        2        3        5         4         0
  19Q LOSS WILD-TYPE      16       23        8        0         2         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  19Q LOSS MUTATED           0         1          0          4          3
  19Q LOSS WILD-TYPE         1         1          1          2          2
                    vv
clus                 STAGE IS
  19Q LOSS MUTATED         16
  19Q LOSS WILD-TYPE       30
D69V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   3                 16
  STAGE IA                  2                 23
  STAGE IB                  3                  8
  STAGE II                  5                  0
  STAGE IIA                 4                  2
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIA                0                  1
  STAGE IIIB                4                  2
  STAGE IIIC                3                  2
  STAGE IS                 16                 30
[1] 12  2
[1] 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
  19Q LOSS MUTATED   19 21  2
  19Q LOSS WILD-TYPE 56 30  4
D69V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               19                 56
  T2               21                 30
  T3                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  19Q LOSS MUTATED   15     8
  19Q LOSS WILD-TYPE 31     5
D69V5, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                  15                 31
  N1+N2                8                  5
[1] 2 2
[1] FALSE
D69V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   37  2
  19Q LOSS WILD-TYPE 77  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     37    2
  19Q LOSS WILD-TYPE   77    2
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               37                 77
  1                2                  2
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         2    39
  19Q LOSS WILD-TYPE     3                         4    79
D69V7, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                   39                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V8, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    3 36
  19Q LOSS WILD-TYPE  8 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3   36
  19Q LOSS WILD-TYPE    8   75
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               36                 75
[1] 2 2
[1] FALSE

Clustering(70) Variable = 20P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    27   1
  20P LOSS WILD-TYPE 102   3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                28                105 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                  3 
$`20P LOSS MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFN TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGJ 
       59.70        14.86        72.20        61.71        63.32        75.09 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH4 
      120.62        59.28        61.45       170.33        60.16       125.69 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AALP TCGA-4K-AA1G TCGA-S6-A8JY TCGA-SN-A84Y 
      229.22       184.41        70.59         3.52         9.14        17.23 
TCGA-VF-A8AC TCGA-WZ-A7V3 TCGA-XE-A8H1 TCGA-XE-AANJ TCGA-XY-A8S2 TCGA-XY-A8S3 
       35.61         3.65         6.87        65.98        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A912 TCGA-ZM-AA0B TCGA-ZM-AA0N 
        6.90         5.29        27.55        10.85 

$`20P LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        38.30       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       71.24        63.22        68.22        72.85        68.38        79.76 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       67.96        92.09       108.16        59.64       106.39       115.00 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
      124.57       128.94        80.94        60.26        59.84        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       61.84        98.53        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      176.15         6.08       122.50       212.65       161.72        95.67 
TCGA-2G-AAL7 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
      131.21         2.73         0.13         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       20.68        18.15        13.58         1.38        16.31         9.63 
TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
       10.26         3.52        37.18        36.79        37.68        24.99 
TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V4 
       33.07        23.90        41.52         4.90        24.26         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.16         0.82        28.14        18.38        40.01        34.22 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        53.03        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43         8.32 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D 
       57.90        54.35        31.92        21.96         0.56        58.88 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0D 
        7.96        40.96         8.15        37.02        39.35        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       16.41        11.34        46.88 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              3.52               0.10 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            229.22             212.65 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             59.49              37.18 
[1] "3.5 - 229.2 (59.5)" "0.1 - 212.7 (37.2)"
[1] "hr="     "2.6e+08"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         4        4        1        2         1         0
  20P LOSS WILD-TYPE      15       21       10        3         5         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  20P LOSS MUTATED           0         0          1          4          1
  20P LOSS WILD-TYPE         1         2          0          2          4
                    vv
clus                 STAGE IS
  20P LOSS MUTATED         10
  20P LOSS WILD-TYPE       36
D70V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   4                 15
  STAGE IA                  4                 21
  STAGE IB                  1                 10
  STAGE II                  2                  3
  STAGE IIA                 1                  5
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                1                  0
  STAGE IIIB                4                  2
  STAGE IIIC                1                  4
  STAGE IS                 10                 36
[1] 12  2
[1] 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
  20P LOSS MUTATED   16 12  0
  20P LOSS WILD-TYPE 59 39  6
D70V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1               16                 59
  T2               12                 39
  T3                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  20P LOSS MUTATED    8     5
  20P LOSS WILD-TYPE 38     8
D70V5, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                   8                 38
  N1+N2                5                  8
[1] 2 2
[1] FALSE
D70V6, binary
                    cls
clus                  0  1
  20P LOSS MUTATED   24  2
  20P LOSS WILD-TYPE 90  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     24    2
  20P LOSS WILD-TYPE   90    2
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               24                 90
  1                2                  2
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         2    26
  20P LOSS WILD-TYPE     4                         4    92
D70V7, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                   26                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V8, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    3 24
  20P LOSS WILD-TYPE  8 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3   24
  20P LOSS WILD-TYPE    8   87
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               24                 87
[1] 2 2
[1] FALSE

