[1] "ofn"        "-oTKICH-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/KICH-TP/15080874/KICH-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KICH-TP/15084587/transformed.cor.cli.txt"

nPatients in clinical file=110, in cluster file=66, common to both=66
[1] "Reduce the number of clustering variables from 82 to 63."
[1] 63 66
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                8                58 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                8                58 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                58 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                58 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               24                42 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               24                42 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               24                42 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               24                42 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8                58 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8                58 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8                58 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8                58 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               24                42 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               24                42 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               24                42 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               24                42 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               17                49 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               17                49 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               18                48 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               18                48 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               10                56 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               10                56 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               10                56 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               10                56 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 62 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 62 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                15                 51 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                15                 51 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                15                 51 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                15                 51 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                19                 47 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                19                 47 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                20                 46 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                20                 46 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                 45 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                 45 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                21                 45 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                21                 45 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                21                 45 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                21                 45 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                21                 45 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                21                 45 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                 49 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                 49 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                16                 50 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                16                 50 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                19                 47 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                19                 47 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                17                 49 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                17                 49 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                20                 46 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                20                 46 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                21                 45 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                21                 45 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 62 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 62 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                 47 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                 47 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                7                59 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                7                59 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                60 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                60 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               53                13 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               53                13 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               52                14 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               52                14 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               46                20 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               46                20 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               46                20 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               46                20 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                57 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                57 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                8                58 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                8                58 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               10                56 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               10                56 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               10                56 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               10                56 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               51                15 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               51                15 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               51                15 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               51                15 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                9                57 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                9                57 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8                58 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8                58 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               10                56 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               10                56 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               10                56 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               10                56 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                48                 18 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                48                 18 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                49                 17 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                49                 17 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 59 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 59 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 59 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 59 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                43                 23 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                43                 23 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 62 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 62 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 61 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 61 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                50                 16 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                50                 16 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                50                 16 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                50                 16 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 8                 58 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 8                 58 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                10                 56 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                10                 56 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 63 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 63 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                 62 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                 62 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 63 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 63 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                35                 31 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                35                 31 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 8                 58 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 8                 58 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               38                28 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               38                28 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               39                27 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               39                27 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "KARNOFSKY_PERFORMANCE_SCORE"           
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "NUMBER_PACK_YEARS_SMOKED"              
[18] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCH_NUMBER"                          

Input Data has 21 rows and 66 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=9,	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=56,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=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 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'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 17:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH_NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER excluded in the analysis because there is no case of (both >= 3) in the table below"
              B226.47.0 B251.42.0
freq.values   "65"      "1"      
freq.contrast "1"       "65"     
both >= 3     "FALSE"   "FALSE"  
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 66 columns, 1 survival variables, and 11 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"   "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[11] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=39, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
21 25 18  2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
   21    25    20 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
21 25 18  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
   21    25    20 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
40  3  2 
[1] "table(vv)"
vv
   N0 N1+N2 
   40     5 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
40  3  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 40

$Class1_nSamples
[1] 5

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   40     5 
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
NUMBER_PACK_YEARS_SMOKED, nv=10, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=8, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 3P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    4  3
  3P GAIN WILD-TYPE 52  6
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                7                58 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                 6 
$`3P GAIN MUTATED`
TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8443 TCGA-KN-8427 
       98.96        28.11        24.79        62.37        49.97         0.99 
TCGA-KN-8428 
       52.27 

$`3P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
       90.48       108.62        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       30.25        44.84        86.56        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        54.74       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       47.24       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       77.85        57.17        61.58        63.95 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.99              2.50 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            98.96            151.96 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            49.97             72.66 
[1] "1.0 - 99.0 (50.0)"  "2.5 - 152.0 (72.7)"
[1] "hr=" "5.4"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         1        4         0        3
  3P GAIN WILD-TYPE      20       21        14        3
D1V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 1                20
  STAGE II                4                21
  STAGE III               0                14
  STAGE IV                3                 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                T1 T2 T3+T4
  3P GAIN MUTATED    1  4     3
  3P GAIN WILD-TYPE 20 21    17
D1V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1                  1                20
  T2                  4                21
  T3+T4               3                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"
                   vv
clus                N0 N1+N2
  3P GAIN MUTATED    5     3
  3P GAIN WILD-TYPE 35     2
D1V5, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0                  5                35
  N1+N2               3                 2
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3  1
  3P GAIN WILD-TYPE 31  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    1
  3P GAIN WILD-TYPE   31    1
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               3                31
  1               1                 1
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    1  7
  3P GAIN WILD-TYPE 26 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    7
  3P GAIN WILD-TYPE   26   32
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               1                26
  MALE                 7                32
[1] 2 2
[1] FALSE
D1V8, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                10 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KO-8411        TCGA-KO-8413 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D1V9, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                 9 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KO-8416 
"3P GAIN WILD-TYPE" 
D1V10, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                 7 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       1                         0     7
  3P GAIN WILD-TYPE     1                         4    51
D1V11, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   7                51
[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"
D1V12, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    0  3
  3P GAIN WILD-TYPE  4 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    3
  3P GAIN WILD-TYPE    4   29
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               3                29
[1] 2 2
[1] FALSE

Clustering(2) Variable = 3Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    4  3
  3Q GAIN WILD-TYPE 52  6
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                7                58 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                 6 
$`3Q GAIN MUTATED`
TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8443 TCGA-KN-8427 
       98.96        28.11        24.79        62.37        49.97         0.99 
TCGA-KN-8428 
       52.27 

$`3Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
       90.48       108.62        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       30.25        44.84        86.56        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        54.74       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       47.24       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       77.85        57.17        61.58        63.95 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.99              2.50 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            98.96            151.96 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            49.97             72.66 
[1] "1.0 - 99.0 (50.0)"  "2.5 - 152.0 (72.7)"
[1] "hr=" "5.4"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED         1        4         0        3
  3Q GAIN WILD-TYPE      20       21        14        3
D2V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 1                20
  STAGE II                4                21
  STAGE III               0                14
  STAGE IV                3                 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                T1 T2 T3+T4
  3Q GAIN MUTATED    1  4     3
  3Q GAIN WILD-TYPE 20 21    17
D2V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1                  1                20
  T2                  4                21
  T3+T4               3                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"
                   vv
clus                N0 N1+N2
  3Q GAIN MUTATED    5     3
  3Q GAIN WILD-TYPE 35     2
D2V5, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0                  5                35
  N1+N2               3                 2
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  1
  3Q GAIN WILD-TYPE 31  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    1
  3Q GAIN WILD-TYPE   31    1
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0               3                31
  1               1                 1
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    1  7
  3Q GAIN WILD-TYPE 26 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1    7
  3Q GAIN WILD-TYPE   26   32
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               1                26
  MALE                 7                32
[1] 2 2
[1] FALSE
D2V8, continuous
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                10 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KO-8411        TCGA-KO-8413 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D2V9, continuous
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 9 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KO-8416 
"3Q GAIN WILD-TYPE" 
D2V10, continuous
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                 7 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       1                         0     7
  3Q GAIN WILD-TYPE     1                         4    51
D2V11, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   7                51
[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"
D2V12, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    0  3
  3Q GAIN WILD-TYPE  4 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0    3
  3Q GAIN WILD-TYPE    4   29
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               3                29
[1] 2 2
[1] FALSE

Clustering(3) Variable = 4P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED   20  3
  4P GAIN WILD-TYPE 36  6
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               23                42 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                 6 
$`4P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 
      141.73       137.06        98.96        28.11        24.79        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 
      151.96        49.97        23.47        25.48        25.91       104.52 
TCGA-KN-8426 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8405 
        3.55         2.50        11.21        42.35        10.68        74.93 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78        86.10        77.85        57.17 

$`4P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.56        66.54        73.91        71.41        28.80        54.74 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
       23.28        44.91        28.80        47.24       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8428 
       31.33       129.37        87.91        65.19         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
       87.12        19.33        59.08       115.00       100.87        76.90 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
       79.04        92.71        16.67       103.27        61.58        63.95 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             2.50              0.99 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           151.96            129.37 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           57.170            68.975 
[1] "2.5 - 152.0 (57.2)" "1.0 - 129.4 (69.0)"
[1] "hr=" "1.1"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         8       10         2        4
  4P GAIN WILD-TYPE      13       15        12        2
D3V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 8                13
  STAGE II               10                15
  STAGE III               2                12
  STAGE IV                4                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  4P GAIN MUTATED    8 10     6
  4P GAIN WILD-TYPE 13 15    14
D3V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1                  8                13
  T2                 10                15
  T3+T4               6                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"
                   vv
clus                N0 N1+N2
  4P GAIN MUTATED   16     2
  4P GAIN WILD-TYPE 24     3
D3V5, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0                 16                24
  N1+N2               2                 3
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   11  2
  4P GAIN WILD-TYPE 23  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     11    2
  4P GAIN WILD-TYPE   23    0
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              11                23
  1               2                 0
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   10 14
  4P GAIN WILD-TYPE 17 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     10   14
  4P GAIN WILD-TYPE   17   25
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              10                17
  MALE                14                25
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
D3V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       1                         1    22
  4P GAIN WILD-TYPE     1                         3    36
D3V11, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                  22                36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    3 12
  4P GAIN WILD-TYPE  1 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3   12
  4P GAIN WILD-TYPE    1   20
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              12                20
[1] 2 2
[1] FALSE

Clustering(4) Variable = 4Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED   20  3
  4Q GAIN WILD-TYPE 36  6
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               23                42 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                 6 
$`4Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 
      141.73       137.06        98.96        28.11        24.79        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 
      151.96        49.97        23.47        25.48        25.91       104.52 
TCGA-KN-8426 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8405 
        3.55         2.50        11.21        42.35        10.68        74.93 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78        86.10        77.85        57.17 

$`4Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.56        66.54        73.91        71.41        28.80        54.74 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
       23.28        44.91        28.80        47.24       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8428 
       31.33       129.37        87.91        65.19         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
       87.12        19.33        59.08       115.00       100.87        76.90 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
       79.04        92.71        16.67       103.27        61.58        63.95 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             2.50              0.99 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           151.96            129.37 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           57.170            68.975 
[1] "2.5 - 152.0 (57.2)" "1.0 - 129.4 (69.0)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         8       10         2        4
  4Q GAIN WILD-TYPE      13       15        12        2
D4V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 8                13
  STAGE II               10                15
  STAGE III               2                12
  STAGE IV                4                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  4Q GAIN MUTATED    8 10     6
  4Q GAIN WILD-TYPE 13 15    14
D4V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1                  8                13
  T2                 10                15
  T3+T4               6                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"
                   vv
clus                N0 N1+N2
  4Q GAIN MUTATED   16     2
  4Q GAIN WILD-TYPE 24     3
D4V5, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0                 16                24
  N1+N2               2                 3
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED   11  2
  4Q GAIN WILD-TYPE 23  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     11    2
  4Q GAIN WILD-TYPE   23    0
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              11                23
  1               2                 0
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED   10 14
  4Q GAIN WILD-TYPE 17 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     10   14
  4Q GAIN WILD-TYPE   17   25
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              10                17
  MALE                14                25
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       1                         1    22
  4Q GAIN WILD-TYPE     1                         3    36
D4V11, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                  22                36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    3 12
  4Q GAIN WILD-TYPE  1 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   12
  4Q GAIN WILD-TYPE    1   20
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              12                20
[1] 2 2
[1] FALSE

Clustering(5) Variable = 5P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    5  3
  5P GAIN WILD-TYPE 51  6
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8                57 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                3                 6 
$`5P GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8339 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8436 
      137.06        28.11         3.55         0.99        52.27        42.35 
TCGA-KO-8404 TCGA-KO-8414 
       10.68        77.85 

$`5P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
       65.19       104.52        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
       59.08       115.00       100.87        76.90        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       57.17        61.58        63.95 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.99              2.50 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           137.06            151.96 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            35.23             71.41 
[1] "1.0 - 137.1 (35.2)" "2.5 - 152.0 (71.4)"
[1] "hr=" "5.4"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED         1        3         0        4
  5P GAIN WILD-TYPE      20       22        14        2
D5V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 1                20
  STAGE II                3                22
  STAGE III               0                14
  STAGE IV                4                 2
[1] 4 2
[1] TRUE
[1] "dimension 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    1  3     4
  5P GAIN WILD-TYPE 20 22    16
D5V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1                  1                20
  T2                  3                22
  T3+T4               4                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"
                   vv
clus                N0 N1+N2
  5P GAIN MUTATED    3     2
  5P GAIN WILD-TYPE 37     3
D5V5, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0                  3                37
  N1+N2               2                 3
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    2  2
  5P GAIN WILD-TYPE 32  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    2
  5P GAIN WILD-TYPE   32    0
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0               2                32
  1               2                 0
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    2  6
  5P GAIN WILD-TYPE 25 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    6
  5P GAIN WILD-TYPE   25   33
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               2                25
  MALE                 6                33
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                10 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KO-8409        TCGA-KO-8416 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
D5V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       0                         0     8
  5P GAIN WILD-TYPE     2                         4    50
D5V11, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   8                50
[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"
D5V12, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    0  4
  5P GAIN WILD-TYPE  4 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      0    4
  5P GAIN WILD-TYPE    4   28
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4                28
[1] 2 2
[1] FALSE

Clustering(6) Variable = 5Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    5  3
  5Q GAIN WILD-TYPE 51  6
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8                57 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                 6 
$`5Q GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8339 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8436 
      137.06        28.11         3.55         0.99        52.27        42.35 
TCGA-KO-8404 TCGA-KO-8414 
       10.68        77.85 

$`5Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
       65.19       104.52        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
       59.08       115.00       100.87        76.90        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       57.17        61.58        63.95 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.99              2.50 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           137.06            151.96 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            35.23             71.41 
[1] "1.0 - 137.1 (35.2)" "2.5 - 152.0 (71.4)"
[1] "hr=" "5.4"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED         1        3         0        4
  5Q GAIN WILD-TYPE      20       22        14        2
D6V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 1                20
  STAGE II                3                22
  STAGE III               0                14
  STAGE IV                4                 2
[1] 4 2
[1] TRUE
[1] "dimension 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    1  3     4
  5Q GAIN WILD-TYPE 20 22    16
D6V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1                  1                20
  T2                  3                22
  T3+T4               4                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"
                   vv
clus                N0 N1+N2
  5Q GAIN MUTATED    3     2
  5Q GAIN WILD-TYPE 37     3
D6V5, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0                  3                37
  N1+N2               2                 3
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    2  2
  5Q GAIN WILD-TYPE 32  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    2
  5Q GAIN WILD-TYPE   32    0
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               2                32
  1               2                 0
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    2  6
  5Q GAIN WILD-TYPE 25 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    6
  5Q GAIN WILD-TYPE   25   33
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               2                25
  MALE                 6                33
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1                10 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KO-8409        TCGA-KO-8416 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D6V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         0     8
  5Q GAIN WILD-TYPE     2                         4    50
D6V11, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   8                50
[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"
D6V12, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    0  4
  5Q GAIN WILD-TYPE  4 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    4
  5Q GAIN WILD-TYPE    4   28
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4                28
[1] 2 2
[1] FALSE

Clustering(7) Variable = 7P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   17  6
  7P GAIN WILD-TYPE 39  3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               23                42 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                6                 3 
$`7P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8343 
      141.73       137.06        98.96        28.11        24.79        71.41 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 
       62.37       151.96        49.97        23.47        25.91       104.52 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8405 
        3.55        52.27        11.21        42.35        10.68        74.93 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67        80.38        86.10        77.85        57.17 

