[1] "ofn"        "-oTMESO-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/MESO-TP/15084766/MESO-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/MESO-TP/15089879/transformed.cor.cli.txt"

nPatients in clinical file=77, in cluster file=87, common to both=77
[1] "Reduce the number of clustering variables from 82 to 73."
[1] 73 77
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                69 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                69 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               18                59 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               18                59 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                4                73 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                4                73 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                71 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                71 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17                60 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17                60 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               19                58 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               19                58 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               19                58 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               19                58 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12                65 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12                65 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                71 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                71 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                73 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                73 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               22                55 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               22                55 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               19                58 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               19                58 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               11                66 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               11                66 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12                65 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12                65 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                74 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                74 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 74 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 74 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                 74 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                 74 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                11                 66 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                11                 66 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                11                 66 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                11                 66 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                18                 59 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                18                 59 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                 59 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                 59 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 4                 73 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 4                 73 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                 67 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                 67 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                 61 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                 61 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                15                 62 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                15                 62 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 6                 71 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 6                 71 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                 61 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                 61 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                 70 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                 70 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 73 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 73 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                13                 64 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                13                 64 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                 68 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                 68 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                 69 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                 69 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                 67 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                 67 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 72 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 72 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                7                70 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                7                70 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                71 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                71 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                8                69 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                8                69 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                74 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                74 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                74 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                74 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                72 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                72 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                74 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                74 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               29                48 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               29                48 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               30                47 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               30                47 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                74 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                74 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8                69 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8                69 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9                68 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9                68 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               26                51 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               26                51 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10                67 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10                67 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                73 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                73 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               26                51 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               26                51 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               18                59 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               18                59 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                22                 55 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                22                 55 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                17                 60 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                17                 60 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 4                 73 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 4                 73 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 72 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 72 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 74 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 74 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                32                 45 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                32                 45 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                31                 46 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                31                 46 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                10                 67 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                10                 67 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 7                 70 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 7                 70 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                 67 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                 67 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                21                 56 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                21                 56 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                 70 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                 70 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 8                 69 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 8                 69 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                14                 63 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                14                 63 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 74 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 74 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 6                 71 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 6                 71 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                14                 63 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                14                 63 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 74 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 74 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                10                 67 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                10                 67 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                59                 18 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                59                 18 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               22                55 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               22                55 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               23                54 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               23                54 
[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] "KARNOFSKY_PERFORMANCE_SCORE"           
[13] "RADIATIONS_RADIATION_REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCH_NUMBER"                          

Input Data has 16 rows and 77 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=63,	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=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
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:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'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 14:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RACE excluded in the analysis because there is no case of (both >= 3) in the table below"
              ASIAN   BLACK OR AFRICAN AMERICAN WHITE  
freq.values   "1"     "1"                       "75"   
freq.contrast "76"    "76"                      "2"    
both >= 3     "FALSE" "FALSE"                   "FALSE"
Variable 15:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'BATCH_NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 77 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"      
[3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
[5] "PATHOLOGY_M_STAGE"           "GENDER"                     
[7] "KARNOFSKY_PERFORMANCE_SCORE"
YEARS_TO_BIRTH, nv=34, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
14 25 28  8 
[1] "table(vv)"
vv
T1 T2 T3 T4 
14 25 28  8 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
14 25 28  8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
14 25 28  8 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
42 10 19  2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
   42    10    21 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 N3 
42 10 19  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
   42    10    21 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=4, binary=FALSE, numeric=TRUE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    0  8
  1P GAIN WILD-TYPE 11 57
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                68 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                57 
$`1P GAIN MUTATED`
TCGA-3H-AB3U TCGA-LK-A4O0 TCGA-SH-A7BC TCGA-SH-A7BH TCGA-UD-AAC5 TCGA-UD-AAC6 
       27.16         6.08        23.90         7.99         8.32        14.99 
TCGA-UD-AAC7 TCGA-YS-A95B 
       13.35         1.28 

$`1P GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 
       26.40        17.95         5.52         8.02         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       66.54        62.27        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-SH-A9CT 
        2.56         9.76        29.42        17.72        15.09        14.76 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       14.76        55.07         8.38        27.75        41.46        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF 
       22.65         9.30        19.43        15.02        32.28        11.77 
TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       10.78        26.14         1.55        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G 
       25.94        23.64        23.77        21.44        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.73         4.67         4.37         2.76        16.41        33.70 
TCGA-ZN-A9VU TCGA-ZN-A9VW 
       24.30         2.76 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.28              0.66 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            27.16             91.73 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           10.835            15.915 
[1] "1.3 - 27.2 (10.8)" "0.7 - 91.7 (15.9)"
[1] "hr=" "2"  
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         1        1        0        2         3        1
  1P GAIN WILD-TYPE       6        1        1       14        37       10
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 1                 6
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                2                14
  STAGE III               3                37
  STAGE IV                1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1P GAIN MUTATED    2  2  3  1
  1P GAIN WILD-TYPE 12 23 25  7
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               2                12
  T2               2                23
  T3               3                25
  T4               1                 7
[1] 4 2
[1] 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+N3
  1P GAIN MUTATED    6  0     2
  1P GAIN WILD-TYPE 36 10    19
D1V5, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0                  6                36
  N1                  0                10
  N2+N3               2                19
[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"
D1V6, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    8  0
  1P GAIN WILD-TYPE 41  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8    0
  1P GAIN WILD-TYPE   41    2
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               8                41
  1               0                 2
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    2  6
  1P GAIN WILD-TYPE 13 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    6
  1P GAIN WILD-TYPE   13   56
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               2                13
  MALE                 6                56
[1] 2 2
[1] FALSE
D1V8, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                 5 
       TCGA-SC-A6LR        TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ZN-A9VU 
"1P GAIN WILD-TYPE" 

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    1 17
  1Q GAIN WILD-TYPE 10 48
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               18                58 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               17                48 
$`1Q GAIN MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O6 
       29.10        27.16        26.40         8.02         6.08        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BH 
       11.51        18.81        23.31        13.61        23.90         7.99 
TCGA-SH-A9CT TCGA-TS-A7PB TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-YS-A95B 
       14.76        32.28         6.48         8.32        13.35         1.28 

$`1Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-LK-A4NW 
       56.38        11.87        42.81        12.66        13.61        17.95 
TCGA-LK-A4NY TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        5.52         1.87        31.20        12.72        80.84        91.73 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        66.54 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ 
       62.27        19.99         0.66        28.96         2.56         9.76 
TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       29.42        17.72        15.09        14.76        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
       27.75        41.46        18.51        22.65         9.30        19.43 
TCGA-TS-A7P8 TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY 
       15.02        11.77        10.78        26.14         1.55        15.42 
TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D 
       27.72        25.94        23.64        14.99        23.77        21.44 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M 
       14.27         2.50         4.73         4.67         4.37         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       16.41        33.70        24.30         2.76 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1.28              0.66 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            32.28             91.73 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           14.170            15.915 
[1] "1.3 - 32.3 (14.2)" "0.7 - 91.7 (15.9)"
[1] "hr=" "1.5"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         1        1        0        5        10        1
  1Q GAIN WILD-TYPE       6        1        1       11        30       10
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 1                 6
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                5                11
  STAGE III              10                30
  STAGE IV                1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1Q GAIN MUTATED    2  7  8  1
  1Q GAIN WILD-TYPE 12 18 20  7
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               2                12
  T2               7                18
  T3               8                20
  T4               1                 7
[1] 4 2
[1] 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+N3
  1Q GAIN MUTATED   10  3     5
  1Q GAIN WILD-TYPE 32  7    16
D2V5, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0                 10                32
  N1                  3                 7
  N2+N3               5                16
[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"
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   17  0
  1Q GAIN WILD-TYPE 32  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     17    0
  1Q GAIN WILD-TYPE   32    2
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              17                32
  1               0                 2
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    5 13
  1Q GAIN WILD-TYPE 10 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5   13
  1Q GAIN WILD-TYPE   10   49
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               5                10
  MALE                13                49
[1] 2 2
[1] FALSE
D2V8, continuous
[1] "Remove cluster labels:" "1Q GAIN MUTATED"       
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                1                 5 
       TCGA-SC-A6LR        TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VS 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-ZN-A9VU 
"1Q GAIN WILD-TYPE" 

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    1  3
  2P GAIN WILD-TYPE 10 62
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                4                72 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3                62 
$`2P GAIN MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4O0 TCGA-SH-A9CU 
       29.10        27.16         6.08        14.76 

$`2P GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X 
       56.38        11.87        42.81        12.66        13.61        26.40 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        66.54 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       62.27        19.99         0.66        28.96        13.61         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
        9.76        29.42        17.72        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       14.76        55.07         8.38        27.75        41.46        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF 
       22.65         9.30        19.43        15.02        32.28        11.77 
TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       10.78        26.14         1.55        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       25.94        23.64         8.32        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       21.44        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        33.70        24.30         2.76 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             6.08              0.66 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            29.10             91.73 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           20.960            15.055 
[1] "6.1 - 29.1 (21.0)" "0.7 - 91.7 (15.1)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  2P GAIN MUTATED         0        1        0        0         2        1
  2P GAIN WILD-TYPE       7        1        1       16        38       10
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                0                16
  STAGE III               2                38
  STAGE IV                1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2P GAIN MUTATED    1  0  2  1
  2P GAIN WILD-TYPE 13 25 26  7
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               1                13
  T2               0                25
  T3               2                26
  T4               1                 7
[1] 4 2
[1] 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+N3
  2P GAIN MUTATED    2  0     2
  2P GAIN WILD-TYPE 40 10    19
D3V5, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0                  2                40
  N1                  0                10
  N2+N3               2                19
[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"
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    4  0
  2P GAIN WILD-TYPE 45  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4    0
  2P GAIN WILD-TYPE   45    2
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               4                45
  1               0                 2
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    1  3
  2P GAIN WILD-TYPE 14 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1    3
  2P GAIN WILD-TYPE   14   59
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               1                14
  MALE                 3                59
[1] 2 2
[1] FALSE
D3V8, continuous

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    1  5
  2Q GAIN WILD-TYPE 10 60
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                70 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                5                60 
$`2Q GAIN MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4O0 TCGA-MQ-A6BS TCGA-SH-A9CU TCGA-TS-A7OU 
       29.10        27.16         6.08        19.99        14.76        55.07 

$`2Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X 
       56.38        11.87        42.81        12.66        13.61        26.40 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        66.54 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       62.27         0.66        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
       29.42        17.72        23.90        15.09         7.99        14.76 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
        8.38        27.75        41.46        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS 
       19.43        15.02        32.28        11.77        10.78        26.14 
TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 
        1.55        15.42        27.72         6.48        25.94        23.64 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E 
        8.32        14.99        13.35        23.77        21.44        14.27 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
        2.50         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       16.41        33.70        24.30         2.76 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             6.08              0.66 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            55.07             91.73 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           23.575            15.005 
[1] "6.1 - 55.1 (23.6)" "0.7 - 91.7 (15.0)"
[1] "hr=" "1.4"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED         0        1        0        1         2        2
  2Q GAIN WILD-TYPE       7        1        1       15        38        9
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               2                38
  STAGE IV                2                 9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2Q GAIN MUTATED    1  1  2  2
  2Q GAIN WILD-TYPE 13 24 26  6
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               1                13
  T2               1                24
  T3               2                26
  T4               2                 6
[1] 4 2
[1] 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+N3
  2Q GAIN MUTATED    4  0     2
  2Q GAIN WILD-TYPE 38 10    19
D4V5, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0                  4                38
  N1                  0                10
  N2+N3               2                19
[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"
D4V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    4  0
  2Q GAIN WILD-TYPE 45  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4    0
  2Q GAIN WILD-TYPE   45    2
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               4                45
  1               0                 2
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    1  5
  2Q GAIN WILD-TYPE 14 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1    5
  2Q GAIN WILD-TYPE   14   57
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               1                14
  MALE                 5                57
[1] 2 2
[1] FALSE
D4V8, continuous

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    3 14
  3P GAIN WILD-TYPE  8 51
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17                59 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               14                51 
$`3P GAIN MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-LK-A4O6 
       11.87        29.10        27.16         6.08        12.72        14.73 
TCGA-MQ-A6BS TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BH TCGA-TS-A7P6 
       19.99        29.42        17.72        23.90         7.99         9.30 
TCGA-TS-A8AS TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       26.14        14.99        13.35        23.77         2.50 

$`3P GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X TCGA-LK-A4NW 
       56.38        42.81        12.66        13.61        26.40        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        5.52         8.02         1.87        31.20        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM 
       10.95        24.89        66.54        62.27         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU 
       13.61         2.56         9.76        15.09        14.76        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AV 
       19.43        15.02        32.28        11.77        10.78         1.55 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 
       15.42        27.72         6.48        25.94        23.64         8.32 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       21.44        14.27         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        2.76        16.41        33.70        24.30         2.76 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             2.50              0.66 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            29.42             91.73 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            14.99             15.09 
[1] "2.5 - 29.4 (15.0)" "0.7 - 91.7 (15.1)"
[1] "hr=" "1.1"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         0        2        0        3        11        1
  3P GAIN WILD-TYPE       7        0        1       13        29       10
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                2                 0
  STAGE IB                0                 1
  STAGE II                3                13
  STAGE III              11                29
  STAGE IV                1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3P GAIN MUTATED    3  3  9  1
  3P GAIN WILD-TYPE 11 22 19  7
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               3                11
  T2               3                22
  T3               9                19
  T4               1                 7
[1] 4 2
[1] 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+N3
  3P GAIN MUTATED    9  1     7
  3P GAIN WILD-TYPE 33  9    14
D5V5, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0                  9                33
  N1                  1                 9
  N2+N3               7                14
[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"
D5V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   14  0
  3P GAIN WILD-TYPE 35  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     14    0
  3P GAIN WILD-TYPE   35    2
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              14                35
  1               0                 2
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    4 13
  3P GAIN WILD-TYPE 11 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4   13
  3P GAIN WILD-TYPE   11   49
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               4                11
  MALE                13                49
[1] 2 2
[1] FALSE
D5V8, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                 4 
       TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    3 16
  3Q GAIN WILD-TYPE  8 49
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               19                57 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               16                49 
$`3Q GAIN MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       11.87        29.10        27.16         6.08         1.87        12.72 
TCGA-LK-A4O6 TCGA-MQ-A6BS TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BH 
       14.73        19.99        29.42        17.72        23.90         7.99 
TCGA-SH-A9CT TCGA-TS-A7P6 TCGA-TS-A8AS TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       14.76         9.30        26.14        14.99        13.35        23.77 
TCGA-UT-A88G 
        2.50 

$`3Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X TCGA-LK-A4NW 
       56.38        42.81        12.66        13.61        26.40        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        5.52         8.02        31.20        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       24.89        66.54        62.27         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BD TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
        2.56         9.76        15.09        14.76        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 
       27.75        41.46        18.51        22.65        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       32.28        11.77        10.78         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UT-A88D TCGA-UT-A88E 
        6.48        25.94        23.64         8.32        21.44        14.27 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ 
        4.73         4.67         1.28         4.37         2.76        16.41 
TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       33.70        24.30         2.76 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             1.87              0.66 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            29.42             91.73 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            14.76             15.42 
[1] "1.9 - 29.4 (14.8)" "0.7 - 91.7 (15.4)"
[1] "hr=" "1.3"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED         0        2        0        4        12        1
  3Q GAIN WILD-TYPE       7        0        1       12        28       10
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                2                 0
  STAGE IB                0                 1
  STAGE II                4                12
  STAGE III              12                28
  STAGE IV                1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED    3  4 10  1
  3Q GAIN WILD-TYPE 11 21 18  7
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               3                11
  T2               4                21
  T3              10                18
  T4               1                 7
[1] 4 2
[1] 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+N3
  3Q GAIN MUTATED   11  1     7
  3Q GAIN WILD-TYPE 31  9    14
D6V5, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0                 11                31
  N1                  1                 9
  N2+N3               7                14
[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"
D6V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   16  0
  3Q GAIN WILD-TYPE 33  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     16    0
  3Q GAIN WILD-TYPE   33    2
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              16                33
  1               0                 2
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    5 14
  3Q GAIN WILD-TYPE 10 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5   14
  3Q GAIN WILD-TYPE   10   48
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               5                10
  MALE                14                48
[1] 2 2
[1] FALSE
D6V8, continuous
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 4 
       TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 

Clustering(7) Variable = 5P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    4 14
  5P GAIN WILD-TYPE  7 51
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               18                58 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               14                51 
$`5P GAIN MUTATED`
TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O7 TCGA-MQ-A4LP 
       27.16        17.95         6.08         1.87        11.51        17.33 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BH 
       62.27        19.99         2.56        29.42        17.72         7.99 
TCGA-SH-A9CU TCGA-TS-A7P1 TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-YS-A95C 
       14.76        18.51         6.48        25.94         8.32         4.37 

$`5P GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3X TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 
       26.40         5.52         8.02        31.20        12.72        14.73 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV 
       80.84        91.73        18.81        23.31         5.19         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       10.95        24.89        66.54         0.66        28.96        13.61 
TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY 
        9.76        23.90        15.09        14.76        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       27.75        41.46        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY 
       32.28        11.77        10.78        26.14         1.55        15.42 
TCGA-UD-AABY TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D 
       27.72        23.64        14.99        13.35        23.77        21.44 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-AA4M 
       14.27         2.50         4.73         4.67         1.28         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       16.41        33.70        24.30         2.76 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             1.87              0.66 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            62.27             91.73 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           16.045            15.055 
[1] "1.9 - 62.3 (16.0)" "0.7 - 91.7 (15.1)"
[1] "hr=" "1.1"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  5P GAIN MUTATED         2        1        0        4         9        3
  5P GAIN WILD-TYPE       5        1        1       12        31        8
D7V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 2                 5
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                4                12
  STAGE III               9                31
  STAGE IV                3                 8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5P GAIN MUTATED    6  5  5  3
  5P GAIN WILD-TYPE  8 20 23  5
D7V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               6                 8
  T2               5                20
  T3               5                23
  T4               3                 5
[1] 4 2
[1] 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+N3
  5P GAIN MUTATED   10  2     6
  5P GAIN WILD-TYPE 32  8    15
D7V5, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0                 10                32
  N1                  2                 8
  N2+N3               6                15
[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"
D7V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   15  0
  5P GAIN WILD-TYPE 34  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     15    0
  5P GAIN WILD-TYPE   34    2
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              15                34
  1               0                 2
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    4 15
  5P GAIN WILD-TYPE 11 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4   15
  5P GAIN WILD-TYPE   11   47
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               4                11
  MALE                15                47
[1] 2 2
[1] FALSE
D7V8, continuous
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                 4 
       TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 

Clustering(8) Variable = 5Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    3  8
  5Q GAIN WILD-TYPE  8 57
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               11                65 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8                57 
$`5Q GAIN MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SC-AA5Z 
        6.08        62.27        19.99         2.56        29.42        17.72 
TCGA-SH-A7BH TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-YS-A95C 
        7.99         6.48        25.94         8.32         4.37 

$`5Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 
       27.16        26.40        17.95         5.52         8.02         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LQ 
       24.89        66.54         0.66        28.96        13.61         9.76 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       23.90        15.09        14.76        14.76        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
       27.75        41.46        18.51        22.65         9.30        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV 
       15.02        32.28        11.77        10.78        26.14         1.55 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       15.42        27.72        23.64        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       21.44        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        2.76        16.41        33.70        24.30         2.76 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             2.56              0.66 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            62.27             91.73 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             8.32             15.09 
[1] "2.6 - 62.3 (8.3)"  "0.7 - 91.7 (15.1)"
[1] "hr=" "1"  
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED         1        1        0        4         5        1
  5Q GAIN WILD-TYPE       6        1        1       12        35       10
D8V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 1                 6
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                4                12
  STAGE III               5                35
  STAGE IV                1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5Q GAIN MUTATED    5  5  1  1
  5Q GAIN WILD-TYPE  9 20 27  7
D8V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               5                 9
  T2               5                20
  T3               1                27
  T4               1                 7
[1] 4 2
[1] 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+N3
  5Q GAIN MUTATED    6  1     4
  5Q GAIN WILD-TYPE 36  9    17
D8V5, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0                  6                36
  N1                  1                 9
  N2+N3               4                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    9  0
  5Q GAIN WILD-TYPE 40  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      9    0
  5Q GAIN WILD-TYPE   40    2
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               9                40
  1               0                 2
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    3  9
  5Q GAIN WILD-TYPE 12 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    9
  5Q GAIN WILD-TYPE   12   53
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               3                12
  MALE                 9                53
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                 4 
       TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 

Clustering(9) Variable = 6P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    3  3
  6P GAIN WILD-TYPE  8 62
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                70 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                62 
$`6P GAIN MUTATED`
TCGA-3H-AB3M TCGA-MQ-A6BS TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A9CU TCGA-UD-AAC6 
       29.10        19.99        29.42        17.72        14.76        14.99 