Clustering(71) Variable = 20Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    14   1
  20Q LOSS WILD-TYPE 115   3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                15                118 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                  3 
$`20Q LOSS MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFN TCGA-2G-AAG6 TCGA-2G-AAGZ TCGA-2G-AAKM TCGA-2G-AAL5 
       59.70        14.86        72.20        60.16       229.22       184.41 
TCGA-4K-AA1G TCGA-S6-A8JY TCGA-SN-A84Y TCGA-VF-A8AC TCGA-XE-A8H1 TCGA-XY-A8S2 
        3.52         9.14        17.23        35.61         6.87        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-ZM-AA0N 
       20.12         6.90        10.85 

$`20Q LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        38.30       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       71.24        61.71        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 
      128.94        61.45       170.33        80.94        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      161.72        95.67       131.21        70.59         2.73         0.13 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 
        7.00         0.10         4.83        20.68        18.15        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 
        1.38        16.31         9.63        10.26         3.52        37.18 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       36.79        37.68        24.99        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
        4.90        24.26         3.65         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
       28.14        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-YU-A90P 
       67.66        41.69        50.96         0.43         8.32        57.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       54.35        31.92        21.96         0.56         5.29        58.88 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        7.96        40.96         8.15        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       17.39        16.41        11.34        46.88 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              3.52               0.10 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            229.22             212.65 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             17.23              39.68 
[1] "3.5 - 229.2 (17.2)" "0.1 - 212.7 (39.7)"
[1] "hr="     "7.7e+07"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         3        1        1        1         0         0
  20Q LOSS WILD-TYPE      16       24       10        4         6         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  20Q LOSS MUTATED           0         0          1          1          0
  20Q LOSS WILD-TYPE         1         2          0          5          5
                    vv
clus                 STAGE IS
  20Q LOSS MUTATED          7
  20Q LOSS WILD-TYPE       39
D71V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   3                 16
  STAGE IA                  1                 24
  STAGE IB                  1                 10
  STAGE II                  1                  4
  STAGE IIA                 0                  6
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                1                  0
  STAGE IIIB                1                  5
  STAGE IIIC                0                  5
  STAGE IS                  7                 39
[1] 12  2
[1] 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
  20Q LOSS MUTATED    6  9  0
  20Q LOSS WILD-TYPE 69 42  6
D71V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                6                 69
  T2                9                 42
  T3                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  20Q LOSS MUTATED    4     2
  20Q LOSS WILD-TYPE 42    11
D71V5, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                   4                 42
  N1+N2                2                 11
[1] 2 2
[1] FALSE
D71V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    14   1
  20Q LOSS WILD-TYPE 100   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     14    1
  20Q LOSS WILD-TYPE  100    3
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0               14                100
  1                1                  3
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         0    15
  20Q LOSS WILD-TYPE     4                         6   103
D71V7, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   15                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V8, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    2 13
  20Q LOSS WILD-TYPE  9 98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2   13
  20Q LOSS WILD-TYPE    9   98
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               13                 98
[1] 2 2
[1] FALSE

Clustering(72) Variable = 22Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   37  1
  22Q LOSS WILD-TYPE 92  3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                38                 95 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                  3 
$`22Q LOSS MUTATED`
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAG6 
       14.14        14.56        17.16         9.57        14.86        72.20 
TCGA-2G-AAG7 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGJ 
       61.71        68.22        72.85        68.38        67.96        75.09 
TCGA-2G-AAGM TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAH3 
       59.64       115.00       120.62       128.94        61.45        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAKD TCGA-2G-AAKL TCGA-2G-AAL5 TCGA-2G-AALP 
      125.69        61.84       122.50        95.67       184.41        70.59 
TCGA-SN-A84W TCGA-SN-A84Y TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-AANR 
        9.63        17.23         0.16        28.14         6.87         0.46 
TCGA-XE-AAO3 TCGA-XE-AAOD TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90Y TCGA-YU-A94I 
       93.93        67.66        12.92        20.12         0.56         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 
       40.96         8.15 