$`7P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 
       86.56        66.54        73.91        28.80        54.74        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       44.91        28.80        47.24       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 
      129.37        87.91        25.48        65.19         0.99        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
       19.33         2.50        59.08       115.00       100.87        76.90 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
       79.04        92.71        87.78       103.27        61.58        63.95 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             3.55              0.99 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           151.96            129.37 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           57.170            70.225 
[1] "3.5 - 152.0 (57.2)" "1.0 - 129.4 (70.2)"
[1] "hr=" "4.2"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED         6       10         4        4
  7P GAIN WILD-TYPE      15       15        10        2
D7V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 6                15
  STAGE II               10                15
  STAGE III               4                10
  STAGE IV                4                 2
[1] 4 2
[1] TRUE
[1] "dimension 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    6 10     8
  7P GAIN WILD-TYPE 15 15    12
D7V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1                  6                15
  T2                 10                15
  T3+T4               8                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"
                   vv
clus                N0 N1+N2
  7P GAIN MUTATED   16     3
  7P GAIN WILD-TYPE 24     2
D7V5, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0                 16                24
  N1+N2               3                 2
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   11  2
  7P GAIN WILD-TYPE 23  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     11    2
  7P GAIN WILD-TYPE   23    0
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              11                23
  1               2                 0
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    7 17
  7P GAIN WILD-TYPE 20 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      7   17
  7P GAIN WILD-TYPE   20   22
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               7                20
  MALE                17                22
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
D7V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       1                         1    22
  7P GAIN WILD-TYPE     1                         3    36
D7V11, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                  22                36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    3 13
  7P GAIN WILD-TYPE  1 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3   13
  7P GAIN WILD-TYPE    1   19
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              13                19
[1] 2 2
[1] FALSE

Clustering(8) Variable = 7Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   17  6
  7Q GAIN WILD-TYPE 39  3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               23                42 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                 3 
$`7Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8343 
      141.73       137.06        98.96        28.11        24.79        71.41 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 
       62.37       151.96        49.97        23.47        25.91       104.52 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8405 
        3.55        52.27        11.21        42.35        10.68        74.93 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67        80.38        86.10        77.85        57.17 

$`7Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 
       86.56        66.54        73.91        28.80        54.74        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       44.91        28.80        47.24       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 
      129.37        87.91        25.48        65.19         0.99        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
       19.33         2.50        59.08       115.00       100.87        76.90 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
       79.04        92.71        87.78       103.27        61.58        63.95 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             3.55              0.99 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           151.96            129.37 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           57.170            70.225 
[1] "3.5 - 152.0 (57.2)" "1.0 - 129.4 (70.2)"
[1] "hr=" "4.2"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED         6       10         4        4
  7Q GAIN WILD-TYPE      15       15        10        2
D8V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 6                15
  STAGE II               10                15
  STAGE III               4                10
  STAGE IV                4                 2
[1] 4 2
[1] TRUE
[1] "dimension 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    6 10     8
  7Q GAIN WILD-TYPE 15 15    12
D8V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1                  6                15
  T2                 10                15
  T3+T4               8                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"
                   vv
clus                N0 N1+N2
  7Q GAIN MUTATED   16     3
  7Q GAIN WILD-TYPE 24     2
D8V5, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0                 16                24
  N1+N2               3                 2
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   11  2
  7Q GAIN WILD-TYPE 23  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     11    2
  7Q GAIN WILD-TYPE   23    0
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              11                23
  1               2                 0
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    7 17
  7Q GAIN WILD-TYPE 20 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7   17
  7Q GAIN WILD-TYPE   20   22
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               7                20
  MALE                17                22
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
D8V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       1                         1    22
  7Q GAIN WILD-TYPE     1                         3    36
D8V11, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                  22                36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    3 13
  7Q GAIN WILD-TYPE  1 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3   13
  7Q GAIN WILD-TYPE    1   19
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              13                19
[1] 2 2
[1] FALSE

Clustering(9) Variable = 8P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   14  2
  8P GAIN WILD-TYPE 42  7
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               16                49 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                 7 
$`8P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      141.73        98.96        28.11        62.37       151.96        49.97 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KO-8405 
       23.47        25.91         0.99        52.27        11.21        74.93 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       80.38        87.78        86.10        77.85 

$`8P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       28.80        54.74        23.28        44.91        28.80        47.24 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      123.12        51.06        31.33       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       65.19       104.52         3.55        87.12        19.33         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87        76.90        10.68 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 
       79.04        92.71        16.67       103.27        57.17        61.58 
TCGA-KO-8417 
       63.95 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.99              2.50 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           151.96            137.06 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            68.65             65.19 
[1] "1.0 - 152.0 (68.7)" "2.5 - 137.1 (65.2)"
[1] "hr=" "1.1"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         4        9         2        2
  8P GAIN WILD-TYPE      17       16        12        4
D9V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 4                17
  STAGE II                9                16
  STAGE III               2                12
  STAGE IV                2                 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                T1 T2 T3+T4
  8P GAIN MUTATED    4  9     4
  8P GAIN WILD-TYPE 17 16    16
D9V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1                  4                17
  T2                  9                16
  T3+T4               4                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"
                   vv
clus                N0 N1+N2
  8P GAIN MUTATED   13     2
  8P GAIN WILD-TYPE 27     3
D9V5, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0                 13                27
  N1+N2               2                 3
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    8  1
  8P GAIN WILD-TYPE 26  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      8    1
  8P GAIN WILD-TYPE   26    1
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               8                26
  1               1                 1
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    6 11
  8P GAIN WILD-TYPE 21 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      6   11
  8P GAIN WILD-TYPE   21   28
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               6                21
  MALE                11                28
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
D9V10, continuous
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                 6 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KO-8408 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       0                         1    16
  8P GAIN WILD-TYPE     2                         3    42
D9V11, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                  16                42
[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"
D9V12, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    2 10
  8P GAIN WILD-TYPE  2 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2   10
  8P GAIN WILD-TYPE    2   22
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              10                22
[1] 2 2
[1] FALSE

Clustering(10) Variable = 8Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   15  2
  8Q GAIN WILD-TYPE 41  7
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               17                48 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                 7 
$`8Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      141.73        98.96        28.11        62.37       151.96        49.97 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 
       23.47        25.91         3.55         0.99        52.27        11.21 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       74.93        80.38        87.78        86.10        77.85 

$`8Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       28.80        54.74        23.28        44.91        28.80        47.24 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      123.12        51.06        31.33       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
       65.19       104.52        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 
      115.00        42.35       100.87        76.90        10.68        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       92.71        16.67       103.27        57.17        61.58        63.95 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.99              2.50 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           151.96            137.06 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           62.370            65.865 
[1] "1.0 - 152.0 (62.4)" "2.5 - 137.1 (65.9)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         4        9         2        3
  8Q GAIN WILD-TYPE      17       16        12        3
D10V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 4                17
  STAGE II                9                16
  STAGE III               2                12
  STAGE IV                3                 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                T1 T2 T3+T4
  8Q GAIN MUTATED    4  9     5
  8Q GAIN WILD-TYPE 17 16    15
D10V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1                  4                17
  T2                  9                16
  T3+T4               5                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"
                   vv
clus                N0 N1+N2
  8Q GAIN MUTATED   13     2
  8Q GAIN WILD-TYPE 27     3
D10V5, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0                 13                27
  N1+N2               2                 3
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    8  2
  8Q GAIN WILD-TYPE 26  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      8    2
  8Q GAIN WILD-TYPE   26    0
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0               8                26
  1               2                 0
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    6 12
  8Q GAIN WILD-TYPE 21 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6   12
  8Q GAIN WILD-TYPE   21   27
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               6                21
  MALE                12                27
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
D10V10, continuous
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                 6 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KO-8408 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       0                         1    17
  8Q GAIN WILD-TYPE     2                         3    41
D10V11, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                  17                41
[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"
D10V12, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    2 10
  8Q GAIN WILD-TYPE  2 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2   10
  8Q GAIN WILD-TYPE    2   22
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              10                22
[1] 2 2
[1] FALSE

Clustering(11) Variable = 9P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    8  2
  9P GAIN WILD-TYPE 48  7
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               10                55 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                 7 
$`9P GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8427 
      137.06        98.96        24.79       151.96        49.97         0.99 
TCGA-KN-8428 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8414 
       52.27        74.93        80.38        77.85 

$`9P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        28.11        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        54.74        62.37        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       47.24       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87        76.90        10.68        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 
       16.67        87.78       103.27        86.10        57.17        61.58 
TCGA-KO-8417 
       63.95 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.99              2.50 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           151.96            141.73 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            76.39             63.95 
[1] "1.0 - 152.0 (76.4)" "2.5 - 141.7 (64.0)"
[1] "hr=" "1.5"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED         1        6         1        2
  9P GAIN WILD-TYPE      20       19        13        4
D11V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 1                20
  STAGE II                6                19
  STAGE III               1                13
  STAGE IV                2                 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                T1 T2 T3+T4
  9P GAIN MUTATED    1  6     3
  9P GAIN WILD-TYPE 20 19    17
D11V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1                  1                20
  T2                  6                19
  T3+T4               3                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"
                   vv
clus                N0 N1+N2
  9P GAIN MUTATED    8     2
  9P GAIN WILD-TYPE 32     3
D11V5, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0                  8                32
  N1+N2               2                 3
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    6  0
  9P GAIN WILD-TYPE 28  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      6    0
  9P GAIN WILD-TYPE   28    2
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               6                28
  1               0                 2
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    4  6
  9P GAIN WILD-TYPE 23 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      4    6
  9P GAIN WILD-TYPE   23   33
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               4                23
  MALE                 6                33
[1] 2 2
[1] FALSE
D11V8, continuous
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                 9 
       TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KO-8411 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KO-8413 
"9P GAIN WILD-TYPE" 
D11V9, continuous
D11V10, continuous
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                 6 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       1                         0     9
  9P GAIN WILD-TYPE     1                         4    49
D11V11, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   9                49
[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"
D11V12, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    1  5
  9P GAIN WILD-TYPE  3 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1    5
  9P GAIN WILD-TYPE    3   27
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               5                27
[1] 2 2
[1] FALSE

Clustering(12) Variable = 9Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    8  2
  9Q GAIN WILD-TYPE 48  7
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               10                55 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                 7 
$`9Q GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8427 
      137.06        98.96        24.79       151.96        49.97         0.99 
TCGA-KN-8428 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8414 
       52.27        74.93        80.38        77.85 

$`9Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        28.11        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        54.74        62.37        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       47.24       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87        76.90        10.68        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 
       16.67        87.78       103.27        86.10        57.17        61.58 
TCGA-KO-8417 
       63.95 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.99              2.50 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           151.96            141.73 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            76.39             63.95 
[1] "1.0 - 152.0 (76.4)" "2.5 - 141.7 (64.0)"
[1] "hr=" "1.5"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         1        6         1        2
  9Q GAIN WILD-TYPE      20       19        13        4
D12V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 1                20
  STAGE II                6                19
  STAGE III               1                13
  STAGE IV                2                 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                T1 T2 T3+T4
  9Q GAIN MUTATED    1  6     3
  9Q GAIN WILD-TYPE 20 19    17
D12V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1                  1                20
  T2                  6                19
  T3+T4               3                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"
                   vv
clus                N0 N1+N2
  9Q GAIN MUTATED    8     2
  9Q GAIN WILD-TYPE 32     3
D12V5, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0                  8                32
  N1+N2               2                 3
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    6  0
  9Q GAIN WILD-TYPE 28  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      6    0
  9Q GAIN WILD-TYPE   28    2
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               6                28
  1               0                 2
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    4  6
  9Q GAIN WILD-TYPE 23 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4    6
  9Q GAIN WILD-TYPE   23   33
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               4                23
  MALE                 6                33
[1] 2 2
[1] FALSE
D12V8, continuous
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                 9 
       TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KO-8411 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KO-8413 
"9Q GAIN WILD-TYPE" 
D12V9, continuous
D12V10, continuous
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                 6 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       1                         0     9
  9Q GAIN WILD-TYPE     1                         4    49
D12V11, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   9                49
[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"
D12V12, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    1  5
  9Q GAIN WILD-TYPE  3 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1    5
  9Q GAIN WILD-TYPE    3   27
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               5                27
[1] 2 2
[1] FALSE

Clustering(13) Variable = 10P GAIN MUTATION ANALYSIS
D13V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    4  0
  10P GAIN WILD-TYPE 52  9
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 61 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  9 
$`10P GAIN MUTATED`
TCGA-KL-8324 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8436 
      141.73         0.99        11.21        42.35 

$`10P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       25.91        65.19       104.52         3.55        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
       19.33         2.50        59.08       115.00       100.87        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68        74.93        79.04        92.71        16.67        80.38 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       87.78       103.27        86.10        77.85        57.17        61.58 
TCGA-KO-8417 
       63.95 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.99               2.50 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            141.73             151.96 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             26.78              66.54 
[1] "1.0 - 141.7 (26.8)" "2.5 - 152.0 (66.5)"
[1] "hr="     "2.6e+07"
D13V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         0        2         1        1
  10P GAIN WILD-TYPE      21       23        13        5
D13V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  0                 21
  STAGE II                 2                 23
  STAGE III                1                 13
  STAGE IV                 1                  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                 T1 T2 T3+T4
  10P GAIN MUTATED    0  2     2
  10P GAIN WILD-TYPE 21 23    18
D13V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                   0                 21
  T2                   2                 23
  T3+T4                2                 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"
                    vv
clus                 N0 N1+N2
  10P GAIN MUTATED    0     1
  10P GAIN WILD-TYPE 40     4
D13V5, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 44 
        TCGA-KL-8326         TCGA-KL-8327         TCGA-KL-8328 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KL-8329         TCGA-KL-8330         TCGA-KL-8331 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KL-8332         TCGA-KL-8333         TCGA-KL-8334 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KL-8335         TCGA-KL-8336         TCGA-KL-8337 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KL-8338         TCGA-KL-8339         TCGA-KL-8340 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8342         TCGA-KL-8343 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KL-8344         TCGA-KL-8345         TCGA-KL-8346 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KM-8438         TCGA-KM-8443         TCGA-KN-8418 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KN-8428         TCGA-KN-8429         TCGA-KN-8430 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KO-8413         TCGA-KO-8414         TCGA-KO-8415 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KO-8416         TCGA-KO-8417 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D13V6, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    1  0
  10P GAIN WILD-TYPE 33  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    0
  10P GAIN WILD-TYPE   33    2
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                1                 33
  1                0                  2
[1] 2 2
[1] FALSE
D13V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    2  2
  10P GAIN WILD-TYPE 25 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    2
  10P GAIN WILD-TYPE   25   37
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                2                 25
  MALE                  2                 37
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                  9 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8428 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8416 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D13V10, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KO-8408 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KO-8409 
"10P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         0     4
  10P GAIN WILD-TYPE     2                         4    54
D13V11, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    4                 54
[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"
D13V12, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    0  2
  10P GAIN WILD-TYPE  4 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0    2
  10P GAIN WILD-TYPE    4   30
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                2                 30
[1] 2 2
[1] FALSE

Clustering(14) Variable = 11P GAIN MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED   12  2
  11P GAIN WILD-TYPE 44  7
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                14                 51 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                  7 
$`11P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8339 TCGA-KL-8341 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 
      141.73        28.11        24.79       151.96        23.47        25.91 
TCGA-KN-8425 TCGA-KN-8433 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      104.52        11.21        74.93        80.38        87.78        86.10 
TCGA-KO-8414 TCGA-KO-8415 
       77.85        57.17 

$`11P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       30.25        44.84        86.56        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        54.74        62.37        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       47.24        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       87.91        25.48        65.19         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       87.12        19.33         2.50        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87        76.90        10.68        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
      103.27        61.58        63.95 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             11.21               0.99 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            151.96             137.06 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             76.39              63.95 
[1] "11.2 - 152.0 (76.4)" "1.0 - 137.1 (64.0)" 
[1] "hr=" "1"  
D14V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         6        5         2        2
  11P GAIN WILD-TYPE      15       20        12        4
D14V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  6                 15
  STAGE II                 5                 20
  STAGE III                2                 12
  STAGE IV                 2                  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                 T1 T2 T3+T4
  11P GAIN MUTATED    6  5     4
  11P GAIN WILD-TYPE 15 20    16
D14V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                   6                 15
  T2                   5                 20
  T3+T4                4                 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"
                    vv
clus                 N0 N1+N2
  11P GAIN MUTATED   11     2
  11P GAIN WILD-TYPE 29     3
D14V5, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                  11                 29
  N1+N2                2                  3
[1] 2 2
[1] FALSE
D14V6, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    8  1
  11P GAIN WILD-TYPE 26  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      8    1
  11P GAIN WILD-TYPE   26    1
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                8                 26
  1                1                  1
[1] 2 2
[1] FALSE
D14V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    6  9
  11P GAIN WILD-TYPE 21 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6    9
  11P GAIN WILD-TYPE   21   30
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                6                 21
  MALE                  9                 30
[1] 2 2
[1] FALSE
D14V8, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KO-8411 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D14V9, continuous
D14V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       1                         1    13
  11P GAIN WILD-TYPE     1                         3    45
D14V11, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   13                 45
[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"
D14V12, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  8
  11P GAIN WILD-TYPE  1 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    8
  11P GAIN WILD-TYPE    1   24
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO                8                 24
[1] 2 2
[1] FALSE