$`6P GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        11.87        42.81        12.66        13.61        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       26.40        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       24.89        66.54        62.27         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
        2.56         9.76        23.90        15.09         7.99        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       26.14         1.55        15.42        27.72         6.48        25.94 
TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E 
       23.64         8.32        13.35        23.77        21.44        14.27 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
        2.50         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       16.41        33.70        24.30         2.76 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            14.76              0.66 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            29.42             91.73 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           18.855            14.890 
[1] "14.8 - 29.4 (18.9)" "0.7 - 91.7 (14.9)" 
[1] "hr=" "2.1"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         0        0        0        2         2        2
  6P GAIN WILD-TYPE       7        2        1       14        38        9
D9V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                2                14
  STAGE III               2                38
  STAGE IV                2                 9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6P GAIN MUTATED    1  2  1  2
  6P GAIN WILD-TYPE 13 23 27  6
D9V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               1                13
  T2               2                23
  T3               1                27
  T4               2                 6
[1] 4 2
[1] 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+N3
  6P GAIN MUTATED    2  0     4
  6P GAIN WILD-TYPE 40 10    17
D9V5, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0                  2                40
  N1                  0                10
  N2+N3               4                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    5  0
  6P GAIN WILD-TYPE 44  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    0
  6P GAIN WILD-TYPE   44    2
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               5                44
  1               0                 2
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    1  5
  6P GAIN WILD-TYPE 14 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1    5
  6P GAIN WILD-TYPE   14   57
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               1                14
  MALE                 5                57
[1] 2 2
[1] FALSE
D9V8, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                 5 
       TCGA-SH-A7BH        TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VS 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ZN-A9VU 
"6P GAIN WILD-TYPE" 

Clustering(10) Variable = 6Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    2  2
  6Q GAIN WILD-TYPE  9 63
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                72 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                63 
$`6Q GAIN MUTATED`
TCGA-MQ-A6BS TCGA-SC-AA5Z TCGA-SH-A9CU TCGA-UD-AAC6 
       19.99        17.72        14.76        14.99 

$`6Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 
       27.16        26.40        17.95         5.52         8.02         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        1.87        31.20        12.72        14.73        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM 
       10.95        24.89        66.54        62.27         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD 
       13.61         2.56         9.76        29.42        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
        7.99        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88C 
        6.48        25.94        23.64         8.32        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       21.44        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        33.70        24.30         2.76 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            14.76              0.66 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            19.99             91.73 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           16.355            15.055 
[1] "14.8 - 20.0 (16.4)" "0.7 - 91.7 (15.1)" 
[1] "hr=" "1.5"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         0        0        0        2         0        2
  6Q GAIN WILD-TYPE       7        2        1       14        40        9
D10V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                2                14
  STAGE III               0                40
  STAGE IV                2                 9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6Q GAIN MUTATED    0  2  0  2
  6Q GAIN WILD-TYPE 14 23 28  6
D10V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               0                14
  T2               2                23
  T3               0                28
  T4               2                 6
[1] 4 2
[1] 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+N3
  6Q GAIN MUTATED    2  0     2
  6Q GAIN WILD-TYPE 40 10    19
D10V5, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0                  2                40
  N1                  0                10
  N2+N3               2                19
[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"
D10V6, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    3  0
  6Q GAIN WILD-TYPE 46  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    0
  6Q GAIN WILD-TYPE   46    2
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               3                46
  1               0                 2
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    0  4
  6Q GAIN WILD-TYPE 15 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    4
  6Q GAIN WILD-TYPE   15   58
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               0                15
  MALE                 4                58
[1] 2 2
[1] FALSE
D10V8, continuous

Clustering(11) Variable = 7P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED    4 17
  7P GAIN WILD-TYPE  7 48
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               21                55 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               17                48 
$`7P GAIN MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O2 
       11.87        29.10        27.16        17.95         6.08         1.87 
TCGA-MQ-A6BS TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BH 
       19.99         9.76        29.42        17.72        23.90         7.99 
TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A8AF TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UD-AAC7 
       14.76        41.46        11.77        25.94        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88G TCGA-YS-A95C 
       23.77         2.50         4.37 

$`7P GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X TCGA-LK-A4NY 
       56.38        42.81        12.66        13.61        26.40         5.52 
TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        8.02        31.20        12.72        14.73        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM 
       10.95        24.89        66.54        62.27         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY 
       13.61         2.56        15.09        14.76        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       27.75        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       32.28        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y 
        6.48        23.64         8.32        21.44        14.27         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        4.67         1.28         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             1.87              0.66 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            41.46             91.73 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            14.99             15.09 
[1] "1.9 - 41.5 (15.0)" "0.7 - 91.7 (15.1)"
[1] "hr=" "1.1"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  7P GAIN MUTATED         0        1        0        4        14        3
  7P GAIN WILD-TYPE       7        1        1       12        26        8
D11V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                4                12
  STAGE III              14                26
  STAGE IV                3                 8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED    3  6  9  3
  7P GAIN WILD-TYPE 11 19 19  5
D11V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               3                11
  T2               6                19
  T3               9                19
  T4               3                 5
[1] 4 2
[1] 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+N3
  7P GAIN MUTATED    9  0    12
  7P GAIN WILD-TYPE 33 10     9
D11V5, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0                  9                33
  N1                  0                10
  N2+N3              12                 9
[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"
D11V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   18  0
  7P GAIN WILD-TYPE 31  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     18    0
  7P GAIN WILD-TYPE   31    2
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              18                31
  1               0                 2
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    5 17
  7P GAIN WILD-TYPE 10 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5   17
  7P GAIN WILD-TYPE   10   45
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               5                10
  MALE                17                45
[1] 2 2
[1] FALSE
D11V8, continuous
[1] "Remove cluster labels:" "7P GAIN MUTATED"       
clus
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                2                 4 
       TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 

Clustering(12) Variable = 7Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED    4 15
  7Q GAIN WILD-TYPE  7 50
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               19                57 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               15                50 
$`7Q GAIN MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-MQ-A6BS 
       11.87        29.10        27.16        17.95         1.87        19.99 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CU 
        9.76        29.42        17.72        23.90         7.99        14.76 
TCGA-TS-A8AF TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       11.77        25.94        14.99        13.35        23.77         2.50 
TCGA-YS-A95C 
        4.37 

$`7Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X TCGA-LK-A4NY 
       56.38        42.81        12.66        13.61        26.40         5.52 
TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
        8.02         6.08        31.20        12.72        14.73        11.51 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       80.84        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
        3.52        10.95        24.89        66.54        62.27         0.66 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU 
       28.96        13.61         2.56        15.09        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
        8.38        27.75        41.46        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV 
       19.43        15.02        32.28        10.78        26.14         1.55 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UT-A88D 
       15.42        27.72         6.48        23.64         8.32        21.44 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VQ 
       14.27         4.73         4.67         1.28         2.76        16.41 
TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       33.70        24.30         2.76 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             1.87              0.66 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            29.42             91.73 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            14.99             15.09 
[1] "1.9 - 29.4 (15.0)" "0.7 - 91.7 (15.1)"
[1] "hr=" "1.2"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED         0        0        0        3        13        3
  7Q GAIN WILD-TYPE       7        2        1       13        27        8
D12V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                3                13
  STAGE III              13                27
  STAGE IV                3                 8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7Q GAIN MUTATED    2  5  8  3
  7Q GAIN WILD-TYPE 12 20 20  5
D12V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               2                12
  T2               5                20
  T3               8                20
  T4               3                 5
[1] 4 2
[1] 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+N3
  7Q GAIN MUTATED    7  0    12
  7Q GAIN WILD-TYPE 35 10     9
D12V5, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0                  7                35
  N1                  0                10
  N2+N3              12                 9
[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"
D12V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   17  0
  7Q GAIN WILD-TYPE 32  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     17    0
  7Q GAIN WILD-TYPE   32    2
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              17                32
  1               0                 2
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    5 14
  7Q GAIN WILD-TYPE 10 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5   14
  7Q GAIN WILD-TYPE   10   48
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               5                10
  MALE                14                48
[1] 2 2
[1] FALSE
D12V8, continuous
[1] "Remove cluster labels:" "7Q GAIN MUTATED"       
clus
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                2                 4 
       TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 

Clustering(13) Variable = 8P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    2  9
  8P GAIN WILD-TYPE  9 56
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               11                65 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                9                56 
$`8P GAIN MUTATED`
TCGA-3H-AB3U TCGA-LK-A4NW TCGA-MQ-A4LM TCGA-SC-A6LR TCGA-SH-A7BH TCGA-TS-A7P0 
       27.16        17.95         5.19        29.42         7.99        41.46 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G TCGA-XT-AASU TCGA-ZN-A9VW 
       13.35        23.77         2.50         4.67         2.76 

$`8P GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3X TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       26.40         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       23.31        17.33         3.52        10.95        24.89        66.54 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       62.27        19.99         0.66        28.96        13.61         2.56 
TCGA-SC-A6LQ TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU 
        9.76        17.72        23.90        15.09        14.76        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
       55.07         8.38        27.75        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS 
       19.43        15.02        32.28        11.77        10.78        26.14 
TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 
        1.55        15.42        27.72         6.48        25.94        23.64 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-YS-A95B 
        8.32        14.99        21.44        14.27         4.73         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        4.37         2.76        16.41        33.70        24.30 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             2.50              0.66 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            41.46             91.73 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            13.35             15.09 
[1] "2.5 - 41.5 (13.3)" "0.7 - 91.7 (15.1)"
[1] "hr=" "1.2"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         0        0        0        1         8        2
  8P GAIN WILD-TYPE       7        2        1       15        32        9
D13V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               8                32
  STAGE IV                2                 9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8P GAIN MUTATED    1  1  7  2
  8P GAIN WILD-TYPE 13 24 21  6
D13V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               1                13
  T2               1                24
  T3               7                21
  T4               2                 6
[1] 4 2
[1] 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+N3
  8P GAIN MUTATED    7  0     3
  8P GAIN WILD-TYPE 35 10    18
D13V5, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0                  7                35
  N1                  0                10
  N2+N3               3                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"
D13V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    8  0
  8P GAIN WILD-TYPE 41  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      8    0
  8P GAIN WILD-TYPE   41    2
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               8                41
  1               0                 2
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    1 10
  8P GAIN WILD-TYPE 14 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   10
  8P GAIN WILD-TYPE   14   52
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               1                14
  MALE                10                52
[1] 2 2
[1] FALSE
D13V8, continuous

Clustering(14) Variable = 8Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED    3  9
  8Q GAIN WILD-TYPE  8 56
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12                64 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                9                56 
$`8Q GAIN MUTATED`
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-MQ-A4LM TCGA-NQ-A57I TCGA-SC-A6LR 
       27.16        26.40        17.95         5.19         0.66        29.42 
TCGA-SH-A7BH TCGA-TS-A7P0 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G TCGA-XT-AASU 
        7.99        41.46        13.35        23.77         2.50         4.67 

$`8Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
        5.52         8.02         6.08         1.87        31.20        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        66.54        62.27 
TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-AA5Z 
       19.99        28.96        13.61         2.56         9.76        17.72 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       23.90        15.09        14.76        14.76        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       27.75        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY 
       32.28        11.77        10.78        26.14         1.55        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 
       27.72         6.48        25.94        23.64         8.32        14.99 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
       21.44        14.27         4.73         1.28         4.37         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       16.41        33.70        24.30         2.76 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.66              1.28 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            41.46             91.73 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           15.650            15.055 
[1] "0.7 - 41.5 (15.6)" "1.3 - 91.7 (15.1)"
[1] "hr=" "1"  
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         0        0        1        1         9        1
  8Q GAIN WILD-TYPE       7        2        0       15        31       10
D14V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                1                 0
  STAGE II                1                15
  STAGE III               9                31
  STAGE IV                1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED    2  1  8  1
  8Q GAIN WILD-TYPE 12 24 20  7
D14V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               2                12
  T2               1                24
  T3               8                20
  T4               1                 7
[1] 4 2
[1] 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+N3
  8Q GAIN MUTATED    7  0     3
  8Q GAIN WILD-TYPE 35 10    18
D14V5, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0                  7                35
  N1                  0                10
  N2+N3               3                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"
D14V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    9  0
  8Q GAIN WILD-TYPE 40  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      9    0
  8Q GAIN WILD-TYPE   40    2
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0               9                40
  1               0                 2
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    1 11
  8Q GAIN WILD-TYPE 14 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   11
  8Q GAIN WILD-TYPE   14   51
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               1                14
  MALE                11                51
[1] 2 2
[1] FALSE
D14V8, continuous

Clustering(15) Variable = 9Q GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    0  3
  9Q GAIN WILD-TYPE 11 62
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                73 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                62 
$`9Q GAIN MUTATED`
TCGA-TS-A8AF TCGA-UD-AAC5 TCGA-ZN-A9VW 
       11.77         8.32         2.76 

$`9Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 
       27.16        26.40        17.95         5.52         8.02         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        1.87        31.20        12.72        14.73        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I 
       10.95        24.89        66.54        62.27        19.99         0.66 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z 
       28.96        13.61         2.56         9.76        29.42        17.72 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU 
       23.90        15.09         7.99        14.76        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
        8.38        27.75        41.46        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV 
       19.43        15.02        32.28        10.78        26.14         1.55 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC6 
       15.42        27.72         6.48        25.94        23.64        14.99 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       13.35        23.77        21.44        14.27         2.50         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.67         1.28         4.37         2.76        16.41        33.70 
TCGA-ZN-A9VU 
       24.30 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             2.76              0.66 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            11.77             91.73 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             8.32             15.42 
[1] "2.8 - 11.8 (8.3)"  "0.7 - 91.7 (15.4)"
[1] "hr=" "4.1"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         1        0        0        0         1        1
  9Q GAIN WILD-TYPE       6        2        1       16        39       10
D15V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 1                 6
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                0                16
  STAGE III               1                39
  STAGE IV                1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9Q GAIN MUTATED    1  1  0  1
  9Q GAIN WILD-TYPE 13 24 28  7
D15V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               1                13
  T2               1                24
  T3               0                28
  T4               1                 7
[1] 4 2
[1] 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+N3
  9Q GAIN MUTATED    2  0     1
  9Q GAIN WILD-TYPE 40 10    20
D15V5, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0                  2                40
  N1                  0                10
  N2+N3               1                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"
D15V6, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    1  0
  9Q GAIN WILD-TYPE 48  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1    0
  9Q GAIN WILD-TYPE   48    2
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               1                48
  1               0                 2
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    0  3
  9Q GAIN WILD-TYPE 15 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    3
  9Q GAIN WILD-TYPE   15   59
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               0                15
  MALE                 3                59
[1] 2 2
[1] FALSE
D15V8, continuous

Clustering(16) Variable = 10P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    1  2
  10P GAIN WILD-TYPE 10 63
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 73 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 63 
$`10P GAIN MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A6BN TCGA-SC-AA5Z 
        6.08        24.89        17.72 

$`10P GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 
       27.16        26.40        17.95         5.52         8.02         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       66.54        62.27        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
        2.56         9.76        29.42        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
       14.76        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
        6.48        25.94        23.64         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       23.77        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              6.08               0.66 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             24.89              91.73 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             17.72              15.02 
[1] "6.1 - 24.9 (17.7)" "0.7 - 91.7 (15.0)"
[1] "hr=" "1"  
D16V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         0        1        0        0         1        1
  10P GAIN WILD-TYPE       7        1        1       16        39       10
D16V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 0                 16
  STAGE III                1                 39
  STAGE IV                 1                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10P GAIN MUTATED    1  1  0  1
  10P GAIN WILD-TYPE 13 24 28  7
D16V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                1                 13
  T2                1                 24
  T3                0                 28
  T4                1                  7
[1] 4 2
[1] 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+N3
  10P GAIN MUTATED    1  1     1
  10P GAIN WILD-TYPE 41  9    20
D16V5, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                   1                 41
  N1                   1                  9
  N2+N3                1                 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"
D16V6, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    2  0
  10P GAIN WILD-TYPE 47  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    0
  10P GAIN WILD-TYPE   47    2
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                2                 47
  1                0                  2
[1] 2 2
[1] FALSE
D16V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    1  2
  10P GAIN WILD-TYPE 14 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    2
  10P GAIN WILD-TYPE   14   60
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                1                 14
  MALE                  2                 60
[1] 2 2
[1] FALSE
D16V8, continuous

Clustering(17) Variable = 10Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED    1  2
  10Q GAIN WILD-TYPE 10 63
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                 73 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 63 
$`10Q GAIN MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A6BN TCGA-SC-AA5Z 
        6.08        24.89        17.72 

$`10Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 
       27.16        26.40        17.95         5.52         8.02         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       66.54        62.27        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
        2.56         9.76        29.42        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
       14.76        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
        6.48        25.94        23.64         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       23.77        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              6.08               0.66 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             24.89              91.73 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             17.72              15.02 
[1] "6.1 - 24.9 (17.7)" "0.7 - 91.7 (15.0)"
[1] "hr=" "1"  
D17V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         0        1        0        0         1        1
  10Q GAIN WILD-TYPE       7        1        1       16        39       10
D17V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 0                 16
  STAGE III                1                 39
  STAGE IV                 1                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10Q GAIN MUTATED    1  1  0  1
  10Q GAIN WILD-TYPE 13 24 28  7
D17V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                1                 13
  T2                1                 24
  T3                0                 28
  T4                1                  7
[1] 4 2
[1] 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+N3
  10Q GAIN MUTATED    1  1     1
  10Q GAIN WILD-TYPE 41  9    20
D17V5, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                   1                 41
  N1                   1                  9
  N2+N3                1                 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"
D17V6, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    2  0
  10Q GAIN WILD-TYPE 47  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    0
  10Q GAIN WILD-TYPE   47    2
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                2                 47
  1                0                  2
[1] 2 2
[1] FALSE
D17V7, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    1  2
  10Q GAIN WILD-TYPE 14 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    2
  10Q GAIN WILD-TYPE   14   60
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                1                 14
  MALE                  2                 60
[1] 2 2
[1] FALSE
D17V8, continuous

Clustering(18) Variable = 11P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    3  7
  11P GAIN WILD-TYPE  8 58
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                 66 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 7                 58 
$`11P GAIN MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3U TCGA-MQ-A6BS TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z 
       11.87        27.16        19.99         9.76        29.42        17.72 
TCGA-SH-A9CU TCGA-TS-A7P6 TCGA-TS-A8AF TCGA-UD-AAC7 
       14.76         9.30        11.77        13.35 

$`11P GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X 
       56.38        29.10        42.81        12.66        13.61        26.40 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       66.54        62.27         0.66        28.96        13.61         2.56 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY 
       23.90        15.09         7.99        14.76        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 
       27.75        41.46        18.51        22.65        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       32.28        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C 
        6.48        25.94        23.64         8.32        14.99        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       21.44        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        33.70        24.30         2.76 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              9.30               0.66 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             29.42              91.73 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            14.055             15.255 
[1] "9.3 - 29.4 (14.1)" "0.7 - 91.7 (15.3)"
[1] "hr=" "1"  
D18V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         0        0        0        3         6        2
  11P GAIN WILD-TYPE       7        2        1       13        34        9
D18V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 3                 13
  STAGE III                6                 34
  STAGE IV                 2                  9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11P GAIN MUTATED    1  4  3  2
  11P GAIN WILD-TYPE 13 21 25  6
D18V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                1                 13
  T2                4                 21
  T3                3                 25
  T4                2                  6
[1] 4 2
[1] 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+N3
  11P GAIN MUTATED    3  0     7
  11P GAIN WILD-TYPE 39 10    14
D18V5, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                   3                 39
  N1                   0                 10
  N2+N3                7                 14
[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"
D18V6, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    7  0
  11P GAIN WILD-TYPE 42  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      7    0
  11P GAIN WILD-TYPE   42    2
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                7                 42
  1                0                  2
[1] 2 2
[1] FALSE
D18V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    1 10
  11P GAIN WILD-TYPE 14 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   10
  11P GAIN WILD-TYPE   14   52
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                1                 14
  MALE                 10                 52
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                  5 
        TCGA-SH-A7BH         TCGA-XT-AASU         TCGA-ZN-A9VQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 

Clustering(19) Variable = 11Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    4  6
  11Q GAIN WILD-TYPE  7 59
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                 66 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                 59 
$`11Q GAIN MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3U TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LR TCGA-SC-AA5Z 
       11.87        27.16        62.27        19.99        29.42        17.72 
TCGA-SH-A9CU TCGA-TS-A7P6 TCGA-TS-A8AF TCGA-UD-AAC7 
       14.76         9.30        11.77        13.35 

$`11Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X 
       56.38        29.10        42.81        12.66        13.61        26.40 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       66.54         0.66        28.96        13.61         2.56         9.76 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY 
       23.90        15.09         7.99        14.76        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 
       27.75        41.46        18.51        22.65        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       32.28        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C 
        6.48        25.94        23.64         8.32        14.99        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       21.44        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        33.70        24.30         2.76 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              9.30               0.66 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             62.27              91.73 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            16.240             15.055 
[1] "9.3 - 62.3 (16.2)" "0.7 - 91.7 (15.1)"
[1] "hr=" "1.6"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         0        0        0        3         6        2
  11Q GAIN WILD-TYPE       7        2        1       13        34        9
D19V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 3                 13
  STAGE III                6                 34
  STAGE IV                 2                  9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11Q GAIN MUTATED    2  4  2  2
  11Q GAIN WILD-TYPE 12 21 26  6
D19V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                2                 12
  T2                4                 21
  T3                2                 26
  T4                2                  6
[1] 4 2
[1] 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+N3
  11Q GAIN MUTATED    3  1     6
  11Q GAIN WILD-TYPE 39  9    15
D19V5, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                   3                 39
  N1                   1                  9
  N2+N3                6                 15
[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"
D19V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    6  0
  11Q GAIN WILD-TYPE 43  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    0
  11Q GAIN WILD-TYPE   43    2
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                6                 43
  1                0                  2
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    1 10
  11Q GAIN WILD-TYPE 14 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   10
  11Q GAIN WILD-TYPE   14   52
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                1                 14
  MALE                 10                 52
[1] 2 2
[1] FALSE
D19V8, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                  5 
        TCGA-SH-A7BH         TCGA-XT-AASU         TCGA-ZN-A9VQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 