$`22Q LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
      154.59       191.31        36.99        16.50        40.70        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAG9 
       36.89        40.01        52.37        71.24        63.22        63.32 
TCGA-2G-AAGF TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGS TCGA-2G-AAGT 
       79.76        92.09       108.16       106.39        59.28       124.57 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAHA 
      170.33        80.94        60.16        60.26        59.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2X-A9D5 TCGA-2X-A9D6 
      212.65       161.72       229.22       131.21         2.73         0.13 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
        3.52         7.00         0.10         4.83        20.68        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X TCGA-SO-A8JP 
        9.14        13.58         1.38        16.31        10.26         3.52 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       37.18        36.79        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       23.90        41.52         4.90        24.26         3.65         5.06 
TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANV 
        0.82        18.38        40.01        34.22        65.98        53.03 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOF TCGA-XE-AAOJ 
       12.07         7.89        16.87         8.88        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
        0.43         8.32         6.90        57.90        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
       21.96         5.29        58.88        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.16               0.10 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            184.41             229.22 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            60.675             36.990 
[1] "0.2 - 184.4 (60.7)" "0.1 - 229.2 (37.0)"
[1] "hr=" "1.3"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         7        2        3        3         3         0
  22Q LOSS WILD-TYPE      12       23        8        2         3         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  22Q LOSS MUTATED           0         1          0          2          4
  22Q LOSS WILD-TYPE         1         1          1          4          1
                    vv
clus                 STAGE IS
  22Q LOSS MUTATED         13
  22Q LOSS WILD-TYPE       33
D72V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   7                 12
  STAGE IA                  2                 23
  STAGE IB                  3                  8
  STAGE II                  3                  2
  STAGE IIA                 3                  3
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  1
  STAGE IIIA                0                  1
  STAGE IIIB                2                  4
  STAGE IIIC                4                  1
  STAGE IS                 13                 33
[1] 12  2
[1] 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
  22Q LOSS MUTATED   16 20  2
  22Q LOSS WILD-TYPE 59 31  4
D72V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               16                 59
  T2               20                 31
  T3                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  22Q LOSS MUTATED   13     5
  22Q LOSS WILD-TYPE 33     8
D72V5, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                  13                 33
  N1+N2                5                  8
[1] 2 2
[1] FALSE
D72V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   31  2
  22Q LOSS WILD-TYPE 83  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     31    2
  22Q LOSS WILD-TYPE   83    2
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               31                 83
  1                2                  2
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       2                         3    32
  22Q LOSS WILD-TYPE     2                         3    86
D72V7, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    2                  2
  BLACK OR AFRICAN AMERICAN                3                  3
  WHITE                                   32                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V8, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    4 30
  22Q LOSS WILD-TYPE  7 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4   30
  22Q LOSS WILD-TYPE    7   81
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               30                 81
[1] 2 2
[1] FALSE

Clustering(73) Variable = XP LOSS MUTATION ANALYSIS
D73V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    23   0
  XP LOSS WILD-TYPE 106   4
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               23               110 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                0                 4 
$`XP LOSS MUTATED`
TCGA-2G-AAFJ TCGA-2G-AAG5 TCGA-2G-AAG7 TCGA-2G-AAGO TCGA-2G-AAGV TCGA-2G-AAH3 
       14.56        71.24        61.71       115.00       128.94        59.90 
TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAL5 TCGA-2X-A9D5 
      125.69        59.80       176.15         6.08       184.41         2.73 
TCGA-S6-A8JY TCGA-SN-A84W TCGA-SO-A8JP TCGA-W4-A7U2 TCGA-XE-AANI TCGA-XE-AANJ 
        9.14         9.63         3.52        41.52        34.22        65.98 
TCGA-XE-AAOJ TCGA-XY-A8S3 TCGA-YU-A912 TCGA-YU-A94I TCGA-ZM-AA0N 
       50.96        20.12         5.29         7.96        10.85 

$`XP LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        36.99        14.14        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       52.37        72.20        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW 
       59.64       106.39       120.62        59.28       124.57        61.45 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH8 
      170.33        80.94        60.16        60.26        59.84        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAKD TCGA-2G-AAKG 
       98.53        59.74        59.80        91.43       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 
      161.72        95.67       229.22       131.21        70.59         0.13 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
        3.52         7.00         0.10         4.83        20.68        18.15 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 
       13.58         1.38        16.31        10.26        17.23        37.18 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       36.79        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
        4.90        24.26         3.65         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANR TCGA-XE-AANV 
       28.14         6.87        18.38        40.01         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A9T9 TCGA-YU-A90P 
       41.69         0.43         8.32        12.92         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-AA4L 
       54.35        31.92        21.96         0.56        58.88        40.96 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
        8.15        37.02        39.35        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H 
       11.34        46.88 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             2.73              0.10 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           184.41            229.22 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            41.52             37.43 
[1] "2.7 - 184.4 (41.5)" "0.1 - 229.2 (37.4)"
[1] "hr="     "8.7e+07"
D73V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP LOSS MUTATED         6        1        1        2         0         0
  XP LOSS WILD-TYPE      13       24       10        3         6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XP LOSS MUTATED           0         0          0          0          1
  XP LOSS WILD-TYPE         1         2          1          6          4
                   vv
clus                STAGE IS
  XP LOSS MUTATED         11
  XP LOSS WILD-TYPE       35
D73V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                  6                13
  STAGE IA                 1                24
  STAGE IB                 1                10
  STAGE II                 2                 3
  STAGE IIA                0                 6
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               1                 4
  STAGE IS                11                35
[1] 12  2
[1] 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
  XP LOSS MUTATED   15  8  0
  XP LOSS WILD-TYPE 60 43  6
D73V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1              15                60
  T2               8                43
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  XP LOSS MUTATED    9     0
  XP LOSS WILD-TYPE 37    13
D73V5, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  N0                  9                37
  N1+N2               0                13
[1] 2 2
[1] FALSE
D73V6, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   20  0
  XP LOSS WILD-TYPE 94  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     20    0
  XP LOSS WILD-TYPE   94    4
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              20                94
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       1                         1    20
  XP LOSS WILD-TYPE     3                         5    98
D73V7, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  20                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V8, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    3 18
  XP LOSS WILD-TYPE  8 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      3   18
  XP LOSS WILD-TYPE    8   93
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              18                93
[1] 2 2
[1] FALSE