Clustering(15) Variable = 11Q GAIN MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED   13  1
  11Q GAIN WILD-TYPE 43  8
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                 51 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                  8 
$`11Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8341 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 
      141.73        24.79       151.96        23.47        25.91       104.52 
TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
        3.55        11.21        74.93        80.38        87.78        86.10 
TCGA-KO-8414 TCGA-KO-8415 
       77.85        57.17 

$`11Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 
       30.25        44.84        86.56        28.11        66.54        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 
       71.41        28.80        54.74        62.37        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       28.80        47.24        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8428 
      129.37        87.91        25.48        65.19         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       87.12        19.33         2.50        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87        76.90        10.68        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
      103.27        61.58        63.95 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              3.55               0.99 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            151.96             137.06 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             76.39              63.95 
[1] "3.5 - 152.0 (76.4)" "1.0 - 137.1 (64.0)"
[1] "hr=" "2.1"
D15V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         6        5         2        2
  11Q GAIN WILD-TYPE      15       20        12        4
D15V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  6                 15
  STAGE II                 5                 20
  STAGE III                2                 12
  STAGE IV                 2                  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                 T1 T2 T3+T4
  11Q GAIN MUTATED    6  5     4
  11Q GAIN WILD-TYPE 15 20    16
D15V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                   6                 15
  T2                   5                 20
  T3+T4                4                 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"
                    vv
clus                 N0 N1+N2
  11Q GAIN MUTATED   11     1
  11Q GAIN WILD-TYPE 29     4
D15V5, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                  11                 29
  N1+N2                1                  4
[1] 2 2
[1] FALSE
D15V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    8  1
  11Q GAIN WILD-TYPE 26  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      8    1
  11Q GAIN WILD-TYPE   26    1
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                8                 26
  1                1                  1
[1] 2 2
[1] FALSE
D15V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    6  9
  11Q GAIN WILD-TYPE 21 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    9
  11Q GAIN WILD-TYPE   21   30
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                6                 21
  MALE                  9                 30
[1] 2 2
[1] FALSE
D15V8, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KO-8411 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D15V9, continuous
D15V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       1                         1    13
  11Q GAIN WILD-TYPE     1                         3    45
D15V11, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   13                 45
[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"
D15V12, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3  8
  11Q GAIN WILD-TYPE  1 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    8
  11Q GAIN WILD-TYPE    1   24
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO                8                 24
[1] 2 2
[1] FALSE

Clustering(16) Variable = 12P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   15  3
  12P GAIN WILD-TYPE 41  6
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                18                 47 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                  6 
$`12P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8343 TCGA-KL-8346 
      141.73       137.06        98.96        28.11        71.41        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
      151.96        49.97        23.47        25.91         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8436 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       52.27        42.35        80.38        87.78        86.10        77.85 

$`12P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 
       86.56        66.54        24.79        73.91        28.80        54.74 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
       23.28        44.91        28.80        47.24       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
       31.33       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       16.67       103.27        57.17        61.58        63.95 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.99               2.50 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            151.96             129.37 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             66.89              65.19 
[1] "1.0 - 152.0 (66.9)" "2.5 - 129.4 (65.2)"
[1] "hr=" "1.3"
D16V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED         5       10         1        3
  12P GAIN WILD-TYPE      16       15        13        3
D16V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  5                 16
  STAGE II                10                 15
  STAGE III                1                 13
  STAGE IV                 3                  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                 T1 T2 T3+T4
  12P GAIN MUTATED    5 10     4
  12P GAIN WILD-TYPE 16 15    16
D16V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                   5                 16
  T2                  10                 15
  T3+T4                4                 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"
                    vv
clus                 N0 N1+N2
  12P GAIN MUTATED   14     2
  12P GAIN WILD-TYPE 26     3
D16V5, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                  14                 26
  N1+N2                2                  3
[1] 2 2
[1] FALSE
D16V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    9  2
  12P GAIN WILD-TYPE 25  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      9    2
  12P GAIN WILD-TYPE   25    0
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                9                 25
  1                2                  0
[1] 2 2
[1] FALSE
D16V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    6 13
  12P GAIN WILD-TYPE 21 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6   13
  12P GAIN WILD-TYPE   21   26
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                6                 21
  MALE                 13                 26
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
D16V10, continuous
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8433 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KO-8408 
"12P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       0                         1    18
  12P GAIN WILD-TYPE     2                         3    40
D16V11, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   18                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1 11
  12P GAIN WILD-TYPE  3 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   11
  12P GAIN WILD-TYPE    3   21
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               11                 21
[1] 2 2
[1] FALSE

Clustering(17) Variable = 12Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   15  4
  12Q GAIN WILD-TYPE 41  5
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                19                 46 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                  5 
$`12Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8343 
      141.73       137.06        98.96        28.11        24.79        71.41 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
      151.96        49.97        23.47        25.91         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       52.27        11.21        42.35        80.38        87.78        86.10 
TCGA-KO-8414 
       77.85 

$`12Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       86.56        66.54        73.91        28.80        54.74        62.37 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
       23.28        44.91        28.80        47.24       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
       31.33       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 
       87.12        19.33         2.50        59.08       115.00       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        57.17        61.58        63.95 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.99               2.50 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            151.96             129.37 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            52.270             65.865 
[1] "1.0 - 152.0 (52.3)" "2.5 - 129.4 (65.9)"
[1] "hr=" "2.2"
D17V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED         5        9         2        4
  12Q GAIN WILD-TYPE      16       16        12        2
D17V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  5                 16
  STAGE II                 9                 16
  STAGE III                2                 12
  STAGE IV                 4                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  12Q GAIN MUTATED    5  9     6
  12Q GAIN WILD-TYPE 16 16    14
D17V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                   5                 16
  T2                   9                 16
  T3+T4                6                 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"
                    vv
clus                 N0 N1+N2
  12Q GAIN MUTATED   13     3
  12Q GAIN WILD-TYPE 27     2
D17V5, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                  13                 27
  N1+N2                3                  2
[1] 2 2
[1] FALSE
D17V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    9  2
  12Q GAIN WILD-TYPE 25  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      9    2
  12Q GAIN WILD-TYPE   25    0
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                9                 25
  1                2                  0
[1] 2 2
[1] FALSE
D17V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    7 13
  12Q GAIN WILD-TYPE 20 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      7   13
  12Q GAIN WILD-TYPE   20   26
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                7                 20
  MALE                 13                 26
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
D17V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       1                         1    18
  12Q GAIN WILD-TYPE     1                         3    40
D17V11, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   18                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1 12
  12Q GAIN WILD-TYPE  3 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   12
  12Q GAIN WILD-TYPE    3   20
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               12                 20
[1] 2 2
[1] FALSE

Clustering(18) Variable = 14Q GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED   17  3
  14Q GAIN WILD-TYPE 39  6
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                20                 45 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                  6 
$`14Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 
      141.73       137.06        98.96        28.11        24.79        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
      151.96        49.97        23.47        25.91       104.52         3.55 
TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       52.27        11.21        42.35        80.38        87.78        86.10 
TCGA-KO-8414 TCGA-KO-8415 
       77.85        57.17 

$`14Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.56        66.54        73.91        71.41        28.80        54.74 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
       23.28        44.91        28.80        47.24       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 
       31.33       129.37        87.91        25.48        65.19         0.99 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 
       87.12        19.33         2.50        59.08       115.00       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
      103.27        61.58        63.95 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              3.55               0.99 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            151.96             129.37 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             59.77              66.54 
[1] "3.5 - 152.0 (59.8)" "1.0 - 129.4 (66.5)"
[1] "hr=" "1.2"
D18V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED         7       10         1        3
  14Q GAIN WILD-TYPE      14       15        13        3
D18V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  7                 14
  STAGE II                10                 15
  STAGE III                1                 13
  STAGE IV                 3                  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                 T1 T2 T3+T4
  14Q GAIN MUTATED    7 10     4
  14Q GAIN WILD-TYPE 14 15    16
D18V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                   7                 14
  T2                  10                 15
  T3+T4                4                 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"
                    vv
clus                 N0 N1+N2
  14Q GAIN MUTATED   15     2
  14Q GAIN WILD-TYPE 25     3
D18V5, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                  15                 25
  N1+N2                2                  3
[1] 2 2
[1] FALSE
D18V6, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   10  2
  14Q GAIN WILD-TYPE 24  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     10    2
  14Q GAIN WILD-TYPE   24    0
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               10                 24
  1                2                  0
[1] 2 2
[1] FALSE
D18V7, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    8 13
  14Q GAIN WILD-TYPE 19 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      8   13
  14Q GAIN WILD-TYPE   19   26
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                8                 19
  MALE                 13                 26
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
D18V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       1                         1    19
  14Q GAIN WILD-TYPE     1                         3    39
D18V11, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   19                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    2 11
  14Q GAIN WILD-TYPE  2 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   11
  14Q GAIN WILD-TYPE    2   21
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO               11                 21
[1] 2 2
[1] FALSE

Clustering(19) Variable = 15Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED   16  4
  15Q GAIN WILD-TYPE 40  5
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                20                 45 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                  5 
$`15Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8336 TCGA-KL-8339 TCGA-KL-8346 
      141.73       137.06        98.96        30.25        28.11        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
      151.96        49.97        23.47       104.52         3.55        52.27 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8413 
       11.21        42.35        74.93        16.67        80.38        86.10 
TCGA-KO-8414 TCGA-KO-8415 
       77.85        57.17 

$`15Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 
       84.89        98.33        96.95        92.55        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
       23.28        44.91        28.80        47.24       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
       31.33       129.37        87.91        25.48        25.91        65.19 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
        0.99        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8410 
      100.87        76.90        10.68        79.04        92.71        87.78 
TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
      103.27        61.58        63.95 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              3.55               0.99 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            151.96             129.37 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             59.77              66.54 
[1] "3.5 - 152.0 (59.8)" "1.0 - 129.4 (66.5)"
[1] "hr=" "1.9"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED         5       10         3        3
  15Q GAIN WILD-TYPE      16       15        11        3
D19V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  5                 16
  STAGE II                10                 15
  STAGE III                3                 11
  STAGE IV                 3                  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                 T1 T2 T3+T4
  15Q GAIN MUTATED    5 10     6
  15Q GAIN WILD-TYPE 16 15    14
D19V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                   5                 16
  T2                  10                 15
  T3+T4                6                 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"
                    vv
clus                 N0 N1+N2
  15Q GAIN MUTATED   14     3
  15Q GAIN WILD-TYPE 26     2
D19V5, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                  14                 26
  N1+N2                3                  2
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   10  2
  15Q GAIN WILD-TYPE 24  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     10    2
  15Q GAIN WILD-TYPE   24    0
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               10                 24
  1                2                  0
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    8 13
  15Q GAIN WILD-TYPE 19 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      8   13
  15Q GAIN WILD-TYPE   19   26
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                8                 19
  MALE                 13                 26
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
D19V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       0                         1    20
  15Q GAIN WILD-TYPE     2                         3    38
D19V11, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   20                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    3 10
  15Q GAIN WILD-TYPE  1 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3   10
  15Q GAIN WILD-TYPE    1   22
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO               10                 22
[1] 2 2
[1] FALSE

Clustering(20) Variable = 16P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   19  1
  16P GAIN WILD-TYPE 37  8
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                20                 45 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                  8 
$`16P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 
      141.73       137.06        98.96        24.79        62.37       151.96 
TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
       49.97        23.47        25.48        25.91       104.52         3.55 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       11.21        42.35        74.93        80.38        87.78        86.10 
TCGA-KO-8414 TCGA-KO-8415 
       77.85        57.17 

$`16P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        28.11        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       54.74        23.28        44.91        28.80        47.24       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8427 
       51.06        31.33       129.37        87.91        65.19         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87        76.90        10.68        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
      103.27        61.58        63.95 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              3.55               0.99 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            151.96             129.37 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             68.65              65.19 
[1] "3.5 - 152.0 (68.7)" "1.0 - 129.4 (65.2)"
[1] "hr=" "3.4"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED         8        9         2        2
  16P GAIN WILD-TYPE      13       16        12        4
D20V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  8                 13
  STAGE II                 9                 16
  STAGE III                2                 12
  STAGE IV                 2                  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                 T1 T2 T3+T4
  16P GAIN MUTATED    8  9     4
  16P GAIN WILD-TYPE 13 16    16
D20V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                   8                 13
  T2                   9                 16
  T3+T4                4                 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"
                    vv
clus                 N0 N1+N2
  16P GAIN MUTATED   16     1
  16P GAIN WILD-TYPE 24     4
D20V5, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                  16                 24
  N1+N2                1                  4
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   11  1
  16P GAIN WILD-TYPE 23  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     11    1
  16P GAIN WILD-TYPE   23    1
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               11                 23
  1                1                  1
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    9 12
  16P GAIN WILD-TYPE 18 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9   12
  16P GAIN WILD-TYPE   18   27
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                9                 18
  MALE                 12                 27
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
D20V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         1    19
  16P GAIN WILD-TYPE     1                         3    39
D20V11, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   19                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    3 10
  16P GAIN WILD-TYPE  1 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3   10
  16P GAIN WILD-TYPE    1   22
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO               10                 22
[1] 2 2
[1] FALSE

Clustering(21) Variable = 16Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   19  1
  16Q GAIN WILD-TYPE 37  8
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                20                 45 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  8 
$`16Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 
      141.73       137.06        98.96        24.79        62.37       151.96 
TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
       49.97        23.47        25.48        25.91       104.52         3.55 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       11.21        42.35        74.93        80.38        87.78        86.10 
TCGA-KO-8414 TCGA-KO-8415 
       77.85        57.17 

$`16Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        28.11        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       54.74        23.28        44.91        28.80        47.24       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8427 
       51.06        31.33       129.37        87.91        65.19         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87        76.90        10.68        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
      103.27        61.58        63.95 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              3.55               0.99 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            151.96             129.37 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             68.65              65.19 
[1] "3.5 - 152.0 (68.7)" "1.0 - 129.4 (65.2)"
[1] "hr=" "3.4"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED         8        9         2        2
  16Q GAIN WILD-TYPE      13       16        12        4
D21V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  8                 13
  STAGE II                 9                 16
  STAGE III                2                 12
  STAGE IV                 2                  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                 T1 T2 T3+T4
  16Q GAIN MUTATED    8  9     4
  16Q GAIN WILD-TYPE 13 16    16
D21V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                   8                 13
  T2                   9                 16
  T3+T4                4                 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"
                    vv
clus                 N0 N1+N2
  16Q GAIN MUTATED   16     1
  16Q GAIN WILD-TYPE 24     4
D21V5, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                  16                 24
  N1+N2                1                  4
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   11  1
  16Q GAIN WILD-TYPE 23  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     11    1
  16Q GAIN WILD-TYPE   23    1
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               11                 23
  1                1                  1
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    9 12
  16Q GAIN WILD-TYPE 18 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      9   12
  16Q GAIN WILD-TYPE   18   27
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                9                 18
  MALE                 12                 27
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
D21V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       1                         1    19
  16Q GAIN WILD-TYPE     1                         3    39
D21V11, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   19                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3 10
  16Q GAIN WILD-TYPE  1 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3   10
  16Q GAIN WILD-TYPE    1   22
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO               10                 22
[1] 2 2
[1] FALSE

Clustering(22) Variable = 18P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED   15  2
  18P GAIN WILD-TYPE 41  7
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                 48 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                  7 
$`18P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8639 TCGA-KN-8419 
      141.73       137.06        62.37       151.96        31.33        23.47 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8436 
       25.48        25.91       104.52         3.55        52.27        42.35 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8415 
       10.68        74.93        80.38        87.78        57.17 