Clustering(20) Variable = 12P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    2 16
  12P GAIN WILD-TYPE  9 49
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                18                 58 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                16                 49 
$`12P GAIN MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       29.10        27.16        17.95         6.08        12.72        80.84 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A9CU TCGA-TS-A7P6 TCGA-TS-A7P7 
       19.99         0.66        23.90        14.76         9.30        19.43 
TCGA-TS-A8AF TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       11.77         8.32        14.99        13.35        23.77         2.50 

$`12P GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X 
       56.38        11.87        42.81        12.66        13.61        26.40 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-LK-A4O7 
        5.52         8.02         1.87        31.20        14.73        11.51 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN 
       10.95        24.89        66.54        62.27        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-SH-A7BH 
        2.56         9.76        29.42        17.72        15.09         7.99 
TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       14.76        55.07         8.38        27.75        41.46        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV 
       22.65        15.02        32.28        10.78        26.14         1.55 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UT-A88D 
       15.42        27.72         6.48        25.94        23.64        21.44 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
       14.27         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       16.41        33.70        24.30         2.76 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.66               1.28 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             80.84              91.73 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            14.875             15.255 
[1] "0.7 - 80.8 (14.9)" "1.3 - 91.7 (15.3)"
[1] "hr=" "1.2"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  12P GAIN MUTATED         2        1        1        3         9        2
  12P GAIN WILD-TYPE       5        1        0       13        31        9
D20V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  2                  5
  STAGE IA                 1                  1
  STAGE IB                 1                  0
  STAGE II                 3                 13
  STAGE III                9                 31
  STAGE IV                 2                  9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12P GAIN MUTATED    4  4  8  2
  12P GAIN WILD-TYPE 10 21 20  6
D20V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                4                 10
  T2                4                 21
  T3                8                 20
  T4                2                  6
[1] 4 2
[1] 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+N3
  12P GAIN MUTATED    9  0     8
  12P GAIN WILD-TYPE 33 10    13
D20V5, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                   9                 33
  N1                   0                 10
  N2+N3                8                 13
[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"
D20V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   13  0
  12P GAIN WILD-TYPE 36  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     13    0
  12P GAIN WILD-TYPE   36    2
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               13                 36
  1                0                  2
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    2 16
  12P GAIN WILD-TYPE 13 46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   16
  12P GAIN WILD-TYPE   13   46
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                2                 13
  MALE                 16                 46
[1] 2 2
[1] FALSE
D20V8, continuous

Clustering(21) Variable = 12Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    2 16
  12Q GAIN WILD-TYPE  9 49
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                 58 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                16                 49 
$`12Q GAIN MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       29.10        27.16        17.95         6.08        12.72        80.84 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A9CU TCGA-TS-A7P6 TCGA-TS-A7P7 
       19.99         0.66        23.90        14.76         9.30        19.43 
TCGA-TS-A8AF TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       11.77         8.32        14.99        13.35        23.77         2.50 

$`12Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X 
       56.38        11.87        42.81        12.66        13.61        26.40 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-LK-A4O7 
        5.52         8.02         1.87        31.20        14.73        11.51 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN 
       10.95        24.89        66.54        62.27        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-SH-A7BH 
        2.56         9.76        29.42        17.72        15.09         7.99 
TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       14.76        55.07         8.38        27.75        41.46        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV 
       22.65        15.02        32.28        10.78        26.14         1.55 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UT-A88D 
       15.42        27.72         6.48        25.94        23.64        21.44 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
       14.27         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       16.41        33.70        24.30         2.76 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.66               1.28 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             80.84              91.73 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            14.875             15.255 
[1] "0.7 - 80.8 (14.9)" "1.3 - 91.7 (15.3)"
[1] "hr=" "1.2"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED         2        1        1        3         9        2
  12Q GAIN WILD-TYPE       5        1        0       13        31        9
D21V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  2                  5
  STAGE IA                 1                  1
  STAGE IB                 1                  0
  STAGE II                 3                 13
  STAGE III                9                 31
  STAGE IV                 2                  9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12Q GAIN MUTATED    4  4  8  2
  12Q GAIN WILD-TYPE 10 21 20  6
D21V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                4                 10
  T2                4                 21
  T3                8                 20
  T4                2                  6
[1] 4 2
[1] 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+N3
  12Q GAIN MUTATED    9  0     8
  12Q GAIN WILD-TYPE 33 10    13
D21V5, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                   9                 33
  N1                   0                 10
  N2+N3                8                 13
[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"
D21V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   13  0
  12Q GAIN WILD-TYPE 36  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     13    0
  12Q GAIN WILD-TYPE   36    2
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               13                 36
  1                0                  2
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    2 16
  12Q GAIN WILD-TYPE 13 46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   16
  12Q GAIN WILD-TYPE   13   46
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                2                 13
  MALE                 16                 46
[1] 2 2
[1] FALSE
D21V8, continuous

Clustering(22) Variable = 13Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    1  3
  13Q GAIN WILD-TYPE 10 62
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 4                 72 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                 62 
$`13Q GAIN MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3X TCGA-TS-A7P0 TCGA-TS-A8AF 
       29.10        26.40        41.46        11.77 

$`13Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        11.87        42.81        12.66        13.61        27.16 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       66.54        62.27        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD 
        2.56         9.76        29.42        17.72        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
        7.99        14.76        14.76        55.07         8.38        27.75 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       10.78        26.14         1.55        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       25.94        23.64         8.32        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       21.44        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        33.70        24.30         2.76 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             11.77               0.66 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             41.46              91.73 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            27.750             15.005 
[1] "11.8 - 41.5 (27.8)" "0.7 - 91.7 (15.0)" 
[1] "hr=" "1.8"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED         0        0        0        0         4        0
  13Q GAIN WILD-TYPE       7        2        1       16        36       11
D22V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 0                 16
  STAGE III                4                 36
  STAGE IV                 0                 11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  13Q GAIN MUTATED    0  1  3  0
  13Q GAIN WILD-TYPE 14 24 25  8
D22V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                0                 14
  T2                1                 24
  T3                3                 25
  T4                0                  8
[1] 4 2
[1] 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+N3
  13Q GAIN MUTATED    2  0     2
  13Q GAIN WILD-TYPE 40 10    19
D22V5, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0                   2                 40
  N1                   0                 10
  N2+N3                2                 19
[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"
D22V6, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    2  0
  13Q GAIN WILD-TYPE 47  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    0
  13Q GAIN WILD-TYPE   47    2
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                2                 47
  1                0                  2
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    1  3
  13Q GAIN WILD-TYPE 14 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1    3
  13Q GAIN WILD-TYPE   14   59
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                1                 14
  MALE                  3                 59
[1] 2 2
[1] FALSE
D22V8, continuous

Clustering(23) Variable = 15Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    1  9
  15Q GAIN WILD-TYPE 10 56
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                 66 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 9                 56 
$`15Q GAIN MUTATED`
TCGA-3H-AB3M TCGA-LK-A4NY TCGA-SC-A6LN TCGA-SC-A6LR TCGA-TS-A7OZ TCGA-TS-A7P0 
       29.10         5.52        13.61        29.42        27.75        41.46 
TCGA-UD-AAC5 TCGA-UT-A88E TCGA-UT-A88G TCGA-YS-A95B 
        8.32        14.27         2.50         1.28 

$`15Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        11.87        42.81        12.66        13.61        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       26.40        17.95         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP 
       66.54        62.27        19.99         0.66        28.96         2.56 
TCGA-SC-A6LQ TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
        9.76        17.72        23.90        15.09         7.99        14.76 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
       14.76        55.07         8.38        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS 
       19.43        15.02        32.28        11.77        10.78        26.14 
TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 
        1.55        15.42        27.72         6.48        25.94        23.64 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A97Y TCGA-XT-AASU 
       14.99        13.35        23.77        21.44         4.73         4.67 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        33.70        24.30         2.76 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.28               0.66 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             41.46              91.73 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            13.940             15.255 
[1] "1.3 - 41.5 (13.9)" "0.7 - 91.7 (15.3)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED         2        0        0        0         7        1
  15Q GAIN WILD-TYPE       5        2        1       16        33       10
D23V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  2                  5
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 0                 16
  STAGE III                7                 33
  STAGE IV                 1                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  15Q GAIN MUTATED    3  1  5  1
  15Q GAIN WILD-TYPE 11 24 23  7
D23V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                3                 11
  T2                1                 24
  T3                5                 23
  T4                1                  7
[1] 4 2
[1] 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+N3
  15Q GAIN MUTATED    5  1     4
  15Q GAIN WILD-TYPE 37  9    17
D23V5, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                   5                 37
  N1                   1                  9
  N2+N3                4                 17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    8  0
  15Q GAIN WILD-TYPE 41  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      8    0
  15Q GAIN WILD-TYPE   41    2
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                8                 41
  1                0                  2
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    3  7
  15Q GAIN WILD-TYPE 12 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    7
  15Q GAIN WILD-TYPE   12   55
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 12
  MALE                  7                 55
[1] 2 2
[1] FALSE
D23V8, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                  5 
        TCGA-SH-A7BH         TCGA-XT-AASU         TCGA-ZN-A9VQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 

Clustering(24) Variable = 16P GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    4 11
  16P GAIN WILD-TYPE  7 54
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                 61 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                11                 54 
$`16P GAIN MUTATED`
TCGA-3H-AB3U TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-NQ-A57I TCGA-SC-A6LR TCGA-SC-AA5Z 
       27.16        18.81        23.31         0.66        29.42        17.72 
TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A8AF 
       23.90         7.99        14.76        41.46         9.30        11.77 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-YS-A95C 
       13.35        23.77         4.37 

$`16P GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       26.40        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        66.54 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       62.27        19.99        28.96        13.61         2.56         9.76 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 
       15.09        14.76        55.07         8.38        27.75        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS 
       22.65        19.43        15.02        32.28        10.78        26.14 
TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 
        1.55        15.42        27.72         6.48        25.94        23.64 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
        8.32        14.99        21.44        14.27         2.50         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        4.67         1.28         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.66               1.28 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             41.46              91.73 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             17.72              15.02 
[1] "0.7 - 41.5 (17.7)" "1.3 - 91.7 (15.0)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  16P GAIN MUTATED         0        0        1        3        10        2
  16P GAIN WILD-TYPE       7        2        0       13        30        9
D24V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 3                 13
  STAGE III               10                 30
  STAGE IV                 2                  9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  16P GAIN MUTATED    3  5  6  2
  16P GAIN WILD-TYPE 11 20 22  6
D24V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                3                 11
  T2                5                 20
  T3                6                 22
  T4                2                  6
[1] 4 2
[1] 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+N3
  16P GAIN MUTATED    5  1     8
  16P GAIN WILD-TYPE 37  9    13
D24V5, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                   5                 37
  N1                   1                  9
  N2+N3                8                 13
[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"
D24V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   11  0
  16P GAIN WILD-TYPE 38  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     11    0
  16P GAIN WILD-TYPE   38    2
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               11                 38
  1                0                  2
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    2 14
  16P GAIN WILD-TYPE 13 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2   14
  16P GAIN WILD-TYPE   13   48
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                2                 13
  MALE                 14                 48
[1] 2 2
[1] FALSE
D24V8, continuous
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                  4 
        TCGA-XT-AASU         TCGA-ZN-A9VQ         TCGA-ZN-A9VS 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ZN-A9VU 
"16P GAIN WILD-TYPE" 

Clustering(25) Variable = 16Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    4 11
  16Q GAIN WILD-TYPE  7 54
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                15                 61 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                11                 54 
$`16Q GAIN MUTATED`
TCGA-3H-AB3U TCGA-LK-A4O2 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-NQ-A57I TCGA-SC-A6LR 
       27.16         1.87        18.81        23.31         0.66        29.42 
TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A7P6 
       17.72        23.90         7.99        14.76        41.46         9.30 
TCGA-TS-A8AF TCGA-UD-AAC7 TCGA-UT-A88C 
       11.77        13.35        23.77 

$`16Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O4 
       26.40        17.95         5.52         8.02         6.08        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM 
       12.72        14.73        11.51        80.84        91.73         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        66.54        62.27 
TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BD 
       19.99        28.96        13.61         2.56         9.76        15.09 
TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 
       14.76        55.07         8.38        27.75        18.51        22.65 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV 
       19.43        15.02        32.28        10.78        26.14         1.55 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 
       15.42        27.72         6.48        25.94        23.64         8.32 
TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       14.99        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.66               1.28 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             41.46              91.73 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             17.72              15.02 
[1] "0.7 - 41.5 (17.7)" "1.3 - 91.7 (15.0)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED         0        0        1        2        10        2
  16Q GAIN WILD-TYPE       7        2        0       14        30        9
D25V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 2                 14
  STAGE III               10                 30
  STAGE IV                 2                  9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  16Q GAIN MUTATED    2  4  7  2
  16Q GAIN WILD-TYPE 12 21 21  6
D25V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                2                 12
  T2                4                 21
  T3                7                 21
  T4                2                  6
[1] 4 2
[1] 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+N3
  16Q GAIN MUTATED    6  1     7
  16Q GAIN WILD-TYPE 36  9    14
D25V5, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                   6                 36
  N1                   1                  9
  N2+N3                7                 14
[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"
D25V6, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   11  0
  16Q GAIN WILD-TYPE 38  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     11    0
  16Q GAIN WILD-TYPE   38    2
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               11                 38
  1                0                  2
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3 12
  16Q GAIN WILD-TYPE 12 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3   12
  16Q GAIN WILD-TYPE   12   50
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                 12
  MALE                 12                 50
[1] 2 2
[1] FALSE
D25V8, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                  4 
        TCGA-XT-AASU         TCGA-ZN-A9VQ         TCGA-ZN-A9VS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ZN-A9VU 
"16Q GAIN WILD-TYPE" 

Clustering(26) Variable = 17P GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    0  6
  17P GAIN WILD-TYPE 11 59
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 6                 70 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 6                 59 
$`17P GAIN MUTATED`
TCGA-3H-AB3K TCGA-3H-AB3U TCGA-LK-A4O0 TCGA-SH-A7BC TCGA-TS-A7P6 TCGA-UT-A88E 
       56.38        27.16         6.08        23.90         9.30        14.27 

$`17P GAIN WILD-TYPE`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X 
       11.87        29.10        42.81        12.66        13.61        26.40 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        66.54 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       62.27        19.99         0.66        28.96        13.61         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
        9.76        29.42        17.72        15.09         7.99        14.76 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       14.76        55.07         8.38        27.75        41.46        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
       22.65        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       26.14         1.55        15.42        27.72         6.48        25.94 
TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D 
       23.64         8.32        14.99        13.35        23.77        21.44 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
        2.50         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       16.41        33.70        24.30         2.76 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              6.08               0.66 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             56.38              91.73 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            19.085             15.055 
[1] "6.1 - 56.4 (19.1)" "0.7 - 91.7 (15.1)"
[1] "hr=" "1"  
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  17P GAIN MUTATED         1        1        0        1         3        0
  17P GAIN WILD-TYPE       6        1        1       15        37       11
D26V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 1                 15
  STAGE III                3                 37
  STAGE IV                 0                 11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17P GAIN MUTATED    2  1  3  0
  17P GAIN WILD-TYPE 12 24 25  8
D26V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                2                 12
  T2                1                 24
  T3                3                 25
  T4                0                  8
[1] 4 2
[1] 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+N3
  17P GAIN MUTATED    4  0     2
  17P GAIN WILD-TYPE 38 10    19
D26V5, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                   4                 38
  N1                   0                 10
  N2+N3                2                 19
[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"
D26V6, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    5  0
  17P GAIN WILD-TYPE 44  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    0
  17P GAIN WILD-TYPE   44    2
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                5                 44
  1                0                  2
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    0  6
  17P GAIN WILD-TYPE 15 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    6
  17P GAIN WILD-TYPE   15   56
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                0                 15
  MALE                  6                 56
[1] 2 2
[1] FALSE
D26V8, continuous

Clustering(27) Variable = 17Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    2 13
  17Q GAIN WILD-TYPE  9 52
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                15                 61 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                13                 52 
$`17Q GAIN MUTATED`
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4O0 
       56.38        29.10        27.16        17.95         5.52         6.08 
TCGA-MQ-A6BS TCGA-SC-A6LR TCGA-SH-A7BC TCGA-TS-A7P6 TCGA-UD-AAC4 TCGA-UD-AAC6 
       19.99        29.42        23.90         9.30        23.64        14.99 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E 
       13.35        23.77        14.27 

$`17Q GAIN WILD-TYPE`
TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X TCGA-LK-A4NZ 
       11.87        42.81        12.66        13.61        26.40         8.02 
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        1.87        31.20        12.72        14.73        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM 
       10.95        24.89        66.54        62.27         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-SH-A7BH 
       13.61         2.56         9.76        17.72        15.09         7.99 
TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
       14.76        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF 
       18.51        22.65        19.43        15.02        32.28        11.77 
TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       10.78        26.14         1.55        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UT-A88D TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       25.94         8.32        21.44         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              5.52               0.66 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             56.38              91.73 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             19.99              14.76 
[1] "5.5 - 56.4 (20.0)" "0.7 - 91.7 (14.8)"
[1] "hr=" "1.1"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED         1        1        0        5         8        1
  17Q GAIN WILD-TYPE       6        1        1       11        32       10
D27V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 5                 11
  STAGE III                8                 32
  STAGE IV                 1                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17Q GAIN MUTATED    3  6  6  1
  17Q GAIN WILD-TYPE 11 19 22  7
D27V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                3                 11
  T2                6                 19
  T3                6                 22
  T4                1                  7
[1] 4 2
[1] 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+N3
  17Q GAIN MUTATED    8  0     7
  17Q GAIN WILD-TYPE 34 10    14
D27V5, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                   8                 34
  N1                   0                 10
  N2+N3                7                 14
[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"
D27V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   13  0
  17Q GAIN WILD-TYPE 36  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     13    0
  17Q GAIN WILD-TYPE   36    2
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               13                 36
  1                0                  2
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    2 14
  17Q GAIN WILD-TYPE 13 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2   14
  17Q GAIN WILD-TYPE   13   48
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                2                 13
  MALE                 14                 48
[1] 2 2
[1] FALSE
D27V8, continuous
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                  5 
        TCGA-SH-A7BH         TCGA-XT-AASU         TCGA-ZN-A9VQ 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 

Clustering(28) Variable = 18P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    1  6
  18P GAIN WILD-TYPE 10 59
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                 69 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 59 
$`18P GAIN MUTATED`
TCGA-3H-AB3M TCGA-LK-A4O0 TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A8AF 
       29.10         6.08         7.99        14.76        41.46        11.77 
TCGA-UD-AAC7 
       13.35 

$`18P GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        11.87        42.81        12.66        13.61        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 
       26.40        17.95         5.52         8.02         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       66.54        62.27        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD 
        2.56         9.76        29.42        17.72        23.90        15.09 
TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 
       14.76        55.07         8.38        27.75        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS 
        9.30        19.43        15.02        32.28        10.78        26.14 
TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 
        1.55        15.42        27.72         6.48        25.94        23.64 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G 
        8.32        14.99        23.77        21.44        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ 
        4.73         4.67         1.28         4.37         2.76        16.41 
TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       33.70        24.30         2.76 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              6.08               0.66 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             41.46              91.73 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             13.35              15.42 
[1] "6.1 - 41.5 (13.3)" "0.7 - 91.7 (15.4)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         0        1        0        1         4        1
  18P GAIN WILD-TYPE       7        1        1       15        36       10
D28V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 1                 15
  STAGE III                4                 36
  STAGE IV                 1                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18P GAIN MUTATED    1  2  3  1
  18P GAIN WILD-TYPE 13 23 25  7
D28V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                1                 13
  T2                2                 23
  T3                3                 25
  T4                1                  7
[1] 4 2
[1] 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+N3
  18P GAIN MUTATED    4  0     3
  18P GAIN WILD-TYPE 38 10    18
D28V5, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                   4                 38
  N1                   0                 10
  N2+N3                3                 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"
D28V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    5  0
  18P GAIN WILD-TYPE 44  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5    0
  18P GAIN WILD-TYPE   44    2
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                5                 44
  1                0                  2
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    2  5
  18P GAIN WILD-TYPE 13 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    5
  18P GAIN WILD-TYPE   13   57
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                2                 13
  MALE                  5                 57
[1] 2 2
[1] FALSE
D28V8, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                  5 
        TCGA-SC-A6LR         TCGA-XT-AASU         TCGA-ZN-A9VQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 

Clustering(29) Variable = 18Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    1  3
  18Q GAIN WILD-TYPE 10 62
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 72 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 62 
$`18Q GAIN MUTATED`
TCGA-LK-A4O0 TCGA-SH-A7BH TCGA-SH-A9CU TCGA-UD-AAC7 
        6.08         7.99        14.76        13.35 