Clustering(74) Variable = XQ LOSS MUTATION ANALYSIS
D74V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    23   0
  XQ LOSS WILD-TYPE 106   4
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               23               110 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                0                 4 
$`XQ LOSS MUTATED`
TCGA-2G-AAFJ TCGA-2G-AAG7 TCGA-2G-AAGV TCGA-2G-AAGY TCGA-2G-AAH3 TCGA-2G-AAH4 
       14.56        61.71       128.94        80.94        59.90       125.69 
TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 
       59.80       176.15         6.08       184.41        70.59         2.73 
TCGA-S6-A8JY TCGA-SN-A84W TCGA-SO-A8JP TCGA-W4-A7U2 TCGA-XE-AANI TCGA-XE-AANJ 
        9.14         9.63         3.52        41.52        34.22        65.98 
TCGA-XE-AAOJ TCGA-XY-A8S3 TCGA-YU-A912 TCGA-YU-A94I TCGA-ZM-AA0N 
       50.96        20.12         5.29         7.96        10.85 

$`XQ LOSS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        36.99        14.14        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       52.37        71.24        72.20        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
      124.57        61.45       170.33        60.16        60.26        59.84 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAKD 
       61.84        98.53        59.74        59.80        91.43       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2X-A9D6 
      212.65       161.72        95.67       229.22       131.21         0.13 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
        3.52         7.00         0.10         4.83        20.68        18.15 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 
       13.58         1.38        16.31        10.26        17.23        37.18 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       36.79        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
        4.90        24.26         3.65         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANR TCGA-XE-AANV 
       28.14         6.87        18.38        40.01         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A9T9 TCGA-YU-A90P 
       41.69         0.43         8.32        12.92         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-AA4L 
       54.35        31.92        21.96         0.56        58.88        40.96 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
        8.15        37.02        39.35        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H 
       11.34        46.88 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             2.73              0.10 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           184.41            229.22 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            41.52             37.43 
[1] "2.7 - 184.4 (41.5)" "0.1 - 229.2 (37.4)"
[1] "hr="     "8.7e+07"
D74V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED         6        1        1        2         0         0
  XQ LOSS WILD-TYPE      13       24       10        3         6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ LOSS MUTATED           0         0          0          1          1
  XQ LOSS WILD-TYPE         1         2          1          5          4
                   vv
clus                STAGE IS
  XQ LOSS MUTATED         10
  XQ LOSS WILD-TYPE       36
D74V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  6                13
  STAGE IA                 1                24
  STAGE IB                 1                10
  STAGE II                 2                 3
  STAGE IIA                0                 6
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               1                 5
  STAGE IIIC               1                 4
  STAGE IS                10                36
[1] 12  2
[1] 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
  XQ LOSS MUTATED   16  7  0
  XQ LOSS WILD-TYPE 59 44  6
D74V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              16                59
  T2               7                44
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  XQ LOSS MUTATED    8     0
  XQ LOSS WILD-TYPE 38    13
D74V5, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0                  8                38
  N1+N2               0                13
[1] 2 2
[1] FALSE
D74V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   19  1
  XQ LOSS WILD-TYPE 95  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     19    1
  XQ LOSS WILD-TYPE   95    3
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              19                95
  1               1                 3
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       1                         1    20
  XQ LOSS WILD-TYPE     3                         5    98
D74V7, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  20                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V8, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    3 18
  XQ LOSS WILD-TYPE  8 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3   18
  XQ LOSS WILD-TYPE    8   93
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              18                93
[1] 2 2
[1] FALSE