$`18P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       71.41        28.80        54.74        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
       47.24        49.97       123.12        51.06       129.37        87.91 
TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
       65.19         0.99        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 
       59.08       115.00       100.87        76.90        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
       16.67       103.27        86.10        77.85        61.58        63.95 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              3.55               0.99 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            151.96             129.37 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            57.170             68.975 
[1] "3.5 - 152.0 (57.2)" "1.0 - 129.4 (69.0)"
[1] "hr=" "1.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         7        7         1        2
  18P GAIN WILD-TYPE      14       18        13        4
D22V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  7                 14
  STAGE II                 7                 18
  STAGE III                1                 13
  STAGE IV                 2                  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                 T1 T2 T3+T4
  18P GAIN MUTATED    7  7     3
  18P GAIN WILD-TYPE 14 18    17
D22V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                   7                 14
  T2                   7                 18
  T3+T4                3                 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"
                    vv
clus                 N0 N1+N2
  18P GAIN MUTATED   12     0
  18P GAIN WILD-TYPE 28     5
D22V5, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                  12                 28
  N1+N2                0                  5
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    7  1
  18P GAIN WILD-TYPE 27  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7    1
  18P GAIN WILD-TYPE   27    1
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                7                 27
  1                1                  1
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    6 11
  18P GAIN WILD-TYPE 21 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6   11
  18P GAIN WILD-TYPE   21   28
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                6                 21
  MALE                 11                 28
[1] 2 2
[1] FALSE
D22V8, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KO-8411         TCGA-KO-8413 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
D22V9, continuous
D22V10, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                  6 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8345         TCGA-KN-8433         TCGA-KO-8408 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       0                         1    16
  18P GAIN WILD-TYPE     2                         3    42
D22V11, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   16                 42
[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"
D22V12, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    2  9
  18P GAIN WILD-TYPE  2 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    9
  18P GAIN WILD-TYPE    2   23
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO                9                 23
[1] 2 2
[1] FALSE

Clustering(23) Variable = 18Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED   15  1
  18Q GAIN WILD-TYPE 41  8
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                16                 49 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                  8 
$`18Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8639 TCGA-KN-8419 
      141.73       137.06        62.37       151.96        31.33        23.47 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8436 
       25.48        25.91       104.52         3.55        52.27        42.35 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8415 
       74.93        80.38        87.78        57.17 

$`18Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       71.41        28.80        54.74        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
       47.24        49.97       123.12        51.06       129.37        87.91 
TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
       65.19         0.99        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 
       59.08       115.00       100.87        76.90        10.68        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 
       92.71        16.67       103.27        86.10        77.85        61.58 
TCGA-KO-8417 
       63.95 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              3.55               0.99 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            151.96             129.37 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             59.77              66.54 
[1] "3.5 - 152.0 (59.8)" "1.0 - 129.4 (66.5)"
[1] "hr=" "2.6"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED         7        7         1        1
  18Q GAIN WILD-TYPE      14       18        13        5
D23V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  7                 14
  STAGE II                 7                 18
  STAGE III                1                 13
  STAGE IV                 1                  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                 T1 T2 T3+T4
  18Q GAIN MUTATED    7  7     2
  18Q GAIN WILD-TYPE 14 18    18
D23V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                   7                 14
  T2                   7                 18
  T3+T4                2                 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"
                    vv
clus                 N0 N1+N2
  18Q GAIN MUTATED   12     0
  18Q GAIN WILD-TYPE 28     5
D23V5, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                  12                 28
  N1+N2                0                  5
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    7  1
  18Q GAIN WILD-TYPE 27  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7    1
  18Q GAIN WILD-TYPE   27    1
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                7                 27
  1                1                  1
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    6 10
  18Q GAIN WILD-TYPE 21 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6   10
  18Q GAIN WILD-TYPE   21   29
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                6                 21
  MALE                 10                 29
[1] 2 2
[1] FALSE
D23V8, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KO-8411         TCGA-KO-8413 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D23V9, continuous
D23V10, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                  6 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8345         TCGA-KN-8433         TCGA-KO-8408 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         1    15
  18Q GAIN WILD-TYPE     2                         3    43
D23V11, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   15                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    2  8
  18Q GAIN WILD-TYPE  2 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    8
  18Q GAIN WILD-TYPE    2   24
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO                8                 24
[1] 2 2
[1] FALSE

Clustering(24) Variable = 19P GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   13  5
  19P GAIN WILD-TYPE 43  4
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                18                 47 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                  4 
$`19P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8336 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 
      141.73        30.25        28.11        24.79        62.37       151.96 
TCGA-KM-8443 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       49.97        25.91       104.52         3.55         0.99        52.27 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8414 
       11.21        42.35        16.67        80.38        87.78        77.85 

$`19P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       44.84        86.56        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       54.74        23.28        44.91        28.80        47.24       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       65.19        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        86.10        57.17        61.58        63.95 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.99               2.50 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            151.96             137.06 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             46.16              73.91 
[1] "1.0 - 152.0 (46.2)" "2.5 - 137.1 (73.9)"
[1] "hr=" "4.2"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED         4        8         2        5
  19P GAIN WILD-TYPE      17       17        12        1
D24V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  4                 17
  STAGE II                 8                 17
  STAGE III                2                 12
  STAGE IV                 5                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  19P GAIN MUTATED    4  8     7
  19P GAIN WILD-TYPE 17 17    13
D24V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                   4                 17
  T2                   8                 17
  T3+T4                7                 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"
                    vv
clus                 N0 N1+N2
  19P GAIN MUTATED   10     5
  19P GAIN WILD-TYPE 30     0
D24V5, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                  10                 30
  N1+N2                5                  0
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    7  2
  19P GAIN WILD-TYPE 27  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7    2
  19P GAIN WILD-TYPE   27    0
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                7                 27
  1                2                  0
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    6 13
  19P GAIN WILD-TYPE 21 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6   13
  19P GAIN WILD-TYPE   21   26
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                6                 21
  MALE                 13                 26
[1] 2 2
[1] FALSE
D24V8, continuous
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8476         TCGA-KM-8477 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KO-8411         TCGA-KO-8413 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D24V9, continuous
D24V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       1                         0    18
  19P GAIN WILD-TYPE     1                         4    40
D24V11, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                   18                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    0 11
  19P GAIN WILD-TYPE  4 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   11
  19P GAIN WILD-TYPE    4   21
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               11                 21
[1] 2 2
[1] FALSE

Clustering(25) Variable = 19Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   12  4
  19Q GAIN WILD-TYPE 44  5
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                16                 49 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                  5 
$`19Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8336 TCGA-KL-8339 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      141.73        30.25        28.11        62.37       151.96        49.97 
TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 
       25.91       104.52         3.55        52.27        11.21        42.35 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8414 
       16.67        80.38        87.78        77.85 

$`19Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       28.80        54.74        23.28        44.91        28.80        47.24 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       25.48        65.19         0.99        87.12        19.33         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       59.08       115.00       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 
       79.04        92.71       103.27        86.10        57.17        61.58 
TCGA-KO-8417 
       63.95 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              3.55               0.99 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            151.96             137.06 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             51.12              71.41 
[1] "3.5 - 152.0 (51.1)" "1.0 - 137.1 (71.4)"
[1] "hr=" "2.8"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED         4        8         2        3
  19Q GAIN WILD-TYPE      17       17        12        3
D25V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  4                 17
  STAGE II                 8                 17
  STAGE III                2                 12
  STAGE IV                 3                  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                 T1 T2 T3+T4
  19Q GAIN MUTATED    4  8     5
  19Q GAIN WILD-TYPE 17 17    15
D25V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                   4                 17
  T2                   8                 17
  T3+T4                5                 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"
                    vv
clus                 N0 N1+N2
  19Q GAIN MUTATED   10     3
  19Q GAIN WILD-TYPE 30     2
D25V5, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                  10                 30
  N1+N2                3                  2
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    6  2
  19Q GAIN WILD-TYPE 28  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      6    2
  19Q GAIN WILD-TYPE   28    0
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                6                 28
  1                2                  0
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    6 11
  19Q GAIN WILD-TYPE 21 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      6   11
  19Q GAIN WILD-TYPE   21   28
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                6                 21
  MALE                 11                 28
[1] 2 2
[1] FALSE
D25V8, continuous
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8476         TCGA-KM-8477 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KO-8411         TCGA-KO-8413 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D25V9, continuous
D25V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       0                         0    17
  19Q GAIN WILD-TYPE     2                         4    41
D25V11, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                   17                 41
[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"
D25V12, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    0 11
  19Q GAIN WILD-TYPE  4 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0   11
  19Q GAIN WILD-TYPE    4   21
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               11                 21
[1] 2 2
[1] FALSE

Clustering(26) Variable = 20P GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   16  3
  20P GAIN WILD-TYPE 40  6
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                19                 46 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                  6 
$`20P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 
      141.73       137.06        98.96        28.11        24.79        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 
      151.96        49.97        25.91       104.52         0.99        52.27 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       11.21        42.35        74.93        80.38        87.78        86.10 
TCGA-KO-8414 
       77.85 

$`20P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.56        66.54        73.91        71.41        28.80        54.74 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
       23.28        44.91        28.80        47.24       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       31.33       129.37        23.47        87.91        25.48        65.19 
TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
        3.55        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87        76.90        10.68        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        57.17        61.58        63.95 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.99               2.50 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            151.96             129.37 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             74.93              64.57 
[1] "1.0 - 152.0 (74.9)" "2.5 - 129.4 (64.6)"
[1] "hr=" "1.2"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED         6        9         2        3
  20P GAIN WILD-TYPE      15       16        12        3
D26V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  6                 15
  STAGE II                 9                 16
  STAGE III                2                 12
  STAGE IV                 3                  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                 T1 T2 T3+T4
  20P GAIN MUTATED    6  9     5
  20P GAIN WILD-TYPE 15 16    15
D26V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                   6                 15
  T2                   9                 16
  T3+T4                5                 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"
                    vv
clus                 N0 N1+N2
  20P GAIN MUTATED   14     3
  20P GAIN WILD-TYPE 26     2
D26V5, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                  14                 26
  N1+N2                3                  2
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   10  1
  20P GAIN WILD-TYPE 24  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     10    1
  20P GAIN WILD-TYPE   24    1
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               10                 24
  1                1                  1
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    7 13
  20P GAIN WILD-TYPE 20 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7   13
  20P GAIN WILD-TYPE   20   26
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                7                 20
  MALE                 13                 26
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
D26V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       1                         0    19
  20P GAIN WILD-TYPE     1                         4    39
D26V11, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                   19                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    2 10
  20P GAIN WILD-TYPE  2 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2   10
  20P GAIN WILD-TYPE    2   22
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO               10                 22
[1] 2 2
[1] FALSE

Clustering(27) Variable = 20Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   16  4
  20Q GAIN WILD-TYPE 40  5
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                20                 45 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 4                  5 
$`20Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 
      141.73       137.06        98.96        28.11        24.79        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 
      151.96        49.97        25.91       104.52         0.99        52.27 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 
       11.21        42.35        10.68        74.93        80.38        87.78 
TCGA-KO-8413 TCGA-KO-8414 
       86.10        77.85 

$`20Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.56        66.54        73.91        71.41        28.80        54.74 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
       23.28        44.91        28.80        47.24       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       31.33       129.37        23.47        87.91        25.48        65.19 
TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
        3.55        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 
      100.87        76.90        79.04        92.71        16.67       103.27 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       57.17        61.58        63.95 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.99               2.50 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            151.96             129.37 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             68.65              65.19 
[1] "1.0 - 152.0 (68.7)" "2.5 - 129.4 (65.2)"
[1] "hr=" "1.9"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED         6        9         2        4
  20Q GAIN WILD-TYPE      15       16        12        2
D27V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  6                 15
  STAGE II                 9                 16
  STAGE III                2                 12
  STAGE IV                 4                  2
[1] 4 2
[1] TRUE
[1] "dimension 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    6  9     6
  20Q GAIN WILD-TYPE 15 16    14
D27V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                   6                 15
  T2                   9                 16
  T3+T4                6                 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"
                    vv
clus                 N0 N1+N2
  20Q GAIN MUTATED   14     3
  20Q GAIN WILD-TYPE 26     2
D27V5, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                  14                 26
  N1+N2                3                  2
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   10  1
  20Q GAIN WILD-TYPE 24  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     10    1
  20Q GAIN WILD-TYPE   24    1
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               10                 24
  1                1                  1
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    7 14
  20Q GAIN WILD-TYPE 20 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      7   14
  20Q GAIN WILD-TYPE   20   25
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                7                 20
  MALE                 14                 25
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
D27V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       1                         0    20
  20Q GAIN WILD-TYPE     1                         4    38
D27V11, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                   20                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    2 11
  20Q GAIN WILD-TYPE  2 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2   11
  20Q GAIN WILD-TYPE    2   21
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO               11                 21
[1] 2 2
[1] FALSE

Clustering(28) Variable = 21Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    4  0
  21Q GAIN WILD-TYPE 52  9
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 61 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                  9 
$`21Q GAIN MUTATED`
TCGA-KM-8438 TCGA-KM-8639 TCGA-KN-8433 TCGA-KN-8436 
      151.96        31.33        11.21        42.35 

$`21Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       51.06       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19       104.52         3.55         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
       19.33         2.50        59.08       115.00       100.87        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68        74.93        79.04        92.71        16.67        80.38 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       87.78       103.27        86.10        77.85        57.17        61.58 
TCGA-KO-8417 
       63.95 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             11.21               0.99 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            151.96             141.73 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             36.84              66.54 
[1] "11.2 - 152.0 (36.8)" "1.0 - 141.7 (66.5)" 
[1] "hr="     "2.6e+07"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED         1        2         1        0
  21Q GAIN WILD-TYPE      20       23        13        6
D28V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  1                 20
  STAGE II                 2                 23
  STAGE III                1                 13
  STAGE IV                 0                  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                 T1 T2 T3+T4
  21Q GAIN MUTATED    1  2     1
  21Q GAIN WILD-TYPE 20 23    19
D28V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                   1                 20
  T2                   2                 23
  T3+T4                1                 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"
                    vv
clus                 N0 N1+N2
  21Q GAIN MUTATED    1     0
  21Q GAIN WILD-TYPE 39     5
D28V5, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 44 
        TCGA-KL-8326         TCGA-KL-8327         TCGA-KL-8328 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8329         TCGA-KL-8330         TCGA-KL-8331 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8332         TCGA-KL-8333         TCGA-KL-8334 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8335         TCGA-KL-8336         TCGA-KL-8337 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8338         TCGA-KL-8339         TCGA-KL-8340 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8342         TCGA-KL-8343 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8344         TCGA-KL-8345         TCGA-KL-8346 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KN-8418         TCGA-KN-8419 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8427 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8428         TCGA-KN-8429         TCGA-KN-8430 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8413         TCGA-KO-8414         TCGA-KO-8415 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8416         TCGA-KO-8417 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D28V6, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    0  0
  21Q GAIN WILD-TYPE 34  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    0
  21Q GAIN WILD-TYPE   34    2
D28V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    2  2
  21Q GAIN WILD-TYPE 25 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    2
  21Q GAIN WILD-TYPE   25   37
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                2                 25
  MALE                  2                 37
[1] 2 2
[1] FALSE
D28V8, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KO-8411         TCGA-KO-8413 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D28V9, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                  9 
        TCGA-KL-8324         TCGA-KL-8330         TCGA-KL-8335 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8345         TCGA-KN-8428 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8416 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D28V10, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                  6 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8345         TCGA-KO-8408         TCGA-KO-8409 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       0                         0     4
  21Q GAIN WILD-TYPE     2                         4    54
D28V11, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    4                 54
[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"
D28V12, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    0  4
  21Q GAIN WILD-TYPE  4 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    4
  21Q GAIN WILD-TYPE    4   28
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                4                 28
[1] 2 2
[1] FALSE

Clustering(29) Variable = 22Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   15  4
  22Q GAIN WILD-TYPE 41  5
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                 46 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                  5 
$`22Q GAIN MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8443 
       38.07       141.73       137.06        24.79        62.37        49.97 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 
       23.47        25.91         3.55         0.99        52.27        11.21 
TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       42.35        74.93        16.67        80.38        87.78        86.10 
TCGA-KO-8414 
       77.85 