$`18Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 
       27.16        26.40        17.95         5.52         8.02         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
       24.89        66.54        62.27        19.99         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC 
       13.61         2.56         9.76        29.42        17.72        23.90 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
       15.09        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C 
        6.48        25.94        23.64         8.32        14.99        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       21.44        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        33.70        24.30         2.76 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              6.08               0.66 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             14.76              91.73 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            10.670             15.915 
[1] "6.1 - 14.8 (10.7)" "0.7 - 91.7 (15.9)"
[1] "hr=" "2"  
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED         0        1        0        1         1        1
  18Q GAIN WILD-TYPE       7        1        1       15        39       10
D29V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 1                 15
  STAGE III                1                 39
  STAGE IV                 1                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18Q GAIN MUTATED    1  1  1  1
  18Q GAIN WILD-TYPE 13 24 27  7
D29V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                1                 13
  T2                1                 24
  T3                1                 27
  T4                1                  7
[1] 4 2
[1] 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+N3
  18Q GAIN MUTATED    3  0     1
  18Q GAIN WILD-TYPE 39 10    20
D29V5, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                   3                 39
  N1                   0                 10
  N2+N3                1                 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"
D29V6, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4  0
  18Q GAIN WILD-TYPE 45  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    0
  18Q GAIN WILD-TYPE   45    2
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                4                 45
  1                0                  2
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    1  3
  18Q GAIN WILD-TYPE 14 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    3
  18Q GAIN WILD-TYPE   14   59
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 14
  MALE                  3                 59
[1] 2 2
[1] FALSE
D29V8, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                  5 
        TCGA-SC-A6LR         TCGA-XT-AASU         TCGA-ZN-A9VQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 

Clustering(30) Variable = 19P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    3  9
  19P GAIN WILD-TYPE  8 56
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                12                 64 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 9                 56 
$`19P GAIN MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3S TCGA-3H-AB3X TCGA-LK-A4O0 TCGA-MQ-A4LP TCGA-SC-A6LR 
       29.10        12.66        26.40         6.08        17.33        29.42 
TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A8AF TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC7 
        7.99        14.76        11.77        23.64         8.32        13.35 

$`19P GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3T TCGA-3H-AB3U TCGA-LK-A4NW 
       56.38        11.87        42.81        13.61        27.16        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         1.87        31.20        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
        3.52        10.95        24.89        66.54        62.27        19.99 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-AA5Z 
        0.66        28.96        13.61         2.56         9.76        17.72 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
       23.90        15.09        14.76        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       41.46        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       32.28        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E 
        6.48        25.94        14.99        23.77        21.44        14.27 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
        2.50         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       16.41        33.70        24.30         2.76 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              6.08               0.66 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             29.42              91.73 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            14.055             15.255 
[1] "6.1 - 29.4 (14.1)" "0.7 - 91.7 (15.3)"
[1] "hr=" "1"  
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  19P GAIN MUTATED         1        1        0        3         7        1
  19P GAIN WILD-TYPE       6        1        1       13        33       10
D30V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 3                 13
  STAGE III                7                 33
  STAGE IV                 1                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19P GAIN MUTATED    3  5  4  1
  19P GAIN WILD-TYPE 11 20 24  7
D30V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                3                 11
  T2                5                 20
  T3                4                 24
  T4                1                  7
[1] 4 2
[1] 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+N3
  19P GAIN MUTATED    7  0     5
  19P GAIN WILD-TYPE 35 10    16
D30V5, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                   7                 35
  N1                   0                 10
  N2+N3                5                 16
[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"
D30V6, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   11  0
  19P GAIN WILD-TYPE 38  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     11    0
  19P GAIN WILD-TYPE   38    2
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               11                 38
  1                0                  2
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    2 11
  19P GAIN WILD-TYPE 13 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2   11
  19P GAIN WILD-TYPE   13   51
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                2                 13
  MALE                 11                 51
[1] 2 2
[1] FALSE
D30V8, continuous
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                  4 
        TCGA-XT-AASU         TCGA-ZN-A9VQ         TCGA-ZN-A9VS 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ZN-A9VU 
"19P GAIN WILD-TYPE" 

Clustering(31) Variable = 19Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    2  6
  19Q GAIN WILD-TYPE  9 59
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 8                 68 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                 59 
$`19Q GAIN MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A4LP TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A8AF TCGA-UD-AAC5 
        6.08        17.33         7.99        14.76        11.77         8.32 
TCGA-UD-AAC7 TCGA-ZN-A9VU 
       13.35        24.30 

$`19Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 
       27.16        26.40        17.95         5.52         8.02         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       18.81        23.31         5.19         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       66.54        62.27        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD 
        2.56         9.76        29.42        17.72        23.90        15.09 
TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       14.76        55.07         8.38        27.75        41.46        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI 
       22.65         9.30        19.43        15.02        32.28        10.78 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       26.14         1.55        15.42        27.72         6.48        25.94 
TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G 
       23.64        14.99        23.77        21.44        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ 
        4.73         4.67         1.28         4.37         2.76        16.41 
TCGA-ZN-A9VS TCGA-ZN-A9VW 
       33.70         2.76 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              6.08               0.66 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             24.30              91.73 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            12.560             15.915 
[1] "6.1 - 24.3 (12.6)" "0.7 - 91.7 (15.9)"
[1] "hr=" "1.5"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED         1        1        0        3         3        1
  19Q GAIN WILD-TYPE       6        1        1       13        37       10
D31V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 3                 13
  STAGE III                3                 37
  STAGE IV                 1                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19Q GAIN MUTATED    2  4  2  1
  19Q GAIN WILD-TYPE 12 21 26  7
D31V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                2                 12
  T2                4                 21
  T3                2                 26
  T4                1                  7
[1] 4 2
[1] 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+N3
  19Q GAIN MUTATED    6  0     2
  19Q GAIN WILD-TYPE 36 10    19
D31V5, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                   6                 36
  N1                   0                 10
  N2+N3                2                 19
[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"
D31V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    6  0
  19Q GAIN WILD-TYPE 43  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      6    0
  19Q GAIN WILD-TYPE   43    2
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                6                 43
  1                0                  2
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    1  8
  19Q GAIN WILD-TYPE 14 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    8
  19Q GAIN WILD-TYPE   14   54
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                1                 14
  MALE                  8                 54
[1] 2 2
[1] FALSE
D31V8, continuous
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                  4 
        TCGA-SC-A6LR         TCGA-XT-AASU         TCGA-ZN-A9VQ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ZN-A9VS 
"19Q GAIN WILD-TYPE" 

Clustering(32) Variable = 20P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    2  6
  20P GAIN WILD-TYPE  9 59
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                 68 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 6                 59 
$`20P GAIN MUTATED`
TCGA-3H-AB3U TCGA-LK-A4NY TCGA-MQ-A6BL TCGA-NQ-A57I TCGA-SC-AA5Z TCGA-SH-A9CU 
       27.16         5.52        10.95         0.66        17.72        14.76 
TCGA-UD-AAC7 TCGA-UT-A88G 
       13.35         2.50 

$`20P GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       26.40        17.95         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       23.31         5.19        17.33         3.52        24.89        66.54 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       62.27        19.99        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU 
       29.42        23.90        15.09         7.99        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
        8.38        27.75        41.46        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS 
       19.43        15.02        32.28        11.77        10.78        26.14 
TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 
        1.55        15.42        27.72         6.48        25.94        23.64 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y 
        8.32        14.99        23.77        21.44        14.27         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.67         1.28         4.37         2.76        16.41        33.70 
TCGA-ZN-A9VU TCGA-ZN-A9VW 
       24.30         2.76 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.66               1.28 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             27.16              91.73 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            12.150             15.915 
[1] "0.7 - 27.2 (12.1)" "1.3 - 91.7 (15.9)"
[1] "hr=" "1.7"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  20P GAIN MUTATED         0        0        1        2         3        2
  20P GAIN WILD-TYPE       7        2        0       14        37        9
D32V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 2                 14
  STAGE III                3                 37
  STAGE IV                 2                  9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20P GAIN MUTATED    1  2  3  2
  20P GAIN WILD-TYPE 13 23 25  6
D32V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                1                 13
  T2                2                 23
  T3                3                 25
  T4                2                  6
[1] 4 2
[1] 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+N3
  20P GAIN MUTATED    5  0     2
  20P GAIN WILD-TYPE 37 10    19
D32V5, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                   5                 37
  N1                   0                 10
  N2+N3                2                 19
[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"
D32V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    7  0
  20P GAIN WILD-TYPE 42  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7    0
  20P GAIN WILD-TYPE   42    2
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0                7                 42
  1                0                  2
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    1  7
  20P GAIN WILD-TYPE 14 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1    7
  20P GAIN WILD-TYPE   14   55
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                1                 14
  MALE                  7                 55
[1] 2 2
[1] FALSE
D32V8, continuous

Clustering(33) Variable = 20Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED    3  7
  20Q GAIN WILD-TYPE  8 58
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                 66 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 7                 58 
$`20Q GAIN MUTATED`
TCGA-3H-AB3U TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-AA5Z TCGA-SH-A9CU 
       27.16        10.95        19.99         0.66        17.72        14.76 
TCGA-TS-A7P0 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       41.46        13.35        23.77         2.50 

$`20Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       26.40        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN 
       18.81        23.31         5.19        17.33         3.52        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       66.54        62.27        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU 
       29.42        23.90        15.09         7.99        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
        8.38        27.75        18.51        22.65         9.30        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV 
       15.02        32.28        11.77        10.78        26.14         1.55 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 
       15.42        27.72         6.48        25.94        23.64         8.32 
TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       14.99        21.44        14.27         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        33.70        24.30         2.76 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.66               1.28 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             41.46              91.73 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            16.240             15.055 
[1] "0.7 - 41.5 (16.2)" "1.3 - 91.7 (15.1)"
[1] "hr=" "1.1"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED         0        0        1        3         4        2
  20Q GAIN WILD-TYPE       7        2        0       13        36        9
D33V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 3                 13
  STAGE III                4                 36
  STAGE IV                 2                  9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20Q GAIN MUTATED    1  3  4  2
  20Q GAIN WILD-TYPE 13 22 24  6
D33V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                1                 13
  T2                3                 22
  T3                4                 24
  T4                2                  6
[1] 4 2
[1] 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+N3
  20Q GAIN MUTATED    6  0     3
  20Q GAIN WILD-TYPE 36 10    18
D33V5, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                   6                 36
  N1                   0                 10
  N2+N3                3                 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"
D33V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    7  0
  20Q GAIN WILD-TYPE 42  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      7    0
  20Q GAIN WILD-TYPE   42    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0                7                 42
  1                0                  2
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    0 10
  20Q GAIN WILD-TYPE 15 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0   10
  20Q GAIN WILD-TYPE   15   52
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                0                 15
  MALE                 10                 52
[1] 2 2
[1] FALSE
D33V8, continuous

Clustering(34) Variable = 21Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    1  4
  21Q GAIN WILD-TYPE 10 61
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 71 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 61 
$`21Q GAIN MUTATED`
TCGA-SH-A7BH TCGA-SH-A9CU TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88G 
        7.99        14.76         6.48        13.35         2.50 

$`21Q GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 
       27.16        26.40        17.95         5.52         8.02         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        1.87        31.20        12.72        14.73        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I 
       10.95        24.89        66.54        62.27        19.99         0.66 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z 
       28.96        13.61         2.56         9.76        29.42        17.72 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
       23.90        15.09        14.76        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       41.46        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY 
       32.28        11.77        10.78        26.14         1.55        15.42 
TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C 
       27.72        25.94        23.64         8.32        14.99        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       21.44        14.27         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        2.76        16.41        33.70        24.30         2.76 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              2.50               0.66 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             14.76              91.73 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              7.99              16.41 
[1] "2.5 - 14.8 (8.0)"  "0.7 - 91.7 (16.4)"
[1] "hr=" "2.6"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED         0        0        0        2         2        1
  21Q GAIN WILD-TYPE       7        2        1       14        38       10
D34V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 2                 14
  STAGE III                2                 38
  STAGE IV                 1                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  21Q GAIN MUTATED    0  2  2  1
  21Q GAIN WILD-TYPE 14 23 26  7
D34V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                0                 14
  T2                2                 23
  T3                2                 26
  T4                1                  7
[1] 4 2
[1] 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+N3
  21Q GAIN MUTATED    4  0     1
  21Q GAIN WILD-TYPE 38 10    20
D34V5, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                   4                 38
  N1                   0                 10
  N2+N3                1                 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"
D34V6, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    5  0
  21Q GAIN WILD-TYPE 44  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5    0
  21Q GAIN WILD-TYPE   44    2
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                5                 44
  1                0                  2
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    1  4
  21Q GAIN WILD-TYPE 14 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    4
  21Q GAIN WILD-TYPE   14   58
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                1                 14
  MALE                  4                 58
[1] 2 2
[1] FALSE
D34V8, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                  5 
        TCGA-SC-A6LR         TCGA-XT-AASU         TCGA-ZN-A9VQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 

Clustering(35) Variable = XP GAIN MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                0  1
  XP GAIN MUTATED    2  5
  XP GAIN WILD-TYPE  9 60
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                7                69 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                5                60 
$`XP GAIN MUTATED`
TCGA-3H-AB3U TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UT-A88G 
       27.16        29.42        17.72        25.94        14.99         2.50 
TCGA-YS-A95B 
        1.28 

$`XP GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       26.40        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
       24.89        66.54        62.27        19.99         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       13.61         2.56         9.76        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
       14.76        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D 
        6.48        23.64         8.32        13.35        23.77        21.44 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ 
       14.27         4.73         4.67         4.37         2.76        16.41 
TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       33.70        24.30         2.76 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             1.28              0.66 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            29.42             91.73 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            17.72             15.02 
[1] "1.3 - 29.4 (17.7)" "0.7 - 91.7 (15.0)"
[1] "hr=" "1.1"
D35V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  XP GAIN MUTATED         0        0        0        1         4        2
  XP GAIN WILD-TYPE       7        2        1       15        36        9
D35V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               4                36
  STAGE IV                2                 9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XP GAIN MUTATED    1  2  2  2
  XP GAIN WILD-TYPE 13 23 26  6
D35V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               1                13
  T2               2                23
  T3               2                26
  T4               2                 6
[1] 4 2
[1] 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+N3
  XP GAIN MUTATED    3  0     4
  XP GAIN WILD-TYPE 39 10    17
D35V5, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  N0                  3                39
  N1                  0                10
  N2+N3               4                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    7  0
  XP GAIN WILD-TYPE 42  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      7    0
  XP GAIN WILD-TYPE   42    2
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0               7                42
  1               0                 2
[1] 2 2
[1] FALSE
D35V7, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    2  5
  XP GAIN WILD-TYPE 13 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2    5
  XP GAIN WILD-TYPE   13   57
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               2                13
  MALE                 5                57
[1] 2 2
[1] FALSE
D35V8, continuous
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                 5 
       TCGA-SH-A7BH        TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VS 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-ZN-A9VU 
"XP GAIN WILD-TYPE" 

Clustering(36) Variable = XQ GAIN MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    2  4
  XQ GAIN WILD-TYPE  9 61
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                70 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                61 
$`XQ GAIN MUTATED`
TCGA-3H-AB3U TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-UD-AAC1 TCGA-UT-A88G TCGA-YS-A95B 
       27.16        29.42        17.72        25.94         2.50         1.28 

$`XQ GAIN WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       26.40        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
       24.89        66.54        62.27        19.99         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       13.61         2.56         9.76        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
       14.76        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        6.48        23.64         8.32        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M 
       21.44        14.27         4.73         4.67         4.37         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       16.41        33.70        24.30         2.76 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             1.28              0.66 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            29.42             91.73 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           21.830            15.005 
[1] "1.3 - 29.4 (21.8)" "0.7 - 91.7 (15.0)"
[1] "hr=" "1.2"
D36V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED         0        0        0        0         4        2
  XQ GAIN WILD-TYPE       7        2        1       16        36        9
D36V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                0                16
  STAGE III               4                36
  STAGE IV                2                 9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XQ GAIN MUTATED    1  1  2  2
  XQ GAIN WILD-TYPE 13 24 26  6
D36V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               1                13
  T2               1                24
  T3               2                26
  T4               2                 6
[1] 4 2
[1] 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+N3
  XQ GAIN MUTATED    2  0     4
  XQ GAIN WILD-TYPE 40 10    17
D36V5, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0                  2                40
  N1                  0                10
  N2+N3               4                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    6  0
  XQ GAIN WILD-TYPE 43  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6    0
  XQ GAIN WILD-TYPE   43    2
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               6                43
  1               0                 2
[1] 2 2
[1] FALSE
D36V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2  4
  XQ GAIN WILD-TYPE 13 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    4
  XQ GAIN WILD-TYPE   13   58
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               2                13
  MALE                 4                58
[1] 2 2
[1] FALSE
D36V8, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                 5 
       TCGA-SH-A7BH        TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VS 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ZN-A9VU 
"XQ GAIN WILD-TYPE" 

Clustering(37) Variable = 1P LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    0  8
  1P LOSS WILD-TYPE 11 57
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                8                68 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                8                57 
$`1P LOSS MUTATED`
TCGA-3H-AB3M TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A6BL TCGA-MQ-A6BS 
       29.10        14.73        11.51        18.81        10.95        19.99 
TCGA-SC-A6LN TCGA-TS-A7P6 
       13.61         9.30 

$`1P LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        11.87        42.81        12.66        13.61        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       26.40        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       31.20        12.72        80.84        91.73        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
       17.33         3.52        24.89        66.54        62.27         0.66 
TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC 
       28.96         2.56         9.76        29.42        17.72        23.90 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       15.09         7.99        14.76        14.76        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 
       27.75        41.46        18.51        22.65        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY 
       32.28        11.77        10.78        26.14         1.55        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 
       27.72         6.48        25.94        23.64         8.32        14.99 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       13.35        23.77        21.44        14.27         2.50         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.67         1.28         4.37         2.76        16.41        33.70 
TCGA-ZN-A9VU TCGA-ZN-A9VW 
       24.30         2.76 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             9.30              0.66 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            29.10             91.73 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           14.170            15.255 
[1] "9.3 - 29.1 (14.2)" "0.7 - 91.7 (15.3)"
[1] "hr=" "1.5"
D37V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  1P LOSS MUTATED         0        0        0        3         5        0
  1P LOSS WILD-TYPE       7        2        1       13        35       11
D37V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                3                13
  STAGE III               5                35
  STAGE IV                0                11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1P LOSS MUTATED    0  4  4  0
  1P LOSS WILD-TYPE 14 21 24  8
D37V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               0                14
  T2               4                21
  T3               4                24
  T4               0                 8
[1] 4 2
[1] 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+N3
  1P LOSS MUTATED    3  2     3
  1P LOSS WILD-TYPE 39  8    18
D37V5, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0                  3                39
  N1                  2                 8
  N2+N3               3                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"
D37V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    6  0
  1P LOSS WILD-TYPE 43  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6    0
  1P LOSS WILD-TYPE   43    2
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0               6                43
  1               0                 2
[1] 2 2
[1] FALSE
D37V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    3  5
  1P LOSS WILD-TYPE 12 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    5
  1P LOSS WILD-TYPE   12   57
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               3                12
  MALE                 5                57
[1] 2 2
[1] FALSE
D37V8, continuous

Clustering(38) Variable = 2P LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    0  3
  2P LOSS WILD-TYPE 11 62
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                73 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                62 
$`2P LOSS MUTATED`
TCGA-MQ-A4LI TCGA-SH-A7BH TCGA-UT-A88G 
       18.81         7.99         2.50 

$`2P LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 
       27.16        26.40        17.95         5.52         8.02         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        1.87        31.20        12.72        14.73        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       91.73        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
       24.89        66.54        62.27        19.99         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC 
       13.61         2.56         9.76        29.42        17.72        23.90 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
       15.09        14.76        14.76        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       41.46        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY 
       32.28        11.77        10.78        26.14         1.55        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 
       27.72         6.48        25.94        23.64         8.32        14.99 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU 
       13.35        23.77        21.44        14.27         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.50              0.66 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            18.81             91.73 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             7.99             15.09 
[1] "2.5 - 18.8 (8.0)"  "0.7 - 91.7 (15.1)"
[1] "hr=" "2.7"
D38V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  2P LOSS MUTATED         0        0        0        1         2        0
  2P LOSS WILD-TYPE       7        2        1       15        38       11
D38V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               2                38
  STAGE IV                0                11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2P LOSS MUTATED    0  1  2  0
  2P LOSS WILD-TYPE 14 24 26  8
D38V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               0                14
  T2               1                24
  T3               2                26
  T4               0                 8
[1] 4 2
[1] 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+N3
  2P LOSS MUTATED    3  0     0
  2P LOSS WILD-TYPE 39 10    21
D38V5, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0                  3                39
  N1                  0                10
  N2+N3               0                21
[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"
D38V6, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    3  0
  2P LOSS WILD-TYPE 46  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    0
  2P LOSS WILD-TYPE   46    2
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               3                46
  1               0                 2
[1] 2 2
[1] FALSE
D38V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    2  1
  2P LOSS WILD-TYPE 13 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    1
  2P LOSS WILD-TYPE   13   61
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               2                13
  MALE                 1                61
[1] 2 2
[1] FALSE
D38V8, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                 5 
       TCGA-SC-A6LR        TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VS 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ZN-A9VU 
"2P LOSS WILD-TYPE" 

Clustering(39) Variable = 2Q LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    0  3
  2Q LOSS WILD-TYPE 11 62
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                73 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                62 
$`2Q LOSS MUTATED`
TCGA-LK-A4O2 TCGA-MQ-A4LI TCGA-SH-A7BH 
        1.87        18.81         7.99 

$`2Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 
       27.16        26.40        17.95         5.52         8.02         6.08 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       66.54        62.27        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD 
        2.56         9.76        29.42        17.72        23.90        15.09 
TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
       14.76        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
        6.48        25.94        23.64         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       23.77        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             1.87              0.66 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            18.81             91.73 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             7.99             15.09 
[1] "1.9 - 18.8 (8.0)"  "0.7 - 91.7 (15.1)"
[1] "hr=" "2.8"
D39V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED         0        0        0        1         2        0
  2Q LOSS WILD-TYPE       7        2        1       15        38       11
D39V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               2                38
  STAGE IV                0                11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2Q LOSS MUTATED    0  1  2  0
  2Q LOSS WILD-TYPE 14 24 26  8
D39V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               0                14
  T2               1                24
  T3               2                26
  T4               0                 8
[1] 4 2
[1] 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+N3
  2Q LOSS MUTATED    3  0     0
  2Q LOSS WILD-TYPE 39 10    21
D39V5, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0                  3                39
  N1                  0                10
  N2+N3               0                21
[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"
D39V6, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    3  0
  2Q LOSS WILD-TYPE 46  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3    0
  2Q LOSS WILD-TYPE   46    2
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               3                46
  1               0                 2
[1] 2 2
[1] FALSE
D39V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    3  0
  2Q LOSS WILD-TYPE 12 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3    0
  2Q LOSS WILD-TYPE   12   62
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               3                12
  MALE                 0                62
[1] 2 2
[1] FALSE
D39V8, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                 5 
       TCGA-SC-A6LR        TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VS 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ZN-A9VU 
"2Q LOSS WILD-TYPE" 

Clustering(40) Variable = 3P LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    1  4
  3P LOSS WILD-TYPE 10 61
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                71 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                61 
$`3P LOSS MUTATED`
TCGA-LK-A4O7 TCGA-NQ-A57I TCGA-SH-A9CU TCGA-TS-A8AF TCGA-UD-AABZ 
       11.51         0.66        14.76        11.77         6.48 

$`3P LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 
       27.16        26.40        17.95         5.52         8.02         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        1.87        31.20        12.72        14.73        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN 
       24.89        66.54        62.27        19.99        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD 
        2.56         9.76        29.42        17.72        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
        7.99        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AAC1 
       10.78        26.14         1.55        15.42        27.72        25.94 
TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D 
       23.64         8.32        14.99        13.35        23.77        21.44 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       14.27         2.50         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        2.76        16.41        33.70        24.30         2.76 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.66              1.28 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            14.76             91.73 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            11.51             16.41 
[1] "0.7 - 14.8 (11.5)" "1.3 - 91.7 (16.4)"
[1] "hr=" "2.6"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         0        0        1        1         2        1
  3P LOSS WILD-TYPE       7        2        0       15        38       10
D40V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                1                 0
  STAGE II                1                15
  STAGE III               2                38
  STAGE IV                1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3P LOSS MUTATED    1  2  1  1
  3P LOSS WILD-TYPE 13 23 27  7
D40V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               1                13
  T2               2                23
  T3               1                27
  T4               1                 7
[1] 4 2
[1] 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+N3
  3P LOSS MUTATED    1  1     2
  3P LOSS WILD-TYPE 41  9    19
D40V5, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0                  1                41
  N1                  1                 9
  N2+N3               2                19
[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"
D40V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    3  0
  3P LOSS WILD-TYPE 46  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3    0
  3P LOSS WILD-TYPE   46    2
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               3                46
  1               0                 2
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    0  5
  3P LOSS WILD-TYPE 15 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    5
  3P LOSS WILD-TYPE   15   57
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               0                15
  MALE                 5                57
[1] 2 2
[1] FALSE
D40V8, continuous

Clustering(41) Variable = 3Q LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    1  2
  3Q LOSS WILD-TYPE 10 63
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                73 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                63 
$`3Q LOSS MUTATED`
TCGA-LK-A4O7 TCGA-NQ-A57I TCGA-SH-A9CU 
       11.51         0.66        14.76 

$`3Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 
       27.16        26.40        17.95         5.52         8.02         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        1.87        31.20        12.72        14.73        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN 
       24.89        66.54        62.27        19.99        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD 
        2.56         9.76        29.42        17.72        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
        7.99        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
        6.48        25.94        23.64         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       23.77        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.66              1.28 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            14.76             91.73 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            11.51             15.42 
[1] "0.7 - 14.8 (11.5)" "1.3 - 91.7 (15.4)"
[1] "hr=" "2"  
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         0        0        1        0         1        1
  3Q LOSS WILD-TYPE       7        2        0       16        39       10
D41V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                1                 0
  STAGE II                0                16
  STAGE III               1                39
  STAGE IV                1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3Q LOSS MUTATED    1  0  1  1
  3Q LOSS WILD-TYPE 13 25 27  7
D41V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               1                13
  T2               0                25
  T3               1                27
  T4               1                 7
[1] 4 2
[1] 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+N3
  3Q LOSS MUTATED    0  1     1
  3Q LOSS WILD-TYPE 42  9    20
D41V5, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                71 
       TCGA-3H-AB3K        TCGA-3H-AB3L        TCGA-3H-AB3M        TCGA-3H-AB3O 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-3H-AB3S        TCGA-3H-AB3T        TCGA-3H-AB3U        TCGA-3H-AB3X 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-LK-A4NW        TCGA-LK-A4NY        TCGA-LK-A4NZ        TCGA-LK-A4O0 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-LK-A4O2        TCGA-LK-A4O4        TCGA-LK-A4O5        TCGA-LK-A4O6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-MQ-A4KX        TCGA-MQ-A4LC        TCGA-MQ-A4LI        TCGA-MQ-A4LJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-MQ-A4LM        TCGA-MQ-A4LP        TCGA-MQ-A4LV        TCGA-MQ-A6BL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-MQ-A6BN        TCGA-MQ-A6BQ        TCGA-MQ-A6BR        TCGA-MQ-A6BS 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SC-A6LP        TCGA-SC-A6LQ        TCGA-SC-A6LR 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SC-AA5Z        TCGA-SH-A7BC        TCGA-SH-A7BD        TCGA-SH-A7BH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SH-A9CT        TCGA-TS-A7OU        TCGA-TS-A7OY        TCGA-TS-A7OZ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-TS-A7P0        TCGA-TS-A7P1        TCGA-TS-A7P3        TCGA-TS-A7P6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-TS-A7P7        TCGA-TS-A7P8        TCGA-TS-A7PB        TCGA-TS-A8AF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-TS-A8AI        TCGA-TS-A8AS        TCGA-TS-A8AV        TCGA-TS-A8AY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-UD-AABY        TCGA-UD-AABZ        TCGA-UD-AAC1        TCGA-UD-AAC4 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-UD-AAC5        TCGA-UD-AAC6        TCGA-UD-AAC7        TCGA-UT-A88C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-UT-A88D        TCGA-UT-A88E        TCGA-UT-A88G        TCGA-UT-A97Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-YS-A95B        TCGA-YS-A95C        TCGA-YS-AA4M        TCGA-ZN-A9VQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ZN-A9VS        TCGA-ZN-A9VU        TCGA-ZN-A9VW 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D41V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  0
  3Q LOSS WILD-TYPE 47  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    0
  3Q LOSS WILD-TYPE   47    2
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               2                47
  1               0                 2
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    0  3
  3Q LOSS WILD-TYPE 15 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    3
  3Q LOSS WILD-TYPE   15   59
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               0                15
  MALE                 3                59
[1] 2 2
[1] FALSE
D41V8, continuous

Clustering(42) Variable = 4P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    4 24
  4P LOSS WILD-TYPE  7 41
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               28                48 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               24                41 
$`4P LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3X TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-LK-A4O6 
       11.87        29.10        26.40         6.08        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BR 
       11.51        18.81         5.19        17.33        10.95        62.27 
TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7P0 
       19.99        13.61         7.99        14.76         8.38        41.46 
TCGA-TS-A7P6 TCGA-TS-A8AI TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
        9.30        10.78         6.48         8.32        14.99        13.35 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-ZN-A9VS 
       14.27         2.50         4.73        33.70 

$`4P LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U TCGA-LK-A4NW 
       56.38        42.81        12.66        13.61        27.16        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        5.52         8.02         1.87        31.20        80.84        91.73 
TCGA-MQ-A4LJ TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SC-A6LM 
       23.31         3.52        24.89        66.54         0.66        28.96 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD 
        2.56         9.76        29.42        17.72        23.90        15.09 
TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 
       14.76        55.07        27.75        18.51        22.65        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY 
       15.02        32.28        11.77        26.14         1.55        15.42 
TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UT-A88C TCGA-UT-A88D TCGA-XT-AASU 
       27.72        25.94        23.64        23.77        21.44         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VU TCGA-ZN-A9VW 
        1.28         4.37         2.76        16.41        24.30         2.76 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             2.50              0.66 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            62.27             91.73 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           13.035            18.970 
[1] "2.5 - 62.3 (13.0)" "0.7 - 91.7 (19.0)"
[1] "hr=" "1.5"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         3        1        0        7        15        3
  4P LOSS WILD-TYPE       4        1        1        9        25        8
D42V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 3                 4
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                7                 9
  STAGE III              15                25
  STAGE IV                3                 8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  4P LOSS MUTATED    5  8 13  2
  4P LOSS WILD-TYPE  9 17 15  6
D42V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               5                 9
  T2               8                17
  T3              13                15
  T4               2                 6
[1] 4 2
[1] 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+N3
  4P LOSS MUTATED   18  4     6
  4P LOSS WILD-TYPE 24  6    15
D42V5, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0                 18                24
  N1                  4                 6
  N2+N3               6                15
[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"
D42V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   21  0
  4P LOSS WILD-TYPE 28  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     21    0
  4P LOSS WILD-TYPE   28    2
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              21                28
  1               0                 2
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    7 22
  4P LOSS WILD-TYPE  8 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      7   22
  4P LOSS WILD-TYPE    8   40
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               7                 8
  MALE                22                40
[1] 2 2
[1] FALSE
D42V8, continuous
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                 4 
       TCGA-SC-A6LR        TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VU 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 

Clustering(43) Variable = 4Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    4 26
  4Q LOSS WILD-TYPE  7 39
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               30                46 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               26                39 
$`4Q LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T TCGA-3H-AB3X TCGA-LK-A4O0 TCGA-LK-A4O5 
       11.87        29.10        13.61        26.40         6.08        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL 
       14.73        11.51        18.81         5.19        17.33        10.95 
TCGA-MQ-A6BR TCGA-SC-A6LN TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OY 
       62.27        13.61         7.99        14.76        14.76         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AI TCGA-TS-A8AY 
       27.75        41.46         9.30        19.43        10.78        15.42 
TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88G TCGA-UT-A97Y TCGA-ZN-A9VS 
        6.48         8.32        13.35         2.50         4.73        33.70 

$`4Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4NY 
       56.38        42.81        12.66        27.16        17.95         5.52 
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ 
        8.02         1.87        31.20        80.84        91.73        23.31 
TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
        3.52        24.89        66.54        19.99         0.66        28.96 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD 
        2.56         9.76        29.42        17.72        23.90        15.09 
TCGA-TS-A7OU TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF 
       55.07        18.51        22.65        15.02        32.28        11.77 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC6 
       26.14         1.55        27.72        25.94        23.64        14.99 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       23.77        21.44        14.27         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VU TCGA-ZN-A9VW 
        2.76        16.41        24.30         2.76 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             2.50              0.66 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            62.27             91.73 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            13.48             19.25 
[1] "2.5 - 62.3 (13.5)" "0.7 - 91.7 (19.2)"
[1] "hr=" "1.4"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         3        1        0        5        18        3
  4Q LOSS WILD-TYPE       4        1        1       11        22        8
D43V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 3                 4
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                5                11
  STAGE III              18                22
  STAGE IV                3                 8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  4Q LOSS MUTATED    5  6 16  2
  4Q LOSS WILD-TYPE  9 19 12  6
D43V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               5                 9
  T2               6                19
  T3              16                12
  T4               2                 6
[1] 4 2
[1] 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+N3
  4Q LOSS MUTATED   17  6     7
  4Q LOSS WILD-TYPE 25  4    14
D43V5, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0                 17                25
  N1                  6                 4
  N2+N3               7                14
[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"
D43V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   21  0
  4Q LOSS WILD-TYPE 28  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     21    0
  4Q LOSS WILD-TYPE   28    2
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              21                28
  1               0                 2
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    8 22
  4Q LOSS WILD-TYPE  7 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8   22
  4Q LOSS WILD-TYPE    7   40
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               8                 7
  MALE                22                40
[1] 2 2
[1] FALSE
D43V8, continuous
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                 4 
       TCGA-SC-A6LR        TCGA-XT-AASU        TCGA-ZN-A9VQ        TCGA-ZN-A9VU 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 

Clustering(44) Variable = 5P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    0  3
  5P LOSS WILD-TYPE 11 62
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                73 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                62 
$`5P LOSS MUTATED`
TCGA-MQ-A4LV TCGA-SC-A6LQ TCGA-UD-AAC7 
        3.52         9.76        13.35 

$`5P LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 
       27.16        26.40        17.95         5.52         8.02         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        1.87        31.20        12.72        14.73        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL 
       91.73        18.81        23.31         5.19        17.33        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
       24.89        66.54        62.27        19.99         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD 
       13.61         2.56        29.42        17.72        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
        7.99        14.76        14.76        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       41.46        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY 
       32.28        11.77        10.78        26.14         1.55        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 
       27.72         6.48        25.94        23.64         8.32        14.99 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       23.77        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             3.52              0.66 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            13.35             91.73 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             9.76             15.42 
[1] "3.5 - 13.3 (9.8)"  "0.7 - 91.7 (15.4)"
[1] "hr=" "3.4"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         0        0        0        1         2        0
  5P LOSS WILD-TYPE       7        2        1       15        38       11
D44V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               2                38
  STAGE IV                0                11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5P LOSS MUTATED    0  1  2  0
  5P LOSS WILD-TYPE 14 24 26  8
D44V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               0                14
  T2               1                24
  T3               2                26
  T4               0                 8
[1] 4 2
[1] 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+N3
  5P LOSS MUTATED    2  0     1
  5P LOSS WILD-TYPE 40 10    20
D44V5, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0                  2                40
  N1                  0                10
  N2+N3               1                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"
D44V6, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    3  0
  5P LOSS WILD-TYPE 46  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3    0
  5P LOSS WILD-TYPE   46    2
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               3                46
  1               0                 2
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    1  2
  5P LOSS WILD-TYPE 14 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    2
  5P LOSS WILD-TYPE   14   60
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               1                14
  MALE                 2                60
[1] 2 2
[1] FALSE
D44V8, continuous

Clustering(45) Variable = 5Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    1  7
  5Q LOSS WILD-TYPE 10 58
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8                68 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                58 
$`5Q LOSS MUTATED`
TCGA-3H-AB3L TCGA-MQ-A4LV TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SH-A9CU TCGA-TS-A7P1 
       11.87         3.52        13.61         9.76        14.76        18.51 
TCGA-TS-A8AF TCGA-UD-AAC7 
       11.77        13.35 

$`5Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        29.10        42.81        12.66        13.61        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       26.40        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN 
       18.81        23.31         5.19        17.33        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP 
       66.54        62.27        19.99         0.66        28.96         2.56 
TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
       29.42        17.72        23.90        15.09         7.99        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A7P6 
       55.07         8.38        27.75        41.46        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV 
       19.43        15.02        32.28        10.78        26.14         1.55 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 
       15.42        27.72         6.48        25.94        23.64         8.32 
TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       14.99        23.77        21.44        14.27         2.50         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.67         1.28         4.37         2.76        16.41        33.70 
TCGA-ZN-A9VU TCGA-ZN-A9VW 
       24.30         2.76 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             3.52              0.66 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            18.51             91.73 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            12.61             16.87 
[1] "3.5 - 18.5 (12.6)" "0.7 - 91.7 (16.9)"
[1] "hr=" "2.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         1        0        0        1         5        1
  5Q LOSS WILD-TYPE       6        2        1       15        35       10
D45V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 1                 6
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               5                35
  STAGE IV                1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    1  3  2  1
  5Q LOSS WILD-TYPE 13 22 26  7
D45V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               1                13
  T2               3                22
  T3               2                26
  T4               1                 7
[1] 4 2
[1] 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+N3
  5Q LOSS MUTATED    3  0     5
  5Q LOSS WILD-TYPE 39 10    16
D45V5, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0                  3                39
  N1                  0                10
  N2+N3               5                16
[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"
D45V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    6  0
  5Q LOSS WILD-TYPE 43  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      6    0
  5Q LOSS WILD-TYPE   43    2
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               6                43
  1               0                 2
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    1  7
  5Q LOSS WILD-TYPE 14 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    7
  5Q LOSS WILD-TYPE   14   55
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               1                14
  MALE                 7                55
[1] 2 2
[1] FALSE
D45V8, continuous

Clustering(46) Variable = 6P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    0  8
  6P LOSS WILD-TYPE 11 57
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                68 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                57 
$`6P LOSS MUTATED`
TCGA-LK-A4O0 TCGA-LK-A4O7 TCGA-MQ-A6BL TCGA-NQ-A57I TCGA-TS-A7P0 TCGA-TS-A7P6 
        6.08        11.51        10.95         0.66        41.46         9.30 
TCGA-TS-A8AS TCGA-UT-A88G 
       26.14         2.50 

$`6P LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 
       27.16        26.40        17.95         5.52         8.02         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       31.20        12.72        14.73        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       23.31         5.19        17.33         3.52        24.89        66.54 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       62.27        19.99        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
       29.42        17.72        23.90        15.09         7.99        14.76 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 
       14.76        55.07         8.38        27.75        18.51        22.65 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AV 
       19.43        15.02        32.28        11.77        10.78         1.55 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 
       15.42        27.72         6.48        25.94        23.64         8.32 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y 
       14.99        13.35        23.77        21.44        14.27         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.67         1.28         4.37         2.76        16.41        33.70 
TCGA-ZN-A9VU TCGA-ZN-A9VW 
       24.30         2.76 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.66              1.28 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            41.46             91.73 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           10.125            15.915 
[1] "0.7 - 41.5 (10.1)" "1.3 - 91.7 (15.9)"
[1] "hr=" "1.9"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  6P LOSS MUTATED         0        2        1        2         4        0
  6P LOSS WILD-TYPE       7        0        0       14        36       11
D46V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                2                 0
  STAGE IB                1                 0
  STAGE II                2                14
  STAGE III               4                36
  STAGE IV                0                11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6P LOSS MUTATED    3  2  4  0
  6P LOSS WILD-TYPE 11 23 24  8
D46V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               3                11
  T2               2                23
  T3               4                24
  T4               0                 8
[1] 4 2
[1] 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+N3
  6P LOSS MUTATED    5  1     1
  6P LOSS WILD-TYPE 37  9    20
D46V5, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0                  5                37
  N1                  1                 9
  N2+N3               1                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"
D46V6, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    4  0
  6P LOSS WILD-TYPE 45  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4    0
  6P LOSS WILD-TYPE   45    2
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0               4                45
  1               0                 2
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    0  9
  6P LOSS WILD-TYPE 15 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    9
  6P LOSS WILD-TYPE   15   53
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               0                15
  MALE                 9                53
[1] 2 2
[1] FALSE
D46V8, continuous

Clustering(47) Variable = 6Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    4 21
  6Q LOSS WILD-TYPE  7 44
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               25                51 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               21                44 
$`6Q LOSS MUTATED`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       56.38        11.87        29.10         8.02         6.08         1.87 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BQ 
       80.84        91.73        18.81         5.19        10.95        66.54 
TCGA-NQ-A57I TCGA-SH-A7BC TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AS 
        0.66        23.90        41.46         9.30        19.43        26.14 
TCGA-TS-A8AY TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88G TCGA-ZN-A9VQ TCGA-ZN-A9VS 
       15.42         8.32        13.35         2.50        16.41        33.70 
TCGA-ZN-A9VU 
       24.30 