$`22Q GAIN WILD-TYPE`
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       102.81        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        28.11        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       54.74       151.96        23.28        44.91        28.80        47.24 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      123.12        51.06        31.33       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
       65.19       104.52        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
      115.00       100.87        76.90        10.68        79.04        92.71 
TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        57.17        61.58        63.95 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.99               2.50 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            141.73             151.96 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             49.97              72.66 
[1] "1.0 - 141.7 (50.0)" "2.5 - 152.0 (72.7)"
[1] "hr=" "2.4"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED         4        8         4        3
  22Q GAIN WILD-TYPE      17       17        10        3
D29V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  4                 17
  STAGE II                 8                 17
  STAGE III                4                 10
  STAGE IV                 3                  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                 T1 T2 T3+T4
  22Q GAIN MUTATED    4  8     7
  22Q GAIN WILD-TYPE 17 17    13
D29V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                   4                 17
  T2                   8                 17
  T3+T4                7                 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"
                    vv
clus                 N0 N1+N2
  22Q GAIN MUTATED   11     3
  22Q GAIN WILD-TYPE 29     2
D29V5, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                  11                 29
  N1+N2                3                  2
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED   10  1
  22Q GAIN WILD-TYPE 24  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     10    1
  22Q GAIN WILD-TYPE   24    1
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               10                 24
  1                1                  1
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    6 13
  22Q GAIN WILD-TYPE 21 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      6   13
  22Q GAIN WILD-TYPE   21   26
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                6                 21
  MALE                 13                 26
[1] 2 2
[1] FALSE
D29V8, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8438         TCGA-KM-8439         TCGA-KM-8440 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8441         TCGA-KM-8442         TCGA-KM-8476 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KO-8411 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
D29V9, continuous
D29V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       1                         1    17
  22Q GAIN WILD-TYPE     1                         3    41
D29V11, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   17                 41
[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"
D29V12, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    2 10
  22Q GAIN WILD-TYPE  2 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2   10
  22Q GAIN WILD-TYPE    2   22
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO               10                 22
[1] 2 2
[1] FALSE

Clustering(30) Variable = XP GAIN MUTATION ANALYSIS
D30V1, survival
                   sevent
clus2                0  1
  XP GAIN MUTATED    7  0
  XP GAIN WILD-TYPE 49  9
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                7                58 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                0                 9 
$`XP GAIN MUTATED`
TCGA-KL-8346 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8410 
       62.37        23.47        25.91         3.55        11.21        87.78 
TCGA-KO-8413 
       86.10 

$`XP GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 
       24.79        73.91        71.41        28.80        54.74       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       51.06        31.33       129.37        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 
       74.93        79.04        92.71        16.67        80.38       103.27 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       77.85        57.17        61.58        63.95 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             3.55              0.99 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            87.78            151.96 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           25.910            68.975 
[1] "3.5 - 87.8 (25.9)"  "1.0 - 152.0 (69.0)"
[1] "hr="     "7.4e+07"
D30V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP GAIN MUTATED         3        2         1        1
  XP GAIN WILD-TYPE      18       23        13        5
D30V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 3                18
  STAGE II                2                23
  STAGE III               1                13
  STAGE IV                1                 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                T1 T2 T3+T4
  XP GAIN MUTATED    3  2     2
  XP GAIN WILD-TYPE 18 23    18
D30V4, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T1                  3                18
  T2                  2                23
  T3+T4               2                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"
                   vv
clus                N0 N1+N2
  XP GAIN MUTATED    5     0
  XP GAIN WILD-TYPE 35     5
D30V5, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  N0                  5                35
  N1+N2               0                 5
[1] 2 2
[1] FALSE
D30V6, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    3  1
  XP GAIN WILD-TYPE 31  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      3    1
  XP GAIN WILD-TYPE   31    1
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0               3                31
  1               1                 1
[1] 2 2
[1] FALSE
D30V7, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    2  5
  XP GAIN WILD-TYPE 25 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2    5
  XP GAIN WILD-TYPE   25   34
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               2                25
  MALE                 5                34
[1] 2 2
[1] FALSE
D30V8, continuous
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                10 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8477 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KO-8411 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
D30V9, continuous
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                10 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8428        TCGA-KO-8408 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-KO-8409        TCGA-KO-8416 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
D30V10, continuous
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                 7 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KO-8408        TCGA-KO-8409 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       0                         1     6
  XP GAIN WILD-TYPE     2                         3    52
D30V11, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   6                52
[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"
D30V12, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    1  4
  XP GAIN WILD-TYPE  3 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1    4
  XP GAIN WILD-TYPE    3   28
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               4                28
[1] 2 2
[1] FALSE

Clustering(31) Variable = XQ GAIN MUTATION ANALYSIS
D31V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    6  0
  XQ GAIN WILD-TYPE 50  9
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                59 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                 9 
$`XQ GAIN MUTATED`
TCGA-KL-8346 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KO-8410 TCGA-KO-8413 
       62.37        23.47        25.91         3.55        87.78        86.10 

$`XQ GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 
       24.79        73.91        71.41        28.80        54.74       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       51.06        31.33       129.37        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
       11.21        59.08       115.00        42.35       100.87        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68        74.93        79.04        92.71        16.67        80.38 
TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        77.85        57.17        61.58        63.95 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             3.55              0.99 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            87.78            151.96 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            44.14             66.54 
[1] "3.5 - 87.8 (44.1)"  "1.0 - 152.0 (66.5)"
[1] "hr="     "7.4e+07"
D31V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED         3        2         0        1
  XQ GAIN WILD-TYPE      18       23        14        5
D31V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 3                18
  STAGE II                2                23
  STAGE III               0                14
  STAGE IV                1                 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                T1 T2 T3+T4
  XQ GAIN MUTATED    3  2     1
  XQ GAIN WILD-TYPE 18 23    19
D31V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1                  3                18
  T2                  2                23
  T3+T4               1                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"
                   vv
clus                N0 N1+N2
  XQ GAIN MUTATED    5     0
  XQ GAIN WILD-TYPE 35     5
D31V5, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0                  5                35
  N1+N2               0                 5
[1] 2 2
[1] FALSE
D31V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    3  1
  XQ GAIN WILD-TYPE 31  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3    1
  XQ GAIN WILD-TYPE   31    1
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               3                31
  1               1                 1
[1] 2 2
[1] FALSE
D31V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    1  5
  XQ GAIN WILD-TYPE 26 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1    5
  XQ GAIN WILD-TYPE   26   34
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               1                26
  MALE                 5                34
[1] 2 2
[1] FALSE
D31V8, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                10 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8477 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KO-8411 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D31V9, continuous
D31V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         1     5
  XQ GAIN WILD-TYPE     2                         3    53
D31V11, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   5                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    1  3
  XQ GAIN WILD-TYPE  3 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1    3
  XQ GAIN WILD-TYPE    3   29
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               3                29
[1] 2 2
[1] FALSE

Clustering(32) Variable = 1P LOSS MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   45  7
  1P LOSS WILD-TYPE 11  2
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               52                13 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7                 2 
$`1P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 
      151.96        44.91        47.24        49.97       123.12       129.37 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8429 
       87.91        25.48        65.19       104.52         0.99        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 
       19.33         2.50        59.08       115.00        42.35        76.90 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 
       74.93        79.04        92.71        16.67        80.38       103.27 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       77.85        57.17        61.58        63.95 

$`1P LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 
       23.28        28.80        51.06        31.33        23.47        25.91 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8410 
        3.55        52.27        11.21       100.87        10.68        87.78 
TCGA-KO-8413 
       86.10 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.99              3.55 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           151.96            100.87 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            74.42             28.80 
[1] "1.0 - 152.0 (74.4)" "3.5 - 100.9 (28.8)"
[1] "hr=" "1.9"
D32V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED        13       23        13        4
  1P LOSS WILD-TYPE       8        2         1        2
D32V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                13                 8
  STAGE II               23                 2
  STAGE III              13                 1
  STAGE IV                4                 2
[1] 4 2
[1] TRUE
[1] "dimension 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   13 23    17
  1P LOSS WILD-TYPE  8  2     3
D32V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1                 13                 8
  T2                 23                 2
  T3+T4              17                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  1P LOSS MUTATED   35     5
  1P LOSS WILD-TYPE  5     0
D32V5, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0                 35                 5
  N1+N2               5                 0
[1] 2 2
[1] FALSE
D32V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   32  1
  1P LOSS WILD-TYPE  2  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     32    1
  1P LOSS WILD-TYPE    2    1
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              32                 2
  1               1                 1
[1] 2 2
[1] FALSE
D32V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   23 30
  1P LOSS WILD-TYPE  4  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     23   30
  1P LOSS WILD-TYPE    4    9
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              23                 4
  MALE                30                 9
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, continuous
D32V10, continuous
[1] "Remove cluster labels:" "1P LOSS WILD-TYPE"     
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                 2 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"1P LOSS MUTATED" "1P LOSS MUTATED" "1P LOSS MUTATED" "1P LOSS MUTATED" 
     TCGA-KO-8408      TCGA-KO-8409 
"1P LOSS MUTATED" "1P LOSS MUTATED" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       2                         3    46
  1P LOSS WILD-TYPE     0                         1    12
D32V11, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   2                 0
  BLACK OR AFRICAN AMERICAN               3                 1
  WHITE                                  46                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"
D32V12, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    3 21
  1P LOSS WILD-TYPE  1 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3   21
  1P LOSS WILD-TYPE    1   11
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              21                11
[1] 2 2
[1] FALSE

Clustering(33) Variable = 1Q LOSS MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED   43  8
  1Q LOSS WILD-TYPE 13  1
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               51                14 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8                 1 
$`1Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 
       44.91        47.24        49.97       123.12       129.37        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       25.48        65.19       104.52        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 
        2.50        59.08       115.00        42.35        76.90        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 
       79.04        92.71        16.67        80.38       103.27        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       57.17        61.58        63.95 

$`1Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 
      109.22        23.28        28.80        51.06        31.33        23.47 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 
       25.91         3.55         0.99        11.21       100.87        10.68 
TCGA-KO-8410 TCGA-KO-8413 
       87.78        86.10 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             2.50              0.99 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           151.96            109.22 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           73.910            27.355 
[1] "2.5 - 152.0 (73.9)" "1.0 - 109.2 (27.4)"
[1] "hr=" "1.3"
D33V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED        13       24        12        3
  1Q LOSS WILD-TYPE       8        1         2        3
D33V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                13                 8
  STAGE II               24                 1
  STAGE III              12                 2
  STAGE IV                3                 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                T1 T2 T3+T4
  1Q LOSS MUTATED   13 24    15
  1Q LOSS WILD-TYPE  8  1     5
D33V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1                 13                 8
  T2                 24                 1
  T3+T4              15                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  1Q LOSS MUTATED   35     4
  1Q LOSS WILD-TYPE  5     1
D33V5, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0                 35                 5
  N1+N2               4                 1
[1] 2 2
[1] FALSE
D33V6, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   31  1
  1Q LOSS WILD-TYPE  3  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     31    1
  1Q LOSS WILD-TYPE    3    1
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              31                 3
  1               1                 1
[1] 2 2
[1] FALSE
D33V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   23 29
  1Q LOSS WILD-TYPE  4 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     23   29
  1Q LOSS WILD-TYPE    4   10
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              23                 4
  MALE                29                10
[1] 2 2
[1] FALSE
D33V8, continuous
D33V9, continuous
[1] "Remove cluster labels:" "1Q LOSS WILD-TYPE"     
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9                 2 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"1Q LOSS MUTATED" "1Q LOSS MUTATED" "1Q LOSS MUTATED" "1Q LOSS MUTATED" 
     TCGA-KL-8345      TCGA-KN-8428      TCGA-KO-8408      TCGA-KO-8409 
"1Q LOSS MUTATED" "1Q LOSS MUTATED" "1Q LOSS MUTATED" "1Q LOSS MUTATED" 
     TCGA-KO-8416 
"1Q LOSS MUTATED" 
D33V10, continuous
[1] "Remove cluster labels:" "1Q LOSS WILD-TYPE"     
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6                 2 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"1Q LOSS MUTATED" "1Q LOSS MUTATED" "1Q LOSS MUTATED" "1Q LOSS MUTATED" 
     TCGA-KO-8408      TCGA-KO-8409 
"1Q LOSS MUTATED" "1Q LOSS MUTATED" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       2                         3    45
  1Q LOSS WILD-TYPE     0                         1    13
D33V11, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   2                 0
  BLACK OR AFRICAN AMERICAN               3                 1
  WHITE                                  45                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"
D33V12, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3 22
  1Q LOSS WILD-TYPE  1 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   22
  1Q LOSS WILD-TYPE    1   10
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              22                10
[1] 2 2
[1] FALSE

Clustering(34) Variable = 2P LOSS MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED   38  7
  2P LOSS WILD-TYPE 18  2
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               45                20 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7                 2 
$`2P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       54.74       151.96        44.91        47.24        49.97       123.12 
TCGA-KN-8418 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      129.37        65.19       104.52        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 
        2.50        59.08       115.00        42.35        76.90        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 
       79.04        92.71        16.67        80.38       103.27        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       57.17        61.58        63.95 

$`2P LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 
      109.22        98.33        71.41        28.80        62.37        23.28 
TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       28.80        51.06        31.33        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 
       25.91         3.55         0.99        11.21       100.87        10.68 
TCGA-KO-8410 TCGA-KO-8413 
       87.78        86.10 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.50              0.99 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           151.96            109.22 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           74.930            30.065 
[1] "2.5 - 152.0 (74.9)" "1.0 - 109.2 (30.1)"
[1] "hr=" "1.1"
D34V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED        12       21        10        3
  2P LOSS WILD-TYPE       9        4         4        3
D34V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                12                 9
  STAGE II               21                 4
  STAGE III              10                 4
  STAGE IV                3                 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                T1 T2 T3+T4
  2P LOSS MUTATED   12 21    13
  2P LOSS WILD-TYPE  9  4     7
D34V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1                 12                 9
  T2                 21                 4
  T3+T4              13                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  2P LOSS MUTATED   29     4
  2P LOSS WILD-TYPE 11     1
D34V5, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0                 29                11
  N1+N2               4                 1
[1] 2 2
[1] FALSE
D34V6, binary
                   cls
clus                 0  1
  2P LOSS MUTATED   27  1
  2P LOSS WILD-TYPE  7  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     27    1
  2P LOSS WILD-TYPE    7    1
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              27                 7
  1               1                 1
[1] 2 2
[1] FALSE
D34V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED   21 25
  2P LOSS WILD-TYPE  6 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     21   25
  2P LOSS WILD-TYPE    6   14
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              21                 6
  MALE                25                14
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
[1] "Remove cluster labels:" "2P LOSS WILD-TYPE"     
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                9                 2 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"2P LOSS MUTATED" "2P LOSS MUTATED" "2P LOSS MUTATED" "2P LOSS MUTATED" 
     TCGA-KL-8345      TCGA-KN-8428      TCGA-KO-8408      TCGA-KO-8409 
"2P LOSS MUTATED" "2P LOSS MUTATED" "2P LOSS MUTATED" "2P LOSS MUTATED" 
     TCGA-KO-8416 
"2P LOSS MUTATED" 
D34V10, continuous
[1] "Remove cluster labels:" "2P LOSS WILD-TYPE"     
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6                 2 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"2P LOSS MUTATED" "2P LOSS MUTATED" "2P LOSS MUTATED" "2P LOSS MUTATED" 
     TCGA-KO-8408      TCGA-KO-8409 
"2P LOSS MUTATED" "2P LOSS MUTATED" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       2                         3    39
  2P LOSS WILD-TYPE     0                         1    19
D34V11, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   2                 0
  BLACK OR AFRICAN AMERICAN               3                 1
  WHITE                                  39                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"
D34V12, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    3 20
  2P LOSS WILD-TYPE  1 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3   20
  2P LOSS WILD-TYPE    1   12
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              20                12
[1] 2 2
[1] FALSE

Clustering(35) Variable = 2Q LOSS MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED   38  7
  2Q LOSS WILD-TYPE 18  2
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               45                20 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                7                 2 
$`2Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       54.74       151.96        44.91        47.24        49.97       123.12 
TCGA-KN-8418 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      129.37        65.19       104.52        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 
        2.50        59.08       115.00        42.35        76.90        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 
       79.04        92.71        16.67        80.38       103.27        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       57.17        61.58        63.95 

$`2Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 
      109.22        98.33        71.41        28.80        62.37        23.28 
TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       28.80        51.06        31.33        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 
       25.91         3.55         0.99        11.21       100.87        10.68 
TCGA-KO-8410 TCGA-KO-8413 
       87.78        86.10 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2.50              0.99 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           151.96            109.22 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           74.930            30.065 
[1] "2.5 - 152.0 (74.9)" "1.0 - 109.2 (30.1)"
[1] "hr=" "1.1"
D35V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED        12       21        10        3
  2Q LOSS WILD-TYPE       9        4         4        3
D35V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                12                 9
  STAGE II               21                 4
  STAGE III              10                 4
  STAGE IV                3                 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                T1 T2 T3+T4
  2Q LOSS MUTATED   12 21    13
  2Q LOSS WILD-TYPE  9  4     7
D35V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1                 12                 9
  T2                 21                 4
  T3+T4              13                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  2Q LOSS MUTATED   29     4
  2Q LOSS WILD-TYPE 11     1
D35V5, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0                 29                11
  N1+N2               4                 1
[1] 2 2
[1] FALSE
D35V6, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   27  1
  2Q LOSS WILD-TYPE  7  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     27    1
  2Q LOSS WILD-TYPE    7    1
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              27                 7
  1               1                 1
[1] 2 2
[1] FALSE
D35V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   21 25
  2Q LOSS WILD-TYPE  6 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     21   25
  2Q LOSS WILD-TYPE    6   14
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              21                 6
  MALE                25                14
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
[1] "Remove cluster labels:" "2Q LOSS WILD-TYPE"     
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                9                 2 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"2Q LOSS MUTATED" "2Q LOSS MUTATED" "2Q LOSS MUTATED" "2Q LOSS MUTATED" 
     TCGA-KL-8345      TCGA-KN-8428      TCGA-KO-8408      TCGA-KO-8409 
"2Q LOSS MUTATED" "2Q LOSS MUTATED" "2Q LOSS MUTATED" "2Q LOSS MUTATED" 
     TCGA-KO-8416 
"2Q LOSS MUTATED" 
D35V10, continuous
[1] "Remove cluster labels:" "2Q LOSS WILD-TYPE"     
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6                 2 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"2Q LOSS MUTATED" "2Q LOSS MUTATED" "2Q LOSS MUTATED" "2Q LOSS MUTATED" 
     TCGA-KO-8408      TCGA-KO-8409 
"2Q LOSS MUTATED" "2Q LOSS MUTATED" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       2                         3    39
  2Q LOSS WILD-TYPE     0                         1    19
D35V11, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   2                 0
  BLACK OR AFRICAN AMERICAN               3                 1
  WHITE                                  39                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"
D35V12, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    3 20
  2Q LOSS WILD-TYPE  1 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3   20
  2Q LOSS WILD-TYPE    1   12
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              20                12
[1] 2 2
[1] FALSE

Clustering(36) Variable = 3P LOSS MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    9  0
  3P LOSS WILD-TYPE 47  9
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                56 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                0                 9 
$`3P LOSS MUTATED`
TCGA-KL-8324 TCGA-KL-8333 TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8432 TCGA-KN-8436 
      141.73        98.33        87.91       104.52         2.50        42.35 
TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 
       80.38        77.85        57.17 

$`3P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
       31.33       129.37        23.47        25.48        25.91        65.19 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 
        3.55         0.99        52.27        87.12        19.33        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       59.08       115.00       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       79.04        92.71        16.67        87.78       103.27        86.10 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.95 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             2.50              0.99 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           141.73            151.96 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            80.38             63.16 
[1] "2.5 - 141.7 (80.4)" "1.0 - 152.0 (63.2)"
[1] "hr="     "8.7e+07"
D36V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         2        7         0        0
  3P LOSS WILD-TYPE      19       18        14        6
D36V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 2                19
  STAGE II                7                18
  STAGE III               0                14
  STAGE IV                0                 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                T1 T2 T3+T4
  3P LOSS MUTATED    2  7     0
  3P LOSS WILD-TYPE 19 18    20
D36V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1                  2                19
  T2                  7                18
  T3+T4               0                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"
                   vv
clus                N0 N1+N2
  3P LOSS MUTATED    6     0
  3P LOSS WILD-TYPE 34     5
D36V5, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0                  6                34
  N1+N2               0                 5
[1] 2 2
[1] FALSE
D36V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    5  0
  3P LOSS WILD-TYPE 29  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    0
  3P LOSS WILD-TYPE   29    2
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               5                29
  1               0                 2
[1] 2 2
[1] FALSE
D36V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    5  4
  3P LOSS WILD-TYPE 22 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    4
  3P LOSS WILD-TYPE   22   35
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               5                22
  MALE                 4                35
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                 9 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433        TCGA-KO-8408 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KO-8416 
"3P LOSS WILD-TYPE" 
D36V10, continuous
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                 7 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       0                         0     9
  3P LOSS WILD-TYPE     2                         4    49
D36V11, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   9                49
[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"
D36V12, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    1  5
  3P LOSS WILD-TYPE  3 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1    5
  3P LOSS WILD-TYPE    3   27
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               5                27
[1] 2 2
[1] FALSE

Clustering(37) Variable = 3Q LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    8  0
  3Q LOSS WILD-TYPE 48  9
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                8                57 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                 9 
$`3Q LOSS MUTATED`
TCGA-KL-8324 TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8409 
      141.73        87.91       104.52         2.50        42.35        80.38 
TCGA-KO-8414 TCGA-KO-8415 
       77.85        57.17 

$`3Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 
       51.06        31.33       129.37        23.47        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       65.19         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       11.21        59.08       115.00       100.87        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 
       74.93        79.04        92.71        16.67        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8416 TCGA-KO-8417 
       86.10        61.58        63.95 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             2.50              0.99 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           141.73            151.96 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           79.115            63.950 
[1] "2.5 - 141.7 (79.1)" "1.0 - 152.0 (64.0)"
[1] "hr="     "8.3e+07"
D37V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         2        6         0        0
  3Q LOSS WILD-TYPE      19       19        14        6
D37V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 2                19
  STAGE II                6                19
  STAGE III               0                14
  STAGE IV                0                 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                T1 T2 T3+T4
  3Q LOSS MUTATED    2  6     0
  3Q LOSS WILD-TYPE 19 19    20
D37V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1                  2                19
  T2                  6                19
  T3+T4               0                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"
                   vv
clus                N0 N1+N2
  3Q LOSS MUTATED    5     0
  3Q LOSS WILD-TYPE 35     5
D37V5, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0                  5                35
  N1+N2               0                 5
[1] 2 2
[1] FALSE
D37V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    4  0
  3Q LOSS WILD-TYPE 30  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      4    0
  3Q LOSS WILD-TYPE   30    2
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               4                30
  1               0                 2
[1] 2 2
[1] FALSE
D37V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    5  3
  3Q LOSS WILD-TYPE 22 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    3
  3Q LOSS WILD-TYPE   22   36
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               5                22
  MALE                 3                36
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                 9 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433        TCGA-KO-8408 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KO-8416 
"3Q LOSS WILD-TYPE" 
D37V10, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                 7 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       0                         0     8
  3Q LOSS WILD-TYPE     2                         4    50
D37V11, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   8                50
[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"
D37V12, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1  5
  3Q LOSS WILD-TYPE  3 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    5
  3Q LOSS WILD-TYPE    3   27
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               5                27
[1] 2 2
[1] FALSE

Clustering(38) Variable = 5P LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    8  1
  5P LOSS WILD-TYPE 48  8
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9                56 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                 8 
$`5P LOSS MUTATED`
TCGA-KL-8324 TCGA-KL-8330 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8442 
      141.73       108.62        24.79        62.37       151.96        47.24 
TCGA-KN-8431 TCGA-KO-8405 TCGA-KO-8409 
       19.33        74.93        80.38 

$`5P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        28.11        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8443 
       28.80        54.74        23.28        44.91        28.80        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87        76.90        10.68        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67        87.78       103.27        86.10        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.95 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            19.33              0.99 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           151.96            137.06 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            74.93             64.57 
[1] "19.3 - 152.0 (74.9)" "1.0 - 137.1 (64.6)" 
[1] "hr=" "1.4"
D38V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         1        7         1        1
  5P LOSS WILD-TYPE      20       18        13        5
D38V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 1                20
  STAGE II                7                18
  STAGE III               1                13
  STAGE IV                1                 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                T1 T2 T3+T4
  5P LOSS MUTATED    1  7     2
  5P LOSS WILD-TYPE 20 18    18
D38V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1                  1                20
  T2                  7                18
  T3+T4               2                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"
                   vv
clus                N0 N1+N2
  5P LOSS MUTATED    6     1
  5P LOSS WILD-TYPE 34     4
D38V5, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0                  6                34
  N1+N2               1                 4
[1] 2 2
[1] FALSE
D38V6, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    6  0
  5P LOSS WILD-TYPE 28  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    0
  5P LOSS WILD-TYPE   28    2
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               6                28
  1               0                 2
[1] 2 2
[1] FALSE
D38V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    4  6
  5P LOSS WILD-TYPE 23 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    6
  5P LOSS WILD-TYPE   23   33
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               4                23
  MALE                 6                33
[1] 2 2
[1] FALSE
D38V8, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                 9 
       TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8443 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KO-8411 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KO-8413 
"5P LOSS WILD-TYPE" 
D38V9, continuous
D38V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       1                         1     6
  5P LOSS WILD-TYPE     1                         3    52
D38V11, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   6                52
[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"
D38V12, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    2  4
  5P LOSS WILD-TYPE  2 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    4
  5P LOSS WILD-TYPE    2   28
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO               4                28
[1] 2 2
[1] FALSE

Clustering(39) Variable = 5Q LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    8  1
  5Q LOSS WILD-TYPE 48  8
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                9                56 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                 8 
$`5Q LOSS MUTATED`
TCGA-KL-8324 TCGA-KL-8330 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8442 
      141.73       108.62        24.79        62.37       151.96        47.24 
TCGA-KN-8431 TCGA-KO-8405 TCGA-KO-8409 
       19.33        74.93        80.38 

$`5Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        28.11        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8443 
       28.80        54.74        23.28        44.91        28.80        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87        76.90        10.68        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67        87.78       103.27        86.10        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.95 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            19.33              0.99 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           151.96            137.06 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            74.93             64.57 
[1] "19.3 - 152.0 (74.9)" "1.0 - 137.1 (64.6)" 
[1] "hr=" "1.4"
D39V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         1        7         1        1
  5Q LOSS WILD-TYPE      20       18        13        5
D39V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 1                20
  STAGE II                7                18
  STAGE III               1                13
  STAGE IV                1                 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                T1 T2 T3+T4
  5Q LOSS MUTATED    1  7     2
  5Q LOSS WILD-TYPE 20 18    18
D39V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1                  1                20
  T2                  7                18
  T3+T4               2                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"
                   vv
clus                N0 N1+N2
  5Q LOSS MUTATED    6     1
  5Q LOSS WILD-TYPE 34     4
D39V5, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0                  6                34
  N1+N2               1                 4
[1] 2 2
[1] FALSE
D39V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    6  0
  5Q LOSS WILD-TYPE 28  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      6    0
  5Q LOSS WILD-TYPE   28    2
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               6                28
  1               0                 2
[1] 2 2
[1] FALSE
D39V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    4  6
  5Q LOSS WILD-TYPE 23 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4    6
  5Q LOSS WILD-TYPE   23   33
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               4                23
  MALE                 6                33
[1] 2 2
[1] FALSE
D39V8, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                 9 
       TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8443 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KO-8411 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KO-8413 
"5Q LOSS WILD-TYPE" 
D39V9, continuous
D39V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       1                         1     6
  5Q LOSS WILD-TYPE     1                         3    52
D39V11, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   6                52
[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"
D39V12, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    2  4
  5Q LOSS WILD-TYPE  2 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2    4
  5Q LOSS WILD-TYPE    2   28
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO               4                28
[1] 2 2
[1] FALSE

Clustering(40) Variable = 6P LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   42  8
  6P LOSS WILD-TYPE 14  1
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               50                15 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                 1 
$`6P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       73.91        54.74       151.96        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
        0.99        52.27        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00        42.35        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 
       92.71        16.67        80.38       103.27        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.95 

$`6P LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 
      109.22        71.41        28.80        62.37        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 
       51.06        31.33        23.47        25.91         3.55        11.21 
TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 
      100.87        87.78        86.10 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.99              3.55 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           151.96            109.22 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            74.42             31.33 
[1] "1.0 - 152.0 (74.4)" "3.5 - 109.2 (31.3)"
[1] "hr=" "1.8"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED        13       23        10        5
  6P LOSS WILD-TYPE       8        2         4        1
D40V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                13                 8
  STAGE II               23                 2
  STAGE III              10                 4
  STAGE IV                5                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  6P LOSS MUTATED   13 23    15
  6P LOSS WILD-TYPE  8  2     5
D40V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1                 13                 8
  T2                 23                 2
  T3+T4              15                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  6P LOSS MUTATED   32     5
  6P LOSS WILD-TYPE  8     0
D40V5, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0                 32                 8
  N1+N2               5                 0
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   28  1
  6P LOSS WILD-TYPE  6  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     28    1
  6P LOSS WILD-TYPE    6    1
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              28                 6
  1               1                 1
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   23 28
  6P LOSS WILD-TYPE  4 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     23   28
  6P LOSS WILD-TYPE    4   11
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              23                 4
  MALE                28                11
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
[1] "Remove cluster labels:" "6P LOSS WILD-TYPE"     
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9                 2 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"6P LOSS MUTATED" "6P LOSS MUTATED" "6P LOSS MUTATED" "6P LOSS MUTATED" 
     TCGA-KL-8345      TCGA-KN-8428      TCGA-KO-8408      TCGA-KO-8409 
"6P LOSS MUTATED" "6P LOSS MUTATED" "6P LOSS MUTATED" "6P LOSS MUTATED" 
     TCGA-KO-8416 
"6P LOSS MUTATED" 
D40V10, continuous
[1] "Remove cluster labels:" "6P LOSS WILD-TYPE"     
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                 2 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"6P LOSS MUTATED" "6P LOSS MUTATED" "6P LOSS MUTATED" "6P LOSS MUTATED" 
     TCGA-KO-8408      TCGA-KO-8409 
"6P LOSS MUTATED" "6P LOSS MUTATED" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       2                         3    44
  6P LOSS WILD-TYPE     0                         1    14
D40V11, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   2                 0
  BLACK OR AFRICAN AMERICAN               3                 1
  WHITE                                  44                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"
D40V12, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    3 22
  6P LOSS WILD-TYPE  1 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3   22
  6P LOSS WILD-TYPE    1   10
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              22                10
[1] 2 2
[1] FALSE

Clustering(41) Variable = 6Q LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   42  8
  6Q LOSS WILD-TYPE 14  1
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               50                15 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                8                 1 
$`6Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       73.91        54.74       151.96        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
        0.99        52.27        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00        42.35        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 
       92.71        16.67        80.38       103.27        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.95 

$`6Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 
      109.22        71.41        28.80        62.37        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 
       51.06        31.33        23.47        25.91         3.55        11.21 
TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 
      100.87        87.78        86.10 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.99              3.55 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           151.96            109.22 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            74.42             31.33 
[1] "1.0 - 152.0 (74.4)" "3.5 - 109.2 (31.3)"
[1] "hr=" "1.8"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED        13       23        10        5
  6Q LOSS WILD-TYPE       8        2         4        1
D41V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                13                 8
  STAGE II               23                 2
  STAGE III              10                 4
  STAGE IV                5                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  6Q LOSS MUTATED   13 23    15
  6Q LOSS WILD-TYPE  8  2     5
D41V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1                 13                 8
  T2                 23                 2
  T3+T4              15                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  6Q LOSS MUTATED   32     5
  6Q LOSS WILD-TYPE  8     0
D41V5, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0                 32                 8
  N1+N2               5                 0
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   28  1
  6Q LOSS WILD-TYPE  6  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     28    1
  6Q LOSS WILD-TYPE    6    1
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              28                 6
  1               1                 1
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   23 28
  6Q LOSS WILD-TYPE  4 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     23   28
  6Q LOSS WILD-TYPE    4   11
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              23                 4
  MALE                28                11
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
[1] "Remove cluster labels:" "6Q LOSS WILD-TYPE"     
clus
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                9                 2 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"6Q LOSS MUTATED" "6Q LOSS MUTATED" "6Q LOSS MUTATED" "6Q LOSS MUTATED" 
     TCGA-KL-8345      TCGA-KN-8428      TCGA-KO-8408      TCGA-KO-8409 
"6Q LOSS MUTATED" "6Q LOSS MUTATED" "6Q LOSS MUTATED" "6Q LOSS MUTATED" 
     TCGA-KO-8416 
"6Q LOSS MUTATED" 
D41V10, continuous
[1] "Remove cluster labels:" "6Q LOSS WILD-TYPE"     
clus
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                6                 2 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"6Q LOSS MUTATED" "6Q LOSS MUTATED" "6Q LOSS MUTATED" "6Q LOSS MUTATED" 
     TCGA-KO-8408      TCGA-KO-8409 
"6Q LOSS MUTATED" "6Q LOSS MUTATED" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       2                         3    44
  6Q LOSS WILD-TYPE     0                         1    14
D41V11, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   2                 0
  BLACK OR AFRICAN AMERICAN               3                 1
  WHITE                                  44                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"
D41V12, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    3 22
  6Q LOSS WILD-TYPE  1 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3   22
  6Q LOSS WILD-TYPE    1   10
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              22                10
[1] 2 2
[1] FALSE