$`6Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW 
       42.81        12.66        13.61        27.16        26.40        17.95 
TCGA-LK-A4NY TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LJ 
        5.52        31.20        12.72        14.73        11.51        23.31 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM 
       17.33         3.52        24.89        62.27        19.99        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BD 
       13.61         2.56         9.76        29.42        17.72        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
        7.99        14.76        14.76        55.07         8.38        27.75 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
       18.51        22.65        15.02        32.28        11.77        10.78 
TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC6 
        1.55        27.72         6.48        25.94        23.64        14.99 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       23.77        21.44        14.27         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VW 
        4.37         2.76         2.76 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.66              1.28 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            91.73             62.27 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            16.41             14.99 
[1] "0.7 - 91.7 (16.4)" "1.3 - 62.3 (15.0)"
[1] "hr=" "1.4"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED         3        2        1        9        11        0
  6Q LOSS WILD-TYPE       4        0        0        7        29       11
D47V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 3                 4
  STAGE IA                2                 0
  STAGE IB                1                 0
  STAGE II                9                 7
  STAGE III              11                29
  STAGE IV                0                11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6Q LOSS MUTATED    6  9 10  0
  6Q LOSS WILD-TYPE  8 16 18  8
D47V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               6                 8
  T2               9                16
  T3              10                18
  T4               0                 8
[1] 4 2
[1] 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+N3
  6Q LOSS MUTATED   18  1     5
  6Q LOSS WILD-TYPE 24  9    16
D47V5, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0                 18                24
  N1                  1                 9
  N2+N3               5                16
[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"
D47V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   15  0
  6Q LOSS WILD-TYPE 34  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     15    0
  6Q LOSS WILD-TYPE   34    2
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              15                34
  1               0                 2
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    4 22
  6Q LOSS WILD-TYPE 11 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4   22
  6Q LOSS WILD-TYPE   11   40
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               4                11
  MALE                22                40
[1] 2 2
[1] FALSE
D47V8, continuous

Clustering(48) Variable = 8P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    2  8
  8P LOSS WILD-TYPE  9 57
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10                66 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                57 
$`8P LOSS MUTATED`
TCGA-3H-AB3K TCGA-LK-A4O0 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A6BQ TCGA-SC-A6LQ 
       56.38         6.08        91.73        18.81        66.54         9.76 
TCGA-SH-A9CU TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-UD-AAC5 
       14.76        27.75        18.51         8.32 

$`8P LOSS WILD-TYPE`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       11.87        29.10        42.81        12.66        13.61        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 
       26.40        17.95         5.52         8.02         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       12.72        14.73        11.51        80.84        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-MQ-A6BS 
       17.33         3.52        10.95        24.89        62.27        19.99 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SC-AA5Z 
        0.66        28.96        13.61         2.56        29.42        17.72 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY 
       23.90        15.09         7.99        14.76        55.07         8.38 
TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       41.46        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        6.48        25.94        23.64        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       21.44        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        33.70        24.30         2.76 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             6.08              0.66 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            91.73             80.84 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           18.660            15.005 
[1] "6.1 - 91.7 (18.7)" "0.7 - 80.8 (15.0)"
[1] "hr=" "2"  
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         2        1        0        4         2        1
  8P LOSS WILD-TYPE       5        1        1       12        38       10
D48V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 2                 5
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                4                12
  STAGE III               2                38
  STAGE IV                1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8P LOSS MUTATED    3  4  2  1
  8P LOSS WILD-TYPE 11 21 26  7
D48V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               3                11
  T2               4                21
  T3               2                26
  T4               1                 7
[1] 4 2
[1] 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+N3
  8P LOSS MUTATED    7  1     2
  8P LOSS WILD-TYPE 35  9    19
D48V5, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0                  7                35
  N1                  1                 9
  N2+N3               2                19
[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"
D48V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    7  0
  8P LOSS WILD-TYPE 42  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      7    0
  8P LOSS WILD-TYPE   42    2
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               7                42
  1               0                 2
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    2  8
  8P LOSS WILD-TYPE 13 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2    8
  8P LOSS WILD-TYPE   13   54
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               2                13
  MALE                 8                54
[1] 2 2
[1] FALSE
D48V8, continuous

Clustering(49) Variable = 8Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    1  3
  8Q LOSS WILD-TYPE 10 62
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                72 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                62 
$`8Q LOSS MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A4LI TCGA-SH-A9CU TCGA-UD-AAC5 
        6.08        18.81        14.76         8.32 

$`8Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 
       27.16        26.40        17.95         5.52         8.02         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       66.54        62.27        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD 
        2.56         9.76        29.42        17.72        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
        7.99        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        6.48        25.94        23.64        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       21.44        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        33.70        24.30         2.76 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             6.08              0.66 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            18.81             91.73 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           11.540            15.255 
[1] "6.1 - 18.8 (11.5)" "0.7 - 91.7 (15.3)"
[1] "hr=" "1.6"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         1        1        0        1         0        1
  8Q LOSS WILD-TYPE       6        1        1       15        40       10
D49V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 1                 6
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               0                40
  STAGE IV                1                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8Q LOSS MUTATED    2  1  0  1
  8Q LOSS WILD-TYPE 12 24 28  7
D49V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               2                12
  T2               1                24
  T3               0                28
  T4               1                 7
[1] 4 2
[1] 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+N3
  8Q LOSS MUTATED    3  0     1
  8Q LOSS WILD-TYPE 39 10    20
D49V5, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0                  3                39
  N1                  0                10
  N2+N3               1                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"
D49V6, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    4  0
  8Q LOSS WILD-TYPE 45  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      4    0
  8Q LOSS WILD-TYPE   45    2
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               4                45
  1               0                 2
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    1  3
  8Q LOSS WILD-TYPE 14 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    3
  8Q LOSS WILD-TYPE   14   59
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               1                14
  MALE                 3                59
[1] 2 2
[1] FALSE
D49V8, continuous

Clustering(50) Variable = 9P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED    1 24
  9P LOSS WILD-TYPE 10 41
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               25                51 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               24                41 
$`9P LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3T TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O7 TCGA-MQ-A4LM 
       11.87        13.61         5.52         6.08        11.51         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       17.33         3.52        19.99         0.66        28.96        13.61 
TCGA-SH-A7BC TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       23.90        14.76         8.38        27.75        41.46        18.51 
TCGA-TS-A7P6 TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AAC7 TCGA-UT-A88E 
        9.30        11.77        10.78        15.42        13.35        14.27 
TCGA-UT-A88G 
        2.50 

$`9P LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3U TCGA-3H-AB3X 
       56.38        29.10        42.81        12.66        27.16        26.40 
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 
       17.95         8.02         1.87        31.20        12.72        14.73 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BL TCGA-MQ-A6BN 
       80.84        91.73        18.81        23.31        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z 
       66.54        62.27         2.56         9.76        29.42        17.72 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7P3 TCGA-TS-A7P7 
       15.09         7.99        14.76        55.07        22.65        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AS TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AABZ 
       15.02        32.28        26.14         1.55        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D 
       25.94        23.64         8.32        14.99        23.77        21.44 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ 
        4.73         4.67         1.28         4.37         2.76        16.41 
TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       33.70        24.30         2.76 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.66              1.28 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            41.46             91.73 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            13.35             18.81 
[1] "0.7 - 41.5 (13.3)" "1.3 - 91.7 (18.8)"
[1] "hr=" "2.1"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         3        1        1        3        14        4
  9P LOSS WILD-TYPE       4        1        0       13        26        7
D50V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 3                 4
  STAGE IA                1                 1
  STAGE IB                1                 0
  STAGE II                3                13
  STAGE III              14                26
  STAGE IV                4                 7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9P LOSS MUTATED    5  5 12  3
  9P LOSS WILD-TYPE  9 20 16  5
D50V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               5                 9
  T2               5                20
  T3              12                16
  T4               3                 5
[1] 4 2
[1] 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+N3
  9P LOSS MUTATED   12  4     7
  9P LOSS WILD-TYPE 30  6    14
D50V5, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0                 12                30
  N1                  4                 6
  N2+N3               7                14
[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"
D50V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   15  0
  9P LOSS WILD-TYPE 34  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     15    0
  9P LOSS WILD-TYPE   34    2
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              15                34
  1               0                 2
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    3 23
  9P LOSS WILD-TYPE 12 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      3   23
  9P LOSS WILD-TYPE   12   39
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               3                12
  MALE                23                39
[1] 2 2
[1] FALSE
D50V8, continuous

Clustering(51) Variable = 9Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    1 16
  9Q LOSS WILD-TYPE 10 49
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               17                59 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               16                49 
$`9Q LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3T TCGA-LK-A4O0 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A4LV 
       11.87        13.61         6.08        18.81         5.19         3.52 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BC TCGA-SH-A9CT TCGA-SH-A9CU 
       19.99         0.66        28.96        23.90        14.76        14.76 
TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G 
        8.38        41.46        13.35        14.27         2.50 

$`9Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3U TCGA-3H-AB3X 
       56.38        29.10        42.81        12.66        27.16        26.40 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LP 
       14.73        11.51        80.84        91.73        23.31        17.33 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LN TCGA-SC-A6LP 
       10.95        24.89        66.54        62.27        13.61         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-SH-A7BH TCGA-TS-A7OU 
        9.76        29.42        17.72        15.09         7.99        55.07 
TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       27.75        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY 
       32.28        11.77        10.78        26.14         1.55        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 
       27.72         6.48        25.94        23.64         8.32        14.99 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       23.77        21.44         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        2.76        16.41        33.70        24.30         2.76 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.66              1.28 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            41.46             91.73 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            13.61             17.33 
[1] "0.7 - 41.5 (13.6)" "1.3 - 91.7 (17.3)"
[1] "hr=" "1.8"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         2        1        1        5         6        3
  9Q LOSS WILD-TYPE       5        1        0       11        34        8
D51V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 2                 5
  STAGE IA                1                 1
  STAGE IB                1                 0
  STAGE II                5                11
  STAGE III               6                34
  STAGE IV                3                 8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9Q LOSS MUTATED    4  5  6  2
  9Q LOSS WILD-TYPE 10 20 22  6
D51V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               4                10
  T2               5                20
  T3               6                22
  T4               2                 6
[1] 4 2
[1] 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+N3
  9Q LOSS MUTATED   11  0     4
  9Q LOSS WILD-TYPE 31 10    17
D51V5, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0                 11                31
  N1                  0                10
  N2+N3               4                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   13  0
  9Q LOSS WILD-TYPE 36  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     13    0
  9Q LOSS WILD-TYPE   36    2
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              13                36
  1               0                 2
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    2 16
  9Q LOSS WILD-TYPE 13 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2   16
  9Q LOSS WILD-TYPE   13   46
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               2                13
  MALE                16                46
[1] 2 2
[1] FALSE
D51V8, continuous

Clustering(52) Variable = 10P LOSS MUTATION ANALYSIS
D52V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    2 19
  10P LOSS WILD-TYPE  9 46
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                21                 55 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                19                 46 
$`10P LOSS MUTATED`
TCGA-3H-AB3L TCGA-LK-A4O7 TCGA-MQ-A4LP TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC 
       11.87        11.51        17.33        19.99         0.66        23.90 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P6 
       15.09         7.99        14.76        41.46        18.51         9.30 
TCGA-TS-A7P8 TCGA-TS-A8AI TCGA-UD-AABY TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88G 
       15.02        10.78        27.72         8.32        13.35         2.50 
TCGA-XT-AASU TCGA-ZN-A9VQ TCGA-ZN-A9VW 
        4.67        16.41         2.76 

$`10P LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        29.10        42.81        12.66        13.61        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       26.40        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       31.20        12.72        14.73        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       23.31         5.19         3.52        10.95        24.89        66.54 
TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
       62.27        28.96        13.61         2.56         9.76        29.42 
TCGA-SC-AA5Z TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P3 
       17.72        14.76        55.07         8.38        27.75        22.65 
TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY 
       19.43        32.28        11.77        26.14         1.55        15.42 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D 
        6.48        25.94        23.64        14.99        23.77        21.44 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VS 
       14.27         4.73         1.28         4.37         2.76        33.70 
TCGA-ZN-A9VU 
       24.30 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.66               1.28 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             41.46              91.73 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             13.35              17.95 
[1] "0.7 - 41.5 (13.3)" "1.3 - 91.7 (17.9)"
[1] "hr=" "1.8"
D52V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         3        0        1        3        11        4
  10P LOSS WILD-TYPE       4        2        0       13        29        7
D52V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  3                  4
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 3                 13
  STAGE III               11                 29
  STAGE IV                 4                  7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10P LOSS MUTATED    4  4  9  3
  10P LOSS WILD-TYPE 10 21 19  5
D52V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                4                 10
  T2                4                 21
  T3                9                 19
  T4                3                  5
[1] 4 2
[1] 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+N3
  10P LOSS MUTATED   12  3     4
  10P LOSS WILD-TYPE 30  7    17
D52V5, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                  12                 30
  N1                   3                  7
  N2+N3                4                 17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   10  1
  10P LOSS WILD-TYPE 39  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     10    1
  10P LOSS WILD-TYPE   39    1
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               10                 39
  1                1                  1
[1] 2 2
[1] FALSE
D52V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    1 21
  10P LOSS WILD-TYPE 14 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   21
  10P LOSS WILD-TYPE   14   41
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                1                 14
  MALE                 21                 41
[1] 2 2
[1] FALSE
D52V8, continuous

Clustering(53) Variable = 10Q LOSS MUTATION ANALYSIS
D53V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    2 15
  10Q LOSS WILD-TYPE  9 50
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                17                 59 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                15                 50 
$`10Q LOSS MUTATED`
TCGA-3H-AB3L TCGA-LK-A4O7 TCGA-MQ-A4LP TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BD 
       11.87        11.51        17.33        19.99         0.66        15.09 
TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A8AI TCGA-UD-AAC5 
        7.99        14.76         9.30        15.02        10.78         8.32 
TCGA-UD-AAC7 TCGA-UT-A88G TCGA-UT-A97Y TCGA-ZN-A9VQ TCGA-ZN-A9VW 
       13.35         2.50         4.73        16.41         2.76 

$`10Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        29.10        42.81        12.66        13.61        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       26.40        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       31.20        12.72        14.73        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       23.31         5.19         3.52        10.95        24.89        66.54 
TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
       62.27        28.96        13.61         2.56         9.76        29.42 
TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
       17.72        23.90        14.76        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AF 
       41.46        18.51        22.65        19.43        32.28        11.77 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       26.14         1.55        15.42        27.72         6.48        25.94 
TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-XT-AASU 
       23.64        14.99        23.77        21.44        14.27         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        33.70        24.30 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.66               1.28 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             19.99              91.73 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             11.51              18.81 
[1] "0.7 - 20.0 (11.5)" "1.3 - 91.7 (18.8)"
[1] "hr=" "2.7"
D53V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         3        0        1        2         7        4
  10Q LOSS WILD-TYPE       4        2        0       14        33        7
D53V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  3                  4
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 2                 14
  STAGE III                7                 33
  STAGE IV                 4                  7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10Q LOSS MUTATED    4  3  5  3
  10Q LOSS WILD-TYPE 10 22 23  5
D53V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                4                 10
  T2                3                 22
  T3                5                 23
  T4                3                  5
[1] 4 2
[1] 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+N3
  10Q LOSS MUTATED   10  3     3
  10Q LOSS WILD-TYPE 32  7    18
D53V5, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                  10                 32
  N1                   3                  7
  N2+N3                3                 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"
D53V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    9  1
  10Q LOSS WILD-TYPE 40  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      9    1
  10Q LOSS WILD-TYPE   40    1
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                9                 40
  1                1                  1
[1] 2 2
[1] FALSE
D53V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    2 15
  10Q LOSS WILD-TYPE 13 47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2   15
  10Q LOSS WILD-TYPE   13   47
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                2                 13
  MALE                 15                 47
[1] 2 2
[1] FALSE
D53V8, continuous
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                  4 
        TCGA-SC-A6LR         TCGA-XT-AASU         TCGA-ZN-A9VS 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ZN-A9VU 
"10Q LOSS WILD-TYPE" 

Clustering(54) Variable = 11P LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    0  4
  11P LOSS WILD-TYPE 11 61
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 4                 72 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 4                 61 
$`11P LOSS MUTATED`
TCGA-3H-AB3M TCGA-LK-A4O0 TCGA-NQ-A57I TCGA-SC-A6LN 
       29.10         6.08         0.66        13.61 

$`11P LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        11.87        42.81        12.66        13.61        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 
       26.40        17.95         5.52         8.02         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ 
       66.54        62.27        19.99        28.96         2.56         9.76 
TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
       29.42        17.72        23.90        15.09         7.99        14.76 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       14.76        55.07         8.38        27.75        41.46        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF 
       22.65         9.30        19.43        15.02        32.28        11.77 
TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       10.78        26.14         1.55        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       25.94        23.64         8.32        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       21.44        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        33.70        24.30         2.76 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.66               1.28 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             29.10              91.73 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             9.845             15.255 
[1] "0.7 - 29.1 (9.8)"  "1.3 - 91.7 (15.3)"
[1] "hr=" "1.8"
D54V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         0        1        1        0         2        0
  11P LOSS WILD-TYPE       7        1        0       16        38       11
D54V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 1                  1
  STAGE IB                 1                  0
  STAGE II                 0                 16
  STAGE III                2                 38
  STAGE IV                 0                 11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11P LOSS MUTATED    2  1  1  0
  11P LOSS WILD-TYPE 12 24 27  8
D54V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                2                 12
  T2                1                 24
  T3                1                 27
  T4                0                  8
[1] 4 2
[1] 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+N3
  11P LOSS MUTATED    1  0     2
  11P LOSS WILD-TYPE 41 10    19
D54V5, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                   1                 41
  N1                   0                 10
  N2+N3                2                 19
[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"
D54V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    3  0
  11P LOSS WILD-TYPE 46  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3    0
  11P LOSS WILD-TYPE   46    2
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                3                 46
  1                0                  2
[1] 2 2
[1] FALSE
D54V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    1  3
  11P LOSS WILD-TYPE 14 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1    3
  11P LOSS WILD-TYPE   14   59
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                1                 14
  MALE                  3                 59
[1] 2 2
[1] FALSE
D54V8, continuous

Clustering(55) Variable = 11Q LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    0  5
  11Q LOSS WILD-TYPE 11 60
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 71 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 60 
$`11Q LOSS MUTATED`
TCGA-3H-AB3M TCGA-LK-A4O0 TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-NQ-A57I 
       29.10         6.08         5.19         3.52         0.66 

$`11Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        11.87        42.81        12.66        13.61        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 
       26.40        17.95         5.52         8.02         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       23.31        17.33        10.95        24.89        66.54        62.27 
TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
       19.99        28.96        13.61         2.56         9.76        29.42 
TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
       17.72        23.90        15.09         7.99        14.76        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       26.14         1.55        15.42        27.72         6.48        25.94 
TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D 
       23.64         8.32        14.99        13.35        23.77        21.44 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       14.27         2.50         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        2.76        16.41        33.70        24.30         2.76 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.66               1.28 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             29.10              91.73 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              5.19              15.42 
[1] "0.7 - 29.1 (5.2)"  "1.3 - 91.7 (15.4)"
[1] "hr=" "2.6"
D55V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         0        1        1        0         3        0
  11Q LOSS WILD-TYPE       7        1        0       16        37       11
D55V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 1                  1
  STAGE IB                 1                  0
  STAGE II                 0                 16
  STAGE III                3                 37
  STAGE IV                 0                 11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED    2  0  3  0
  11Q LOSS WILD-TYPE 12 25 25  8
D55V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                2                 12
  T2                0                 25
  T3                3                 25
  T4                0                  8
[1] 4 2
[1] 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+N3
  11Q LOSS MUTATED    3  0     1
  11Q LOSS WILD-TYPE 39 10    20
D55V5, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                   3                 39
  N1                   0                 10
  N2+N3                1                 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"
D55V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    4  0
  11Q LOSS WILD-TYPE 45  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4    0
  11Q LOSS WILD-TYPE   45    2
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                4                 45
  1                0                  2
[1] 2 2
[1] FALSE
D55V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    1  4
  11Q LOSS WILD-TYPE 14 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1    4
  11Q LOSS WILD-TYPE   14   58
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                1                 14
  MALE                  4                 58
[1] 2 2
[1] FALSE
D55V8, continuous

Clustering(56) Variable = 12P LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    0  3
  12P LOSS WILD-TYPE 11 62
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 73 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 62 
$`12P LOSS MUTATED`
TCGA-3H-AB3T TCGA-SH-A7BH TCGA-SH-A9CT 
       13.61         7.99        14.76 

$`12P LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3U 
       56.38        11.87        29.10        42.81        12.66        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       26.40        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
       24.89        66.54        62.27        19.99         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC 
       13.61         2.56         9.76        29.42        17.72        23.90 
TCGA-SH-A7BD TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
       15.09        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
        6.48        25.94        23.64         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       23.77        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              7.99               0.66 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             14.76              91.73 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             13.61              15.42 
[1] "8.0 - 14.8 (13.6)" "0.7 - 91.7 (15.4)"
[1] "hr=" "2.3"
D56V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  12P LOSS MUTATED         1        0        0        1         1        0
  12P LOSS WILD-TYPE       6        2        1       15        39       11
D56V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 1                 15
  STAGE III                1                 39
  STAGE IV                 0                 11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12P LOSS MUTATED    1  1  1  0
  12P LOSS WILD-TYPE 13 24 27  8
D56V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                1                 13
  T2                1                 24
  T3                1                 27
  T4                0                  8
[1] 4 2
[1] 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+N3
  12P LOSS MUTATED    3  0     0
  12P LOSS WILD-TYPE 39 10    21
D56V5, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                   3                 39
  N1                   0                 10
  N2+N3                0                 21
[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"
D56V6, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    3  0
  12P LOSS WILD-TYPE 46  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    0
  12P LOSS WILD-TYPE   46    2
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                3                 46
  1                0                  2
[1] 2 2
[1] FALSE
D56V7, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    1  2
  12P LOSS WILD-TYPE 14 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1    2
  12P LOSS WILD-TYPE   14   60
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                1                 14
  MALE                  2                 60
[1] 2 2
[1] FALSE
D56V8, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                  5 
        TCGA-SC-A6LR         TCGA-XT-AASU         TCGA-ZN-A9VQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 