Clustering(42) Variable = 8P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    9  0
  8P LOSS WILD-TYPE 47  9
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                9                56 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                 9 
$`8P LOSS MUTATED`
TCGA-KL-8327 TCGA-KL-8337 TCGA-KM-8476 TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8436 
      137.06        44.84       123.12         2.50       115.00        42.35 
TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
      103.27        61.58        63.95 

$`8P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 
       44.91        28.80        47.24        49.97        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      104.52         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       11.21        59.08       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       79.04        92.71        16.67        80.38        87.78        86.10 
TCGA-KO-8414 TCGA-KO-8415 
       77.85        57.17 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             2.50              0.99 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           137.06            151.96 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           63.950            65.865 
[1] "2.5 - 137.1 (64.0)" "1.0 - 152.0 (65.9)"
[1] "hr="     "8.5e+07"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         4        4         1        0
  8P LOSS WILD-TYPE      17       21        13        6
D42V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 4                17
  STAGE II                4                21
  STAGE III               1                13
  STAGE IV                0                 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                T1 T2 T3+T4
  8P LOSS MUTATED    4  4     1
  8P LOSS WILD-TYPE 17 21    19
D42V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1                  4                17
  T2                  4                21
  T3+T4               1                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"
                   vv
clus                N0 N1+N2
  8P LOSS MUTATED    4     0
  8P LOSS WILD-TYPE 36     5
D42V5, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0                  4                36
  N1+N2               0                 5
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    5  0
  8P LOSS WILD-TYPE 29  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5    0
  8P LOSS WILD-TYPE   29    2
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               5                29
  1               0                 2
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    3  6
  8P LOSS WILD-TYPE 24 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    6
  8P LOSS WILD-TYPE   24   33
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               3                24
  MALE                 6                33
[1] 2 2
[1] FALSE
D42V8, continuous
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                 9 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8477        TCGA-KM-8639 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KO-8413 
"8P LOSS WILD-TYPE" 
D42V9, continuous
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                10 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KO-8408        TCGA-KO-8409 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D42V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       0                         1     8
  8P LOSS WILD-TYPE     2                         3    50
D42V11, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   8                50
[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"
D42V12, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    0  7
  8P LOSS WILD-TYPE  4 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0    7
  8P LOSS WILD-TYPE    4   25
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7                25
[1] 2 2
[1] FALSE

Clustering(43) Variable = 8Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    8  0
  8Q LOSS WILD-TYPE 48  9
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8                57 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                 9 
$`8Q LOSS MUTATED`
TCGA-KL-8327 TCGA-KL-8337 TCGA-KM-8476 TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8411 
      137.06        44.84       123.12         2.50        42.35       103.27 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.95 

$`8Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 
       44.91        28.80        47.24        49.97        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      104.52         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       11.21        59.08       115.00       100.87        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
       74.93        79.04        92.71        16.67        80.38        87.78 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       86.10        77.85        57.17 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             2.50              0.99 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           137.06            151.96 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           62.765            66.540 
[1] "2.5 - 137.1 (62.8)" "1.0 - 152.0 (66.5)"
[1] "hr="     "8.2e+07"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         4        3         1        0
  8Q LOSS WILD-TYPE      17       22        13        6
D43V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 4                17
  STAGE II                3                22
  STAGE III               1                13
  STAGE IV                0                 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                T1 T2 T3+T4
  8Q LOSS MUTATED    4  3     1
  8Q LOSS WILD-TYPE 17 22    19
D43V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1                  4                17
  T2                  3                22
  T3+T4               1                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"
                   vv
clus                N0 N1+N2
  8Q LOSS MUTATED    4     0
  8Q LOSS WILD-TYPE 36     5
D43V5, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0                  4                36
  N1+N2               0                 5
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    5  0
  8Q LOSS WILD-TYPE 29  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5    0
  8Q LOSS WILD-TYPE   29    2
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               5                29
  1               0                 2
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    3  5
  8Q LOSS WILD-TYPE 24 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    5
  8Q LOSS WILD-TYPE   24   34
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               3                24
  MALE                 5                34
[1] 2 2
[1] FALSE
D43V8, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                 9 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8477        TCGA-KM-8639 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KO-8413 
"8Q LOSS WILD-TYPE" 
D43V9, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                10 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KO-8408        TCGA-KO-8409 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D43V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         1     7
  8Q LOSS WILD-TYPE     2                         3    51
D43V11, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   7                51
[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"
D43V12, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    0  6
  8Q LOSS WILD-TYPE  4 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    6
  8Q LOSS WILD-TYPE    4   26
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6                26
[1] 2 2
[1] FALSE

Clustering(44) Variable = 9P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED    5  4
  9P LOSS WILD-TYPE 51  5
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                9                56 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4                 5 
$`9P LOSS MUTATED`
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8332 TCGA-KL-8343 TCGA-KL-8346 TCGA-KN-8436 
      141.73        23.84        84.89        71.41        62.37        42.35 
TCGA-KO-8404 TCGA-KO-8408 TCGA-KO-8415 
       10.68        16.67        57.17 

$`9P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.22       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       98.96        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8344 
       86.56        28.11        66.54        24.79        73.91        28.80 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       54.74       151.96        23.28        44.91        28.80        47.24 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
       59.08       115.00       100.87        76.90        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       92.71        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.95 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            10.68              0.99 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           141.73            151.96 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           57.170            70.225 
[1] "10.7 - 141.7 (57.2)" "1.0 - 152.0 (70.2)" 
[1] "hr=" "5.8"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         3        4         2        1
  9P LOSS WILD-TYPE      18       21        12        5
D44V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 3                18
  STAGE II                4                21
  STAGE III               2                12
  STAGE IV                1                 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                T1 T2 T3+T4
  9P LOSS MUTATED    3  4     3
  9P LOSS WILD-TYPE 18 21    17
D44V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1                  3                18
  T2                  4                21
  T3+T4               3                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"
                   vv
clus                N0 N1+N2
  9P LOSS MUTATED    5     1
  9P LOSS WILD-TYPE 35     4
D44V5, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0                  5                35
  N1+N2               1                 4
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    6  0
  9P LOSS WILD-TYPE 28  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6    0
  9P LOSS WILD-TYPE   28    2
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0               6                28
  1               0                 2
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    3  7
  9P LOSS WILD-TYPE 24 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      3    7
  9P LOSS WILD-TYPE   24   32
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               3                24
  MALE                 7                32
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
[1] "Remove cluster labels:" "9P LOSS MUTATED"       
clus
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                2                 9 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433        TCGA-KO-8409 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KO-8416 
"9P LOSS WILD-TYPE" 
D44V10, continuous
[1] "Remove cluster labels:" "9P LOSS MUTATED"       
clus
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                1                 7 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8409 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       0                         0    10
  9P LOSS WILD-TYPE     2                         4    48
D44V11, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                  10                48
[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"
D44V12, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    1  5
  9P LOSS WILD-TYPE  3 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1    5
  9P LOSS WILD-TYPE    3   27
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               5                27
[1] 2 2
[1] FALSE

Clustering(45) Variable = 9Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    5  4
  9Q LOSS WILD-TYPE 51  5
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                9                56 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                4                 5 
$`9Q LOSS MUTATED`
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8332 TCGA-KL-8343 TCGA-KL-8346 TCGA-KN-8436 
      141.73        23.84        84.89        71.41        62.37        42.35 
TCGA-KO-8404 TCGA-KO-8408 TCGA-KO-8415 
       10.68        16.67        57.17 

$`9Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.22       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       98.96        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8344 
       86.56        28.11        66.54        24.79        73.91        28.80 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       54.74       151.96        23.28        44.91        28.80        47.24 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
       59.08       115.00       100.87        76.90        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       92.71        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.95 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            10.68              0.99 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           141.73            151.96 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           57.170            70.225 
[1] "10.7 - 141.7 (57.2)" "1.0 - 152.0 (70.2)" 
[1] "hr=" "5.8"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         3        4         2        1
  9Q LOSS WILD-TYPE      18       21        12        5
D45V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 3                18
  STAGE II                4                21
  STAGE III               2                12
  STAGE IV                1                 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                T1 T2 T3+T4
  9Q LOSS MUTATED    3  4     3
  9Q LOSS WILD-TYPE 18 21    17
D45V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1                  3                18
  T2                  4                21
  T3+T4               3                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"
                   vv
clus                N0 N1+N2
  9Q LOSS MUTATED    5     1
  9Q LOSS WILD-TYPE 35     4
D45V5, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0                  5                35
  N1+N2               1                 4
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    6  0
  9Q LOSS WILD-TYPE 28  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      6    0
  9Q LOSS WILD-TYPE   28    2
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0               6                28
  1               0                 2
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    3  7
  9Q LOSS WILD-TYPE 24 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3    7
  9Q LOSS WILD-TYPE   24   32
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               3                24
  MALE                 7                32
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                 9 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433        TCGA-KO-8409 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KO-8416 
"9Q LOSS WILD-TYPE" 
D45V10, continuous
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                 7 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8409 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       0                         0    10
  9Q LOSS WILD-TYPE     2                         4    48
D45V11, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                  10                48
[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"
D45V12, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    1  5
  9Q LOSS WILD-TYPE  3 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1    5
  9Q LOSS WILD-TYPE    3   27
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               5                27
[1] 2 2
[1] FALSE

Clustering(46) Variable = 10P LOSS MUTATION ANALYSIS
D46V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   38  9
  10P LOSS WILD-TYPE 18  0
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                47                 18 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 9                  0 
$`10P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       71.41        54.74        62.37        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 
       52.27        87.12         2.50        59.08       115.00        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68        74.93        79.04        92.71        16.67        80.38 
TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        77.85        57.17        61.58        63.95 

$`10P LOSS WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8344 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 
      141.73       109.22        28.80       151.96        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
       51.06        31.33        23.47        25.91         3.55         0.99 
TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 
       19.33        11.21        42.35       100.87        87.78        86.10 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              2.50               0.99 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            137.06             151.96 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            73.910             30.065 
[1] "2.5 - 137.1 (73.9)" "1.0 - 152.0 (30.1)"
[1] "hr="     "2.6e+08"
D46V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED        13       20        11        4
  10P LOSS WILD-TYPE       8        5         3        2
D46V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                 13                  8
  STAGE II                20                  5
  STAGE III               11                  3
  STAGE IV                 4                  2
[1] 4 2
[1] TRUE
[1] "dimension 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   13 20    15
  10P LOSS WILD-TYPE  8  5     5
D46V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                  13                  8
  T2                  20                  5
  T3+T4               15                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  10P LOSS MUTATED   33     4
  10P LOSS WILD-TYPE  7     1
D46V5, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                  33                  7
  N1+N2                4                  1
[1] 2 2
[1] FALSE
D46V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   29  1
  10P LOSS WILD-TYPE  5  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     29    1
  10P LOSS WILD-TYPE    5    1
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               29                  5
  1                1                  1
[1] 2 2
[1] FALSE
D46V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   20 28
  10P LOSS WILD-TYPE  7 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     20   28
  10P LOSS WILD-TYPE    7   11
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               20                  7
  MALE                 28                 11
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
D46V10, continuous
[1] "Remove cluster labels:" "10P LOSS WILD-TYPE"    
clus
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                  2 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"10P LOSS MUTATED" "10P LOSS MUTATED" "10P LOSS MUTATED" "10P LOSS MUTATED" 
      TCGA-KO-8408       TCGA-KO-8409 
"10P LOSS MUTATED" "10P LOSS MUTATED" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       2                         3    42
  10P LOSS WILD-TYPE     0                         1    16
D46V11, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    2                  0
  BLACK OR AFRICAN AMERICAN                3                  1
  WHITE                                   42                 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"
D46V12, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    3 21
  10P LOSS WILD-TYPE  1 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3   21
  10P LOSS WILD-TYPE    1   11
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO               21                 11
[1] 2 2
[1] FALSE

Clustering(47) Variable = 10Q LOSS MUTATION ANALYSIS
D47V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   39  9
  10Q LOSS WILD-TYPE 17  0
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                48                 17 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 9                  0 
$`10Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       71.41        54.74        62.37        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       52.27        87.12         2.50        59.08       115.00        42.35 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       80.38       103.27        77.85        57.17        61.58        63.95 

$`10Q LOSS WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8344 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 
      141.73       109.22        28.80       151.96        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
       51.06        31.33        23.47        25.91         3.55         0.99 
TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 
       19.33        11.21       100.87        87.78        86.10 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              2.50               0.99 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            137.06             151.96 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             72.66              28.80 
[1] "2.5 - 137.1 (72.7)" "1.0 - 152.0 (28.8)"
[1] "hr="     "2.5e+08"
D47V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED        13       21        11        4
  10Q LOSS WILD-TYPE       8        4         3        2
D47V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                 13                  8
  STAGE II                21                  4
  STAGE III               11                  3
  STAGE IV                 4                  2
[1] 4 2
[1] TRUE
[1] "dimension 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   13 21    15
  10Q LOSS WILD-TYPE  8  4     5
D47V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                  13                  8
  T2                  21                  4
  T3+T4               15                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  10Q LOSS MUTATED   33     4
  10Q LOSS WILD-TYPE  7     1
D47V5, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                  33                  7
  N1+N2                4                  1
[1] 2 2
[1] FALSE
D47V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   29  1
  10Q LOSS WILD-TYPE  5  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     29    1
  10Q LOSS WILD-TYPE    5    1
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               29                  5
  1                1                  1
[1] 2 2
[1] FALSE
D47V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   20 29
  10Q LOSS WILD-TYPE  7 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     20   29
  10Q LOSS WILD-TYPE    7   10
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               20                  7
  MALE                 29                 10
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
D47V10, continuous
[1] "Remove cluster labels:" "10Q LOSS WILD-TYPE"    
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                  2 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"10Q LOSS MUTATED" "10Q LOSS MUTATED" "10Q LOSS MUTATED" "10Q LOSS MUTATED" 
      TCGA-KO-8408       TCGA-KO-8409 
"10Q LOSS MUTATED" "10Q LOSS MUTATED" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       2                         3    43
  10Q LOSS WILD-TYPE     0                         1    15
D47V11, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    2                  0
  BLACK OR AFRICAN AMERICAN                3                  1
  WHITE                                   43                 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"
D47V12, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    3 22
  10Q LOSS WILD-TYPE  1 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3   22
  10Q LOSS WILD-TYPE    1   10
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO               22                 10
[1] 2 2
[1] FALSE

Clustering(48) Variable = 11P LOSS MUTATION ANALYSIS
D48V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    7  0
  11P LOSS WILD-TYPE 49  9
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 58 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 0                  9 
$`11P LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8331 TCGA-KL-8345 TCGA-KM-8443 TCGA-KN-8427 TCGA-KN-8434 
      102.81        98.96        54.74        49.97         0.99        59.08 
TCGA-KN-8436 
       42.35 