Clustering(57) Variable = 13Q LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    4 28
  13Q LOSS WILD-TYPE  7 37
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                32                 44 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                28                 37 
$`13Q LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3T TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       11.87        13.61        17.95         6.08         1.87        12.72 
TCGA-MQ-A4KX TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL 
       80.84        18.81        23.31         5.19         3.52        10.95 
TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       19.99        13.61         2.56        23.90        15.09         7.99 
TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AI TCGA-TS-A8AS 
       14.76         8.38         9.30        19.43        10.78        26.14 
TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G TCGA-YS-AA4M 
       15.42         6.48        13.35        23.77         2.50         2.76 
TCGA-ZN-A9VS TCGA-ZN-A9VU 
       33.70        24.30 

$`13Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3U TCGA-3H-AB3X 
       56.38        29.10        42.81        12.66        27.16        26.40 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LC 
        5.52         8.02        31.20        14.73        11.51        91.73 
TCGA-MQ-A4LP TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM 
       17.33        24.89        66.54        62.27         0.66        28.96 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OZ 
        9.76        29.42        17.72        14.76        55.07        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF 
       41.46        18.51        22.65        15.02        32.28        11.77 
TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 
        1.55        27.72        25.94        23.64         8.32        14.99 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       21.44        14.27         4.73         4.67         1.28         4.37 
TCGA-ZN-A9VQ TCGA-ZN-A9VW 
       16.41         2.76 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              1.87               0.66 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             80.84              91.73 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            13.480             18.115 
[1] "1.9 - 80.8 (13.5)" "0.7 - 91.7 (18.1)"
[1] "hr=" "1.7"
D57V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         2        2        0        7        15        6
  13Q LOSS WILD-TYPE       5        0        1        9        25        5
D57V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  2                  5
  STAGE IA                 2                  0
  STAGE IB                 0                  1
  STAGE II                 7                  9
  STAGE III               15                 25
  STAGE IV                 6                  5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  13Q LOSS MUTATED    5 10 13  3
  13Q LOSS WILD-TYPE  9 15 15  5
D57V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                5                  9
  T2               10                 15
  T3               13                 15
  T4                3                  5
[1] 4 2
[1] 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+N3
  13Q LOSS MUTATED   20  3     9
  13Q LOSS WILD-TYPE 22  7    12
D57V5, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                  20                 22
  N1                   3                  7
  N2+N3                9                 12
[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"
D57V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   21  2
  13Q LOSS WILD-TYPE 28  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     21    2
  13Q LOSS WILD-TYPE   28    0
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               21                 28
  1                2                  0
[1] 2 2
[1] FALSE
D57V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    5 27
  13Q LOSS WILD-TYPE 10 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      5   27
  13Q LOSS WILD-TYPE   10   35
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                5                 10
  MALE                 27                 35
[1] 2 2
[1] FALSE
D57V8, continuous

Clustering(58) Variable = 14Q LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    3 27
  14Q LOSS WILD-TYPE  8 38
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                30                 46 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                27                 38 
$`14Q LOSS MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3S TCGA-3H-AB3X TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
       29.10        12.66        26.40         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SC-A6LQ 
       11.51        18.81        23.31        19.99        13.61         9.76 
TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7OZ 
       23.90         7.99        14.76        14.76         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A8AF TCGA-TS-A8AY TCGA-UD-AABZ 
       41.46         9.30        15.02        11.77        15.42         6.48 
TCGA-UD-AAC7 TCGA-UT-A88G TCGA-UT-A97Y TCGA-YS-A95B TCGA-YS-A95C TCGA-ZN-A9VS 
       13.35         2.50         4.73         1.28         4.37        33.70 

$`14Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3T TCGA-3H-AB3U TCGA-LK-A4NW 
       56.38        11.87        42.81        13.61        27.16        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        5.52         8.02         6.08        31.20        80.84        91.73 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        66.54 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SC-AA5Z 
       62.27         0.66        28.96         2.56        29.42        17.72 
TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7PB 
       15.09        55.07        18.51        22.65        19.43        32.28 
TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC4 
       10.78        26.14         1.55        27.72        25.94        23.64 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-XT-AASU 
        8.32        14.99        23.77        21.44        14.27         4.67 
TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VU TCGA-ZN-A9VW 
        2.76        16.41        24.30         2.76 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              1.28               0.66 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             41.46              91.73 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             13.48              18.23 
[1] "1.3 - 41.5 (13.5)" "0.7 - 91.7 (18.2)"
[1] "hr=" "1.7"
D58V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED         1        0        0        7        20        3
  14Q LOSS WILD-TYPE       6        2        1        9        20        8
D58V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 7                  9
  STAGE III               20                 20
  STAGE IV                 3                  8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  14Q LOSS MUTATED    2 10 16  2
  14Q LOSS WILD-TYPE 12 15 12  6
D58V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                2                 12
  T2               10                 15
  T3               16                 12
  T4                2                  6
[1] 4 2
[1] 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+N3
  14Q LOSS MUTATED   14  6    10
  14Q LOSS WILD-TYPE 28  4    11
D58V5, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                  14                 28
  N1                   6                  4
  N2+N3               10                 11
[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"
D58V6, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   21  0
  14Q LOSS WILD-TYPE 28  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     21    0
  14Q LOSS WILD-TYPE   28    2
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               21                 28
  1                0                  2
[1] 2 2
[1] FALSE
D58V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   10 21
  14Q LOSS WILD-TYPE  5 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10   21
  14Q LOSS WILD-TYPE    5   41
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               10                  5
  MALE                 21                 41
[1] 2 2
[1] FALSE
D58V8, continuous
[1] "Remove cluster labels:" "14Q LOSS MUTATED"      
clus
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 2                  4 
        TCGA-SC-A6LR         TCGA-XT-AASU         TCGA-ZN-A9VQ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ZN-A9VU 
"14Q LOSS WILD-TYPE" 

Clustering(59) Variable = 15Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    1  9
  15Q LOSS WILD-TYPE 10 56
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                10                 66 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 9                 56 
$`15Q LOSS MUTATED`
TCGA-3H-AB3T TCGA-LK-A4O0 TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC 
       13.61         6.08         3.52        19.99         0.66        23.90 
TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P6 TCGA-UD-AABZ 
        7.99        14.76         9.30         6.48 

$`15Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3U 
       56.38        11.87        29.10        42.81        12.66        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 
       26.40        17.95         5.52         8.02         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       23.31         5.19        17.33        10.95        24.89        66.54 
TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
       62.27        28.96        13.61         2.56         9.76        29.42 
TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
       17.72        15.09        14.76        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       41.46        18.51        22.65        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       25.94        23.64         8.32        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       21.44        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        33.70        24.30         2.76 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.66               1.28 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             23.90              91.73 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             8.645             16.870 
[1] "0.7 - 23.9 (8.6)"  "1.3 - 91.7 (16.9)"
[1] "hr=" "2.4"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         1        1        1        2         4        1
  15Q LOSS WILD-TYPE       6        1        0       14        36       10
D59V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 1                  1
  STAGE IB                 1                  0
  STAGE II                 2                 14
  STAGE III                4                 36
  STAGE IV                 1                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  15Q LOSS MUTATED    3  2  4  1
  15Q LOSS WILD-TYPE 11 23 24  7
D59V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                3                 11
  T2                2                 23
  T3                4                 24
  T4                1                  7
[1] 4 2
[1] 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+N3
  15Q LOSS MUTATED    6  0     3
  15Q LOSS WILD-TYPE 36 10    18
D59V5, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                   6                 36
  N1                   0                 10
  N2+N3                3                 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"
D59V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    7  0
  15Q LOSS WILD-TYPE 42  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7    0
  15Q LOSS WILD-TYPE   42    2
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0                7                 42
  1                0                  2
[1] 2 2
[1] FALSE
D59V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  9
  15Q LOSS WILD-TYPE 14 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    9
  15Q LOSS WILD-TYPE   14   53
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                1                 14
  MALE                  9                 53
[1] 2 2
[1] FALSE
D59V8, continuous
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                  5 
        TCGA-SC-A6LR         TCGA-XT-AASU         TCGA-ZN-A9VQ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 

Clustering(60) Variable = 16P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    2  5
  16P LOSS WILD-TYPE  9 60
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 7                 69 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 60 
$`16P LOSS MUTATED`
TCGA-3H-AB3X TCGA-LK-A4O0 TCGA-MQ-A4LM TCGA-MQ-A6BS TCGA-UT-A88G TCGA-UT-A97Y 
       26.40         6.08         5.19        19.99         2.50         4.73 
TCGA-ZN-A9VQ 
       16.41 

$`16P LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 
       27.16        17.95         5.52         8.02         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       23.31        17.33         3.52        10.95        24.89        66.54 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       62.27         0.66        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
       29.42        17.72        23.90        15.09         7.99        14.76 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       14.76        55.07         8.38        27.75        41.46        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF 
       22.65         9.30        19.43        15.02        32.28        11.77 
TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       10.78        26.14         1.55        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       25.94        23.64         8.32        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
       21.44        14.27         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       33.70        24.30         2.76 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              2.50               0.66 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             26.40              91.73 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              6.08              15.09 
[1] "2.5 - 26.4 (6.1)"  "0.7 - 91.7 (15.1)"
[1] "hr=" "1.5"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         2        1        0        1         3        0
  16P LOSS WILD-TYPE       5        1        1       15        37       11
D60V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  2                  5
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 1                 15
  STAGE III                3                 37
  STAGE IV                 0                 11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  16P LOSS MUTATED    3  1  3  0
  16P LOSS WILD-TYPE 11 24 25  8
D60V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                3                 11
  T2                1                 24
  T3                3                 25
  T4                0                  8
[1] 4 2
[1] 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+N3
  16P LOSS MUTATED    7  0     0
  16P LOSS WILD-TYPE 35 10    21
D60V5, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                   7                 35
  N1                   0                 10
  N2+N3                0                 21
[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"
D60V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    5  0
  16P LOSS WILD-TYPE 44  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5    0
  16P LOSS WILD-TYPE   44    2
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                5                 44
  1                0                  2
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  6
  16P LOSS WILD-TYPE 14 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    6
  16P LOSS WILD-TYPE   14   56
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                1                 14
  MALE                  6                 56
[1] 2 2
[1] FALSE
D60V8, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                  5 
        TCGA-SC-A6LR         TCGA-SH-A7BH         TCGA-XT-AASU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 

Clustering(61) Variable = 16Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    2  7
  16Q LOSS WILD-TYPE  9 58
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 9                 67 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                 58 
$`16Q LOSS MUTATED`
TCGA-3H-AB3T TCGA-3H-AB3X TCGA-LK-A4O0 TCGA-LK-A4O6 TCGA-MQ-A6BS TCGA-UD-AABZ 
       13.61        26.40         6.08        14.73        19.99         6.48 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-ZN-A9VQ 
        2.50         4.73        16.41 

$`16Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3U 
       56.38        11.87        29.10        42.81        12.66        27.16 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.72 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        66.54        62.27 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
        0.66        28.96        13.61         2.56         9.76        29.42 
TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
       17.72        23.90        15.09         7.99        14.76        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC4 
       26.14         1.55        15.42        27.72        25.94        23.64 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E 
        8.32        14.99        13.35        23.77        21.44        14.27 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VS TCGA-ZN-A9VU 
        4.67         1.28         4.37         2.76        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              2.50               0.66 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             26.40              91.73 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             13.61              15.42 
[1] "2.5 - 26.4 (13.6)" "0.7 - 91.7 (15.4)"
[1] "hr=" "1.6"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         3        1        0        3         3        0
  16Q LOSS WILD-TYPE       4        1        1       13        37       11
D61V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  3                  4
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 3                 13
  STAGE III                3                 37
  STAGE IV                 0                 11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  16Q LOSS MUTATED    4  3  3  0
  16Q LOSS WILD-TYPE 10 22 25  8
D61V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                4                 10
  T2                3                 22
  T3                3                 25
  T4                0                  8
[1] 4 2
[1] 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+N3
  16Q LOSS MUTATED    8  1     0
  16Q LOSS WILD-TYPE 34  9    21
D61V5, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                   8                 34
  N1                   1                  9
  N2+N3                0                 21
[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"
D61V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    7  0
  16Q LOSS WILD-TYPE 42  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7    0
  16Q LOSS WILD-TYPE   42    2
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                7                 42
  1                0                  2
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    2  8
  16Q LOSS WILD-TYPE 13 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    8
  16Q LOSS WILD-TYPE   13   54
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                2                 13
  MALE                  8                 54
[1] 2 2
[1] FALSE
D61V8, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                  5 
        TCGA-SC-A6LR         TCGA-SH-A7BH         TCGA-XT-AASU 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 

Clustering(62) Variable = 17P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED    3 18
  17P LOSS WILD-TYPE  8 47
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                21                 55 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                18                 47 
$`17P LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T TCGA-LK-A4NW TCGA-MQ-A6BS TCGA-NQ-A57I 
       11.87        29.10        13.61        17.95        19.99         0.66 
TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU 
       13.61         9.76         7.99        14.76        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A8AY TCGA-UD-AAC7 TCGA-UT-A88C 
        8.38        41.46        22.65        15.42        13.35        23.77 
TCGA-UT-A88G TCGA-YS-A95B TCGA-ZN-A9VS 
        2.50         1.28        33.70 

$`17P LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NY 
       56.38        42.81        12.66        27.16        26.40         5.52 
TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 
        8.02         6.08         1.87        31.20        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        66.54        62.27 
TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD 
       28.96         2.56        29.42        17.72        23.90        15.09 
TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       27.75        18.51         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AABZ 
       11.77        10.78        26.14         1.55        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A88E 
       25.94        23.64         8.32        14.99        21.44        14.27 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VU 
        4.73         4.67         4.37         2.76        16.41        24.30 
TCGA-ZN-A9VW 
        2.76 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.66               1.55 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             55.07              91.73 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             14.76              16.41 
[1] "0.7 - 55.1 (14.8)" "1.6 - 91.7 (16.4)"
[1] "hr=" "1.2"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         1        0        1        3        11        5
  17P LOSS WILD-TYPE       6        2        0       13        29        6
D62V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 3                 13
  STAGE III               11                 29
  STAGE IV                 5                  6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17P LOSS MUTATED    2  4 10  4
  17P LOSS WILD-TYPE 12 21 18  4
D62V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                2                 12
  T2                4                 21
  T3               10                 18
  T4                4                  4
[1] 4 2
[1] 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+N3
  17P LOSS MUTATED    9  1    10
  17P LOSS WILD-TYPE 33  9    11
D62V5, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                   9                 33
  N1                   1                  9
  N2+N3               10                 11
[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"
D62V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   13  0
  17P LOSS WILD-TYPE 36  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     13    0
  17P LOSS WILD-TYPE   36    2
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               13                 36
  1                0                  2
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    5 16
  17P LOSS WILD-TYPE 10 46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5   16
  17P LOSS WILD-TYPE   10   46
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                5                 10
  MALE                 16                 46
[1] 2 2
[1] FALSE
D62V8, continuous
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                  4 
        TCGA-SC-A6LR         TCGA-XT-AASU         TCGA-ZN-A9VQ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ZN-A9VU 
"17P LOSS WILD-TYPE" 

Clustering(63) Variable = 17Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    2  5
  17Q LOSS WILD-TYPE  9 60
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                 69 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 60 
$`17Q LOSS MUTATED`
TCGA-NQ-A57I TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-UT-A88G TCGA-YS-A95B 
        0.66         7.99        14.76        41.46         2.50         1.28 
TCGA-ZN-A9VS 
       33.70 

$`17Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 
       27.16        26.40        17.95         5.52         8.02         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        1.87        31.20        12.72        14.73        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM 
       10.95        24.89        66.54        62.27        19.99        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC 
       13.61         2.56         9.76        29.42        17.72        23.90 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 
       15.09        14.76        55.07         8.38        27.75        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF 
       22.65         9.30        19.43        15.02        32.28        11.77 
TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       10.78        26.14         1.55        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       25.94        23.64         8.32        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M 
       21.44        14.27         4.73         4.67         4.37         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VU TCGA-ZN-A9VW 
       16.41        24.30         2.76 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.66               1.55 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             41.46              91.73 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              7.99              15.42 
[1] "0.7 - 41.5 (8.0)"  "1.6 - 91.7 (15.4)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED         0        0        1        0         4        2
  17Q LOSS WILD-TYPE       7        2        0       16        36        9
D63V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 0                 16
  STAGE III                4                 36
  STAGE IV                 2                  9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17Q LOSS MUTATED    1  0  4  2
  17Q LOSS WILD-TYPE 13 25 24  6
D63V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                1                 13
  T2                0                 25
  T3                4                 24
  T4                2                  6
[1] 4 2
[1] 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+N3
  17Q LOSS MUTATED    4  0     2
  17Q LOSS WILD-TYPE 38 10    19
D63V5, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                   4                 38
  N1                   0                 10
  N2+N3                2                 19
[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"
D63V6, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    4  0
  17Q LOSS WILD-TYPE 45  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    0
  17Q LOSS WILD-TYPE   45    2
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0                4                 45
  1                0                  2
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    2  5
  17Q LOSS WILD-TYPE 13 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    5
  17Q LOSS WILD-TYPE   13   57
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                2                 13
  MALE                  5                 57
[1] 2 2
[1] FALSE
D63V8, continuous
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                  4 
        TCGA-SC-A6LR         TCGA-XT-AASU         TCGA-ZN-A9VQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ZN-A9VU 
"17Q LOSS WILD-TYPE" 

Clustering(64) Variable = 18P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    1  7
  18P LOSS WILD-TYPE 10 58
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 8                 68 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                 58 
$`18P LOSS MUTATED`
TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-TS-A7P8 TCGA-UT-A88G 
       18.81         5.19        10.95        19.99        15.02         2.50 
TCGA-YS-A95C TCGA-ZN-A9VS 
        4.37        33.70 

$`18P LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 
       27.16        26.40        17.95         5.52         8.02         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        1.87        31.20        12.72        14.73        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       91.73        23.31        17.33         3.52        24.89        66.54 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       62.27         0.66        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
       29.42        17.72        23.90        15.09         7.99        14.76 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       14.76        55.07         8.38        27.75        41.46        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
       22.65         9.30        19.43        32.28        11.77        10.78 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       26.14         1.55        15.42        27.72         6.48        25.94 
TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D 
       23.64         8.32        14.99        13.35        23.77        21.44 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VQ 
       14.27         4.73         4.67         1.28         2.76        16.41 
TCGA-ZN-A9VU TCGA-ZN-A9VW 
       24.30         2.76 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              2.50               0.66 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             33.70              91.73 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            12.985             15.255 
[1] "2.5 - 33.7 (13.0)" "0.7 - 91.7 (15.3)"
[1] "hr=" "1.5"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  18P LOSS MUTATED         0        0        0        3         5        0
  18P LOSS WILD-TYPE       7        2        1       13        35       11
D64V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 3                 13
  STAGE III                5                 35
  STAGE IV                 0                 11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18P LOSS MUTATED    1  3  3  0
  18P LOSS WILD-TYPE 13 22 25  8
D64V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                1                 13
  T2                3                 22
  T3                3                 25
  T4                0                  8
[1] 4 2
[1] 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+N3
  18P LOSS MUTATED    6  1     1
  18P LOSS WILD-TYPE 36  9    20
D64V5, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                   6                 36
  N1                   1                  9
  N2+N3                1                 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"
D64V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    5  0
  18P LOSS WILD-TYPE 44  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      5    0
  18P LOSS WILD-TYPE   44    2
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0                5                 44
  1                0                  2
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    1  7
  18P LOSS WILD-TYPE 14 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    7
  18P LOSS WILD-TYPE   14   55
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                1                 14
  MALE                  7                 55
[1] 2 2
[1] FALSE
D64V8, continuous
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                  5 
        TCGA-SC-A6LR         TCGA-SH-A7BH         TCGA-XT-AASU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ZN-A9VQ         TCGA-ZN-A9VU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 

Clustering(65) Variable = 18Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    1 13
  18Q LOSS WILD-TYPE 10 52
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                14                 62 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                13                 52 
$`18Q LOSS MUTATED`
TCGA-3H-AB3M TCGA-LK-A4NY TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BS 
       29.10         5.52        18.81         5.19        10.95        19.99 
TCGA-SC-A6LM TCGA-SC-A6LQ TCGA-TS-A7P0 TCGA-TS-A7P8 TCGA-TS-A8AF TCGA-UT-A88G 
       28.96         9.76        41.46        15.02        11.77         2.50 
TCGA-YS-A95C TCGA-ZN-A9VS 
        4.37        33.70 

$`18Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        11.87        42.81        12.66        13.61        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       26.40        17.95         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ 
       12.72        14.73        11.51        80.84        91.73        23.31 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
       17.33         3.52        24.89        66.54        62.27         0.66 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD 
       13.61         2.56        29.42        17.72        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
        7.99        14.76        14.76        55.07         8.38        27.75 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AI 
       18.51        22.65         9.30        19.43        32.28        10.78 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       26.14         1.55        15.42        27.72         6.48        25.94 
TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D 
       23.64         8.32        14.99        13.35        23.77        21.44 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VQ 
       14.27         4.73         4.67         1.28         2.76        16.41 
TCGA-ZN-A9VU TCGA-ZN-A9VW 
       24.30         2.76 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              2.50               0.66 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             41.46              91.73 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            13.395             15.255 
[1] "2.5 - 41.5 (13.4)" "0.7 - 91.7 (15.3)"
[1] "hr=" "1.3"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED         0        0        0        3        10        1
  18Q LOSS WILD-TYPE       7        2        1       13        30       10
D65V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 3                 13
  STAGE III               10                 30
  STAGE IV                 1                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS MUTATED    1  4  7  1
  18Q LOSS WILD-TYPE 13 21 21  7
D65V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                1                 13
  T2                4                 21
  T3                7                 21
  T4                1                  7
[1] 4 2
[1] 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+N3
  18Q LOSS MUTATED    8  1     4
  18Q LOSS WILD-TYPE 34  9    17
D65V5, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                   8                 34
  N1                   1                  9
  N2+N3                4                 17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    9  0
  18Q LOSS WILD-TYPE 40  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      9    0
  18Q LOSS WILD-TYPE   40    2
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0                9                 40
  1                0                  2
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    5  9
  18Q LOSS WILD-TYPE 10 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5    9
  18Q LOSS WILD-TYPE   10   53
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                5                 10
  MALE                  9                 53
[1] 2 2
[1] FALSE
D65V8, continuous
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                  5 
        TCGA-SC-A6LR         TCGA-SH-A7BH         TCGA-XT-AASU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ZN-A9VQ         TCGA-ZN-A9VU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 

Clustering(66) Variable = 19P LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    0  3
  19P LOSS WILD-TYPE 11 62
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 73 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 62 
$`19P LOSS MUTATED`
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-TS-A7OZ 
       19.99         0.66        27.75 

$`19P LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 
       27.16        26.40        17.95         5.52         8.02         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        1.87        31.20        12.72        14.73        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN 
       10.95        24.89        66.54        62.27        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD 
        2.56         9.76        29.42        17.72        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7P0 
        7.99        14.76        14.76        55.07         8.38        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
        6.48        25.94        23.64         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       23.77        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.66               1.28 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             27.75              91.73 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             19.99              15.02 
[1] "0.7 - 27.8 (20.0)" "1.3 - 91.7 (15.0)"
[1] "hr=" "1.3"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         0        0        1        1         1        0
  19P LOSS WILD-TYPE       7        2        0       15        39       11
D66V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 1                 15
  STAGE III                1                 39
  STAGE IV                 0                 11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19P LOSS MUTATED    1  1  1  0
  19P LOSS WILD-TYPE 13 24 27  8
D66V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                1                 13
  T2                1                 24
  T3                1                 27
  T4                0                  8
[1] 4 2
[1] 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+N3
  19P LOSS MUTATED    1  1     0
  19P LOSS WILD-TYPE 41  9    21
D66V5, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 71 
        TCGA-3H-AB3K         TCGA-3H-AB3L         TCGA-3H-AB3M 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-3H-AB3O         TCGA-3H-AB3S         TCGA-3H-AB3T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-3H-AB3U         TCGA-3H-AB3X         TCGA-LK-A4NW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-LK-A4NY         TCGA-LK-A4NZ         TCGA-LK-A4O0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-LK-A4O2         TCGA-LK-A4O4         TCGA-LK-A4O5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-LK-A4O6         TCGA-LK-A4O7         TCGA-MQ-A4KX 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MQ-A4LC         TCGA-MQ-A4LI         TCGA-MQ-A4LJ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MQ-A4LM         TCGA-MQ-A4LP         TCGA-MQ-A4LV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MQ-A6BL         TCGA-MQ-A6BN         TCGA-MQ-A6BQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MQ-A6BR         TCGA-SC-A6LN         TCGA-SC-A6LP 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-SC-A6LQ         TCGA-SC-A6LR         TCGA-SC-AA5Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-SH-A7BC         TCGA-SH-A7BD         TCGA-SH-A7BH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-SH-A9CT         TCGA-SH-A9CU         TCGA-TS-A7OU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-TS-A7OY         TCGA-TS-A7P0         TCGA-TS-A7P1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-TS-A7P3         TCGA-TS-A7P6         TCGA-TS-A7P7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-TS-A7P8         TCGA-TS-A7PB         TCGA-TS-A8AF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-TS-A8AI         TCGA-TS-A8AS         TCGA-TS-A8AV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-TS-A8AY         TCGA-UD-AABY         TCGA-UD-AABZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UD-AAC1         TCGA-UD-AAC4         TCGA-UD-AAC5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UD-AAC6         TCGA-UD-AAC7         TCGA-UT-A88C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UT-A88D         TCGA-UT-A88E         TCGA-UT-A88G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UT-A97Y         TCGA-YS-A95B         TCGA-YS-A95C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-YS-AA4M         TCGA-ZN-A9VQ         TCGA-ZN-A9VS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ZN-A9VU         TCGA-ZN-A9VW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D66V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    0  0
  19P LOSS WILD-TYPE 49  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    0
  19P LOSS WILD-TYPE   49    2
D66V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    0  3
  19P LOSS WILD-TYPE 15 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    3
  19P LOSS WILD-TYPE   15   59
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                0                 15
  MALE                  3                 59
[1] 2 2
[1] FALSE
D66V8, continuous

Clustering(67) Variable = 19Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    2  4
  19Q LOSS WILD-TYPE  9 61
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 6                 70 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 61 
$`19Q LOSS MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3X TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-TS-A7OZ 
       29.10        26.40        66.54        19.99         0.66        27.75 

$`19Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        11.87        42.81        12.66        13.61        27.16 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
       62.27        28.96        13.61         2.56         9.76        29.42 
TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
       17.72        23.90        15.09         7.99        14.76        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
       55.07         8.38        41.46        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS 
       19.43        15.02        32.28        11.77        10.78        26.14 
TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 
        1.55        15.42        27.72         6.48        25.94        23.64 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E 
        8.32        14.99        13.35        23.77        21.44        14.27 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
        2.50         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       16.41        33.70        24.30         2.76 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.66               1.28 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             66.54              91.73 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            27.075             14.875 
[1] "0.7 - 66.5 (27.1)" "1.3 - 91.7 (14.9)"
[1] "hr=" "2"  
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         0        0        1        2         3        0
  19Q LOSS WILD-TYPE       7        2        0       14        37       11
D67V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 2                 14
  STAGE III                3                 37
  STAGE IV                 0                 11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19Q LOSS MUTATED    1  2  3  0
  19Q LOSS WILD-TYPE 13 23 25  8
D67V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                1                 13
  T2                2                 23
  T3                3                 25
  T4                0                  8
[1] 4 2
[1] 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+N3
  19Q LOSS MUTATED    3  1     1
  19Q LOSS WILD-TYPE 39  9    20
D67V5, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                   3                 39
  N1                   1                  9
  N2+N3                1                 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"
D67V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  0
  19Q LOSS WILD-TYPE 47  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    0
  19Q LOSS WILD-TYPE   47    2
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                2                 47
  1                0                  2
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    1  5
  19Q LOSS WILD-TYPE 14 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    5
  19Q LOSS WILD-TYPE   14   57
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                1                 14
  MALE                  5                 57
[1] 2 2
[1] FALSE
D67V8, continuous

Clustering(68) Variable = 20P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    3 11
  20P LOSS WILD-TYPE  8 54
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                14                 62 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                11                 54 
$`20P LOSS MUTATED`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O5 
       56.38        11.87        29.10        17.95         6.08        12.72 
TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-TS-A7P0 TCGA-TS-A7P7 TCGA-UT-A88E 
       66.54        19.99        13.61        41.46        19.43        14.27 
TCGA-ZN-A9VQ TCGA-ZN-A9VU 
       16.41        24.30 

$`20P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NY 
       42.81        12.66        13.61        27.16        26.40         5.52 
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        8.02         1.87        31.20        14.73        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP 
       10.95        24.89        62.27         0.66        28.96         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
        9.76        29.42        17.72        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 
       14.76        14.76        55.07         8.38        27.75        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
       22.65         9.30        15.02        32.28        11.77        10.78 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       26.14         1.55        15.42        27.72         6.48        25.94 
TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D 
       23.64         8.32        14.99        13.35        23.77        21.44 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
        2.50         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VS TCGA-ZN-A9VW 
       33.70         2.76 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              6.08               0.66 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             66.54              91.73 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            18.690             14.875 
[1] "6.1 - 66.5 (18.7)" "0.7 - 91.7 (14.9)"
[1] "hr=" "1.4"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         2        1        0        4         6        1
  20P LOSS WILD-TYPE       5        1        1       12        34       10
D68V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  2                  5
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 4                 12
  STAGE III                6                 34
  STAGE IV                 1                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20P LOSS MUTATED    3  5  4  1
  20P LOSS WILD-TYPE 11 20 24  7
D68V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                3                 11
  T2                5                 20
  T3                4                 24
  T4                1                  7
[1] 4 2
[1] 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+N3
  20P LOSS MUTATED    9  0     5
  20P LOSS WILD-TYPE 33 10    16
D68V5, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                   9                 33
  N1                   0                 10
  N2+N3                5                 16
[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"
D68V6, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    8  0
  20P LOSS WILD-TYPE 41  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8    0
  20P LOSS WILD-TYPE   41    2
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                8                 41
  1                0                  2
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    2 12
  20P LOSS WILD-TYPE 13 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   12
  20P LOSS WILD-TYPE   13   50
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                2                 13
  MALE                 12                 50
[1] 2 2
[1] FALSE
D68V8, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                  4 
        TCGA-SC-A6LR         TCGA-SH-A7BH         TCGA-XT-AASU 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ZN-A9VS 
"20P LOSS WILD-TYPE" 

Clustering(69) Variable = 20Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    0  3
  20Q LOSS WILD-TYPE 11 62
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 73 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 62 
$`20Q LOSS MUTATED`
TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-TS-A7P7 
        6.08        12.72        19.43 

$`20Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 
       27.16        26.40        17.95         5.52         8.02         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       31.20        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       66.54        62.27        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD 
        2.56         9.76        29.42        17.72        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
        7.99        14.76        14.76        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A7PB 
       41.46        18.51        22.65         9.30        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
        6.48        25.94        23.64         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       23.77        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              6.08               0.66 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             19.43              91.73 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             12.72              15.09 
[1] "6.1 - 19.4 (12.7)" "0.7 - 91.7 (15.1)"
[1] "hr=" "2"  
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  20Q LOSS MUTATED         0        1        0        0         2        0
  20Q LOSS WILD-TYPE       7        1        1       16        38       11
D69V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 0                 16
  STAGE III                2                 38
  STAGE IV                 0                 11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20Q LOSS MUTATED    1  0  2  0
  20Q LOSS WILD-TYPE 13 25 26  8
D69V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                1                 13
  T2                0                 25
  T3                2                 26
  T4                0                  8
[1] 4 2
[1] 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+N3
  20Q LOSS MUTATED    2  0     1
  20Q LOSS WILD-TYPE 40 10    20
D69V5, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                   2                 40
  N1                   0                 10
  N2+N3                1                 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"
D69V6, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    2  0
  20Q LOSS WILD-TYPE 47  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    0
  20Q LOSS WILD-TYPE   47    2
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                2                 47
  1                0                  2
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  2
  20Q LOSS WILD-TYPE 14 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    2
  20Q LOSS WILD-TYPE   14   60
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                 14
  MALE                  2                 60
[1] 2 2
[1] FALSE
D69V8, continuous

Clustering(70) Variable = 21Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    1  8
  21Q LOSS WILD-TYPE 10 57
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 9                 67 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                 57 
$`21Q LOSS MUTATED`
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-AA5Z TCGA-SH-A9CT 
        6.08         1.87        19.99         0.66        17.72        14.76 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A8AF 
       41.46        18.51        11.77 

$`21Q LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O4 
       27.16        26.40        17.95         5.52         8.02        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       66.54        62.27        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7OU 
       29.42        23.90        15.09         7.99        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
        8.38        27.75        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       32.28        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
        6.48        25.94        23.64         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       23.77        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.66               1.28 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             41.46              91.73 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             14.76              15.09 
[1] "0.7 - 41.5 (14.8)" "1.3 - 91.7 (15.1)"
[1] "hr=" "1.5"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED         1        1        1        3         3        1
  21Q LOSS WILD-TYPE       6        1        0       13        37       10
D70V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 1                  1
  STAGE IB                 1                  0
  STAGE II                 3                 13
  STAGE III                3                 37
  STAGE IV                 1                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS MUTATED    3  4  2  1
  21Q LOSS WILD-TYPE 11 21 26  7
D70V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                3                 11
  T2                4                 21
  T3                2                 26
  T4                1                  7
[1] 4 2
[1] 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+N3
  21Q LOSS MUTATED    6  0     2
  21Q LOSS WILD-TYPE 36 10    19
D70V5, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                   6                 36
  N1                   0                 10
  N2+N3                2                 19
[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"
D70V6, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    4  0
  21Q LOSS WILD-TYPE 45  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4    0
  21Q LOSS WILD-TYPE   45    2
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0                4                 45
  1                0                  2
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    1  9
  21Q LOSS WILD-TYPE 14 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1    9
  21Q LOSS WILD-TYPE   14   53
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                1                 14
  MALE                  9                 53
[1] 2 2
[1] FALSE
D70V8, continuous

Clustering(71) Variable = 22Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    8 50
  22Q LOSS WILD-TYPE  3 15
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                58                 18 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                50                 15 
$`22Q LOSS MUTATED`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X 
       56.38        11.87        29.10        12.66        13.61        26.40 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       11.51        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
        3.52        24.89        66.54        19.99         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU 
       13.61         9.76        23.90        15.09        14.76        14.76 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
        8.38        27.75        41.46        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-UD-AABY 
       19.43        15.02        32.28        11.77        10.78        27.72 
TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        6.48        23.64         8.32        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-YS-A95B TCGA-YS-A95C 
       21.44        14.27         2.50         4.73         1.28         4.37 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       16.41        33.70        24.30         2.76 

$`22Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A6BL 
       42.81        27.16        17.95        31.20        80.84        10.95 
TCGA-MQ-A6BR TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BH TCGA-TS-A7OU 
       62.27         2.56        29.42        17.72         7.99        55.07 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AAC1 TCGA-XT-AASU TCGA-YS-AA4M 
       26.14         1.55        15.42        25.94         4.67         2.76 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.66               1.55 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             91.73              80.84 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            14.760             21.945 
[1] "0.7 - 91.7 (14.8)" "1.6 - 80.8 (21.9)"
[1] "hr=" "1.5"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED         6        1        1       14        30        7
  22Q LOSS WILD-TYPE       1        1        0        2        10        4
D71V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  6                  1
  STAGE IA                 1                  1
  STAGE IB                 1                  0
  STAGE II                14                  2
  STAGE III               30                 10
  STAGE IV                 7                  4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  22Q LOSS MUTATED    9 20 23  5
  22Q LOSS WILD-TYPE  5  5  5  3
D71V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                9                  5
  T2               20                  5
  T3               23                  5
  T4                5                  3
[1] 4 2
[1] 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+N3
  22Q LOSS MUTATED   33  7    16
  22Q LOSS WILD-TYPE  9  3     5
D71V5, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                  33                  9
  N1                   7                  3
  N2+N3               16                  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"
D71V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   38  1
  22Q LOSS WILD-TYPE 11  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     38    1
  22Q LOSS WILD-TYPE   11    1
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               38                 11
  1                1                  1
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   11 48
  22Q LOSS WILD-TYPE  4 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     11   48
  22Q LOSS WILD-TYPE    4   14
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               11                  4
  MALE                 48                 14
[1] 2 2
[1] FALSE
D71V8, continuous

Clustering(72) Variable = XP LOSS MUTATION ANALYSIS
D72V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED    4 18
  XP LOSS WILD-TYPE  7 47
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               22                54 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               18                47 
$`XP LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3X TCGA-LK-A4NY TCGA-LK-A4O7 TCGA-MQ-A4LI 
       11.87        29.10        26.40         5.52        11.51        18.81 
TCGA-MQ-A4LP TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU 
       17.33        19.99        13.61        15.09        14.76        14.76 
TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P7 TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABZ 
       27.75        18.51        19.43        10.78        15.42         6.48 
TCGA-UD-AAC7 TCGA-UT-A88E TCGA-ZN-A9VQ TCGA-ZN-A9VS 
       13.35        14.27        16.41        33.70 

$`XP LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U TCGA-LK-A4NW 
       56.38        42.81        12.66        13.61        27.16        17.95 
TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 
        8.02         6.08         1.87        31.20        12.72        14.73 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL 
       80.84        91.73        23.31         5.19         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP 
       24.89        66.54        62.27         0.66        28.96         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BH TCGA-TS-A7OU 
        9.76        29.42        17.72        23.90         7.99        55.07 
TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A7PB 
        8.38        41.46        22.65         9.30        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AS TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC4 
       11.77        26.14         1.55        27.72        25.94        23.64 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88G TCGA-UT-A97Y 
        8.32        14.99        23.77        21.44         2.50         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.67         1.28         4.37         2.76        24.30         2.76 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             5.52              0.66 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            33.70             91.73 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           15.255            15.005 
[1] "5.5 - 33.7 (15.3)" "0.7 - 91.7 (15.0)"
[1] "hr=" "1.1"
D72V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  XP LOSS MUTATED         3        0        0        5        11        3
  XP LOSS WILD-TYPE       4        2        1       11        29        8
D72V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 3                 4
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                5                11
  STAGE III              11                29
  STAGE IV                3                 8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XP LOSS MUTATED    3  7  9  2
  XP LOSS WILD-TYPE 11 18 19  6
D72V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               3                11
  T2               7                18
  T3               9                19
  T4               2                 6
[1] 4 2
[1] 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+N3
  XP LOSS MUTATED   13  4     5
  XP LOSS WILD-TYPE 29  6    16
D72V5, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  N0                 13                29
  N1                  4                 6
  N2+N3               5                16
[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"
D72V6, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   13  1
  XP LOSS WILD-TYPE 36  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     13    1
  XP LOSS WILD-TYPE   36    1
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              13                36
  1               1                 1
[1] 2 2
[1] FALSE
D72V7, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    4 18
  XP LOSS WILD-TYPE 11 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      4   18
  XP LOSS WILD-TYPE   11   44
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE               4                11
  MALE                18                44
[1] 2 2
[1] FALSE
D72V8, continuous
[1] "Remove cluster labels:" "XP LOSS MUTATED"       
clus
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                2                 4 
       TCGA-SC-A6LR        TCGA-SH-A7BH        TCGA-XT-AASU        TCGA-ZN-A9VU 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 

Clustering(73) Variable = XQ LOSS MUTATION ANALYSIS
D73V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    4 19
  XQ LOSS WILD-TYPE  7 46
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               23                53 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               19                46 
$`XQ LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3X TCGA-LK-A4NY TCGA-LK-A4O7 TCGA-MQ-A4LI 
       11.87        29.10        26.40         5.52        11.51        18.81 
TCGA-MQ-A4LP TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU 
       17.33        19.99        13.61        15.09        14.76        14.76 
TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P7 TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABZ 
       27.75        18.51        19.43        10.78        15.42         6.48 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88E TCGA-ZN-A9VQ TCGA-ZN-A9VS 
       14.99        13.35        14.27        16.41        33.70 

$`XQ LOSS WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U TCGA-LK-A4NW 
       56.38        42.81        12.66        13.61        27.16        17.95 
TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 
        8.02         6.08         1.87        31.20        12.72        14.73 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL 
       80.84        91.73        23.31         5.19         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP 
       24.89        66.54        62.27         0.66        28.96         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BH TCGA-TS-A7OU 
        9.76        29.42        17.72        23.90         7.99        55.07 
TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A7PB 
        8.38        41.46        22.65         9.30        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AS TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC4 
       11.77        26.14         1.55        27.72        25.94        23.64 
TCGA-UD-AAC5 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
        8.32        23.77        21.44         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VU TCGA-ZN-A9VW 
        1.28         4.37         2.76        24.30         2.76 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             5.52              0.66 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            33.70             91.73 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            15.09             15.02 
[1] "5.5 - 33.7 (15.1)" "0.7 - 91.7 (15.0)"
[1] "hr=" "1.2"
D73V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         3        0        0        6        11        3
  XQ LOSS WILD-TYPE       4        2        1       10        29        8
D73V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 3                 4
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                6                10
  STAGE III              11                29
  STAGE IV                3                 8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XQ LOSS MUTATED    3  8  9  2
  XQ LOSS WILD-TYPE 11 17 19  6
D73V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               3                11
  T2               8                17
  T3               9                19
  T4               2                 6
[1] 4 2
[1] 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+N3
  XQ LOSS MUTATED   14  4     5
  XQ LOSS WILD-TYPE 28  6    16
D73V5, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0                 14                28
  N1                  4                 6
  N2+N3               5                16
[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"
D73V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   14  1
  XQ LOSS WILD-TYPE 35  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     14    1
  XQ LOSS WILD-TYPE   35    1
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              14                35
  1               1                 1
[1] 2 2
[1] FALSE
D73V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    4 19
  XQ LOSS WILD-TYPE 11 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4   19
  XQ LOSS WILD-TYPE   11   43
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               4                11
  MALE                19                43
[1] 2 2
[1] FALSE
D73V8, continuous
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                 4 
       TCGA-SC-A6LR        TCGA-SH-A7BH        TCGA-XT-AASU        TCGA-ZN-A9VU 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