$`11P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       71.41        28.80        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       28.80        47.24       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        3.55        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       77.85        57.17        61.58        63.95 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.99               2.50 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            102.81             151.96 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            54.740             68.975 
[1] "1.0 - 102.8 (54.7)" "2.5 - 152.0 (69.0)"
[1] "hr="     "7.9e+07"
D48V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         0        5         1        1
  11P LOSS WILD-TYPE      21       20        13        5
D48V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  0                 21
  STAGE II                 5                 20
  STAGE III                1                 13
  STAGE IV                 1                  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                 T1 T2 T3+T4
  11P LOSS MUTATED    0  5     2
  11P LOSS WILD-TYPE 21 20    18
D48V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                   0                 21
  T2                   5                 20
  T3+T4                2                 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"
                    vv
clus                 N0 N1+N2
  11P LOSS MUTATED    4     1
  11P LOSS WILD-TYPE 36     4
D48V5, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                   4                 36
  N1+N2                1                  4
[1] 2 2
[1] FALSE
D48V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    3  0
  11P LOSS WILD-TYPE 31  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3    0
  11P LOSS WILD-TYPE   31    2
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                3                 31
  1                0                  2
[1] 2 2
[1] FALSE
D48V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    2  5
  11P LOSS WILD-TYPE 25 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2    5
  11P LOSS WILD-TYPE   25   34
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                2                 25
  MALE                  5                 34
[1] 2 2
[1] FALSE
D48V8, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 10 
        TCGA-KM-8438         TCGA-KM-8439         TCGA-KM-8440 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8441         TCGA-KM-8442         TCGA-KM-8476 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KO-8411 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8413 
"11P LOSS WILD-TYPE" 
D48V9, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 10 
        TCGA-KL-8324         TCGA-KL-8330         TCGA-KL-8335 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8341         TCGA-KM-8639         TCGA-KN-8428 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8433         TCGA-KO-8408         TCGA-KO-8409 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8416 
"11P LOSS WILD-TYPE" 
D48V10, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8433         TCGA-KO-8408 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8409 
"11P LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       0                         0     7
  11P LOSS WILD-TYPE     2                         4    51
D48V11, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    7                 51
[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"
D48V12, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    0  3
  11P LOSS WILD-TYPE  4 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0    3
  11P LOSS WILD-TYPE    4   29
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                3                 29
[1] 2 2
[1] FALSE

Clustering(49) Variable = 11Q LOSS MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    7  0
  11Q LOSS WILD-TYPE 49  9
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 58 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 0                  9 
$`11Q LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8331 TCGA-KL-8345 TCGA-KM-8443 TCGA-KN-8427 TCGA-KN-8434 
      102.81        98.96        54.74        49.97         0.99        59.08 
TCGA-KN-8436 
       42.35 

$`11Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       71.41        28.80        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       28.80        47.24       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        3.55        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       77.85        57.17        61.58        63.95 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.99               2.50 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            102.81             151.96 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            54.740             68.975 
[1] "1.0 - 102.8 (54.7)" "2.5 - 152.0 (69.0)"
[1] "hr="     "7.9e+07"
D49V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         0        5         1        1
  11Q LOSS WILD-TYPE      21       20        13        5
D49V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  0                 21
  STAGE II                 5                 20
  STAGE III                1                 13
  STAGE IV                 1                  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                 T1 T2 T3+T4
  11Q LOSS MUTATED    0  5     2
  11Q LOSS WILD-TYPE 21 20    18
D49V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                   0                 21
  T2                   5                 20
  T3+T4                2                 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"
                    vv
clus                 N0 N1+N2
  11Q LOSS MUTATED    4     1
  11Q LOSS WILD-TYPE 36     4
D49V5, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                   4                 36
  N1+N2                1                  4
[1] 2 2
[1] FALSE
D49V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    3  0
  11Q LOSS WILD-TYPE 31  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    0
  11Q LOSS WILD-TYPE   31    2
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                3                 31
  1                0                  2
[1] 2 2
[1] FALSE
D49V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    2  5
  11Q LOSS WILD-TYPE 25 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    5
  11Q LOSS WILD-TYPE   25   34
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                2                 25
  MALE                  5                 34
[1] 2 2
[1] FALSE
D49V8, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                 10 
        TCGA-KM-8438         TCGA-KM-8439         TCGA-KM-8440 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8441         TCGA-KM-8442         TCGA-KM-8476 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KO-8411 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8413 
"11Q LOSS WILD-TYPE" 
D49V9, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                 10 
        TCGA-KL-8324         TCGA-KL-8330         TCGA-KL-8335 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8341         TCGA-KM-8639         TCGA-KN-8428 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8433         TCGA-KO-8408         TCGA-KO-8409 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8416 
"11Q LOSS WILD-TYPE" 
D49V10, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8433         TCGA-KO-8408 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8409 
"11Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       0                         0     7
  11Q LOSS WILD-TYPE     2                         4    51
D49V11, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    7                 51
[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"
D49V12, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    0  3
  11Q LOSS WILD-TYPE  4 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    3
  11Q LOSS WILD-TYPE    4   29
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                3                 29
[1] 2 2
[1] FALSE

Clustering(50) Variable = 13Q LOSS MUTATION ANALYSIS
D50V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   35  7
  13Q LOSS WILD-TYPE 21  2
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                42                 23 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 7                  2 
$`13Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       141.73       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       98.96        84.89        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8440 
       86.56        28.11        66.54        24.79       151.96        44.91 
TCGA-KM-8442 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       47.24       123.12       129.37        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       59.08       115.00        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
       92.71        16.67        80.38        77.85        61.58        63.95 

$`13Q LOSS WILD-TYPE`
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       23.84       109.22        98.33        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8443 TCGA-KM-8477 
       54.74        62.37        23.28        28.80        49.97        51.06 
TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KN-8436 
       31.33        23.47        25.91         3.55        11.21        42.35 
TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 
      100.87        87.78       103.27        86.10        57.17 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.99               3.55 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            151.96             109.22 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            77.375             51.060 
[1] "1.0 - 152.0 (77.4)" "3.5 - 109.2 (51.1)"
[1] "hr=" "1.6"
D50V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED        11       18         9        5
  13Q LOSS WILD-TYPE      10        7         5        1
D50V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                 11                 10
  STAGE II                18                  7
  STAGE III                9                  5
  STAGE IV                 5                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  13Q LOSS MUTATED   11 18    14
  13Q LOSS WILD-TYPE 10  7     6
D50V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                  11                 10
  T2                  18                  7
  T3+T4               14                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  13Q LOSS MUTATED   27     5
  13Q LOSS WILD-TYPE 13     0
D50V5, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                  27                 13
  N1+N2                5                  0
[1] 2 2
[1] FALSE
D50V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   22  1
  13Q LOSS WILD-TYPE 12  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     22    1
  13Q LOSS WILD-TYPE   12    1
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               22                 12
  1                1                  1
[1] 2 2
[1] FALSE
D50V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   20 23
  13Q LOSS WILD-TYPE  7 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     20   23
  13Q LOSS WILD-TYPE    7   16
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               20                  7
  MALE                 23                 16
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, continuous
D50V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       2                         3    36
  13Q LOSS WILD-TYPE     0                         1    22
D50V11, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    2                  0
  BLACK OR AFRICAN AMERICAN                3                  1
  WHITE                                   36                 22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    2 19
  13Q LOSS WILD-TYPE  2 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   19
  13Q LOSS WILD-TYPE    2   13
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO               19                 13
[1] 2 2
[1] FALSE

Clustering(51) Variable = 16P LOSS MUTATION ANALYSIS
D51V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    1  3
  16P LOSS WILD-TYPE 55  6
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 61 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                  6 
$`16P LOSS MUTATED`
TCGA-KL-8336 TCGA-KL-8339 TCGA-KN-8427 TCGA-KO-8408 
       30.25        28.11         0.99        16.67 

$`16P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       92.55        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       65.19       104.52         3.55        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        59.08       115.00        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 
       76.90        10.68        74.93        79.04        92.71        80.38 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       87.78       103.27        86.10        77.85        57.17        61.58 
TCGA-KO-8417 
       63.95 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.99               2.50 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             30.25             151.96 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             22.39              71.41 
[1] "1.0 - 30.2 (22.4)"  "2.5 - 152.0 (71.4)"
[1] "hr=" "26" 
D51V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         0        0         1        3
  16P LOSS WILD-TYPE      21       25        13        3
D51V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  0                 21
  STAGE II                 0                 25
  STAGE III                1                 13
  STAGE IV                 3                  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                 T1 T2 T3+T4
  16P LOSS MUTATED    0  0     4
  16P LOSS WILD-TYPE 21 25    16
D51V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                   0                 21
  T2                   0                 25
  T3+T4                4                 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"
                    vv
clus                 N0 N1+N2
  16P LOSS MUTATED    0     4
  16P LOSS WILD-TYPE 40     1
D51V5, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                   0                 40
  N1+N2                4                  1
[1] 2 2
[1] FALSE
D51V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  1
  16P LOSS WILD-TYPE 33  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    1
  16P LOSS WILD-TYPE   33    1
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                1                 33
  1                1                  1
[1] 2 2
[1] FALSE
D51V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  3
  16P LOSS WILD-TYPE 26 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    3
  16P LOSS WILD-TYPE   26   36
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                1                 26
  MALE                  3                 36
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 10 
        TCGA-KL-8324         TCGA-KL-8330         TCGA-KL-8335 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8345         TCGA-KM-8639 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8428         TCGA-KN-8433         TCGA-KO-8409 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8416 
"16P LOSS WILD-TYPE" 
D51V10, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8433 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8409 
"16P LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       0                         0     4
  16P LOSS WILD-TYPE     2                         4    54
D51V11, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    4                 54
[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"
D51V12, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    0  1
  16P LOSS WILD-TYPE  4 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    1
  16P LOSS WILD-TYPE    4   31
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                1                 31
[1] 2 2
[1] FALSE

Clustering(52) Variable = 16Q LOSS MUTATION ANALYSIS
D52V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    1  4
  16Q LOSS WILD-TYPE 55  5
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 60 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                  5 
$`16Q LOSS MUTATED`
TCGA-KL-8336 TCGA-KL-8339 TCGA-KN-8427 TCGA-KN-8428 TCGA-KO-8408 
       30.25        28.11         0.99        52.27        16.67 

$`16Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       92.55        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       65.19       104.52         3.55        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
       11.21        59.08       115.00        42.35       100.87        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 
       10.68        74.93        79.04        92.71        80.38        87.78 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        86.10        77.85        57.17        61.58        63.95 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.99               2.50 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             52.27             151.96 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             28.11              72.66 
[1] "1.0 - 52.3 (28.1)"  "2.5 - 152.0 (72.7)"
[1] "hr=" "21" 
D52V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         0        1         1        3
  16Q LOSS WILD-TYPE      21       24        13        3
D52V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  0                 21
  STAGE II                 1                 24
  STAGE III                1                 13
  STAGE IV                 3                  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                 T1 T2 T3+T4
  16Q LOSS MUTATED    0  1     4
  16Q LOSS WILD-TYPE 21 24    16
D52V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                   0                 21
  T2                   1                 24
  T3+T4                4                 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"
                    vv
clus                 N0 N1+N2
  16Q LOSS MUTATED    1     4
  16Q LOSS WILD-TYPE 39     1
D52V5, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                   1                 39
  N1+N2                4                  1
[1] 2 2
[1] FALSE
D52V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    1  1
  16Q LOSS WILD-TYPE 33  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    1
  16Q LOSS WILD-TYPE   33    1
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                1                 33
  1                1                  1
[1] 2 2
[1] FALSE
D52V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    1  4
  16Q LOSS WILD-TYPE 26 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    4
  16Q LOSS WILD-TYPE   26   35
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                1                 26
  MALE                  4                 35
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                  9 
        TCGA-KL-8324         TCGA-KL-8330         TCGA-KL-8335 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8345         TCGA-KM-8639 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8433         TCGA-KO-8409         TCGA-KO-8416 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D52V10, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8433 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8409 
"16Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       0                         0     5
  16Q LOSS WILD-TYPE     2                         4    53
D52V11, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    5                 53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    0  2
  16Q LOSS WILD-TYPE  4 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0    2
  16Q LOSS WILD-TYPE    4   30
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                2                 30
[1] 2 2
[1] FALSE

Clustering(53) Variable = 17P LOSS MUTATION ANALYSIS
D53V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   42  7
  17P LOSS WILD-TYPE 14  2
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                49                 16 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                  2 
$`17P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       54.74        62.37       151.96        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
        0.99        52.27        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      115.00        42.35        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       16.67        80.38       103.27        77.85        57.17        61.58 
TCGA-KO-8417 
       63.95 

$`17P LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KM-8439 TCGA-KM-8441 
      109.22        98.33        71.41        28.80        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 
       51.06        31.33        23.47        25.91         3.55        11.21 
TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8410 TCGA-KO-8413 
      100.87        10.68        87.78        86.10 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.99               3.55 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            151.96             109.22 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            73.910             30.065 
[1] "1.0 - 152.0 (73.9)" "3.5 - 109.2 (30.1)"
[1] "hr=" "1.2"
D53V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED        13       23        10        4
  17P LOSS WILD-TYPE       8        2         4        2
D53V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                 13                  8
  STAGE II                23                  2
  STAGE III               10                  4
  STAGE IV                 4                  2
[1] 4 2
[1] TRUE
[1] "dimension 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   13 23    14
  17P LOSS WILD-TYPE  8  2     6
D53V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                  13                  8
  T2                  23                  2
  T3+T4               14                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  17P LOSS MUTATED   32     5
  17P LOSS WILD-TYPE  8     0
D53V5, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                  32                  8
  N1+N2                5                  0
[1] 2 2
[1] FALSE
D53V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   28  1
  17P LOSS WILD-TYPE  6  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     28    1
  17P LOSS WILD-TYPE    6    1
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               28                  6
  1                1                  1
[1] 2 2
[1] FALSE
D53V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   23 27
  17P LOSS WILD-TYPE  4 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     23   27
  17P LOSS WILD-TYPE    4   12
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               23                  4
  MALE                 27                 12
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
[1] "Remove cluster labels:" "17P LOSS WILD-TYPE"    
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                  2 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" 
      TCGA-KL-8345       TCGA-KN-8428       TCGA-KO-8408       TCGA-KO-8409 
"17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" 
      TCGA-KO-8416 
"17P LOSS MUTATED" 
D53V10, continuous
[1] "Remove cluster labels:" "17P LOSS WILD-TYPE"    
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 6                  2 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" 
      TCGA-KO-8408       TCGA-KO-8409 
"17P LOSS MUTATED" "17P LOSS MUTATED" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       2                         3    43
  17P LOSS WILD-TYPE     0                         1    15
D53V11, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    2                  0
  BLACK OR AFRICAN AMERICAN                3                  1
  WHITE                                   43                 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"
D53V12, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    3 21
  17P LOSS WILD-TYPE  1 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3   21
  17P LOSS WILD-TYPE    1   11
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO               21                 11
[1] 2 2
[1] FALSE

Clustering(54) Variable = 17Q LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   42  7
  17Q LOSS WILD-TYPE 14  2
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                49                 16 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                  2 
$`17Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       54.74        62.37       151.96        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
        0.99        52.27        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      115.00        42.35        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       16.67        80.38       103.27        77.85        57.17        61.58 
TCGA-KO-8417 
       63.95 

$`17Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KM-8439 TCGA-KM-8441 
      109.22        98.33        71.41        28.80        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 
       51.06        31.33        23.47        25.91         3.55        11.21 
TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8410 TCGA-KO-8413 
      100.87        10.68        87.78        86.10 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.99               3.55 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            151.96             109.22 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            73.910             30.065 
[1] "1.0 - 152.0 (73.9)" "3.5 - 109.2 (30.1)"
[1] "hr=" "1.2"
D54V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED        13       23        10        4
  17Q LOSS WILD-TYPE       8        2         4        2
D54V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                 13                  8
  STAGE II                23                  2
  STAGE III               10                  4
  STAGE IV                 4                  2
[1] 4 2
[1] TRUE
[1] "dimension 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   13 23    14
  17Q LOSS WILD-TYPE  8  2     6
D54V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                  13                  8
  T2                  23                  2
  T3+T4               14                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  17Q LOSS MUTATED   32     5
  17Q LOSS WILD-TYPE  8     0
D54V5, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                  32                  8
  N1+N2                5                  0
[1] 2 2
[1] FALSE
D54V6, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   28  1
  17Q LOSS WILD-TYPE  6  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     28    1
  17Q LOSS WILD-TYPE    6    1
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               28                  6
  1                1                  1
[1] 2 2
[1] FALSE
D54V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   23 27
  17Q LOSS WILD-TYPE  4 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     23   27
  17Q LOSS WILD-TYPE    4   12
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               23                  4
  MALE                 27                 12
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
[1] "Remove cluster labels:" "17Q LOSS WILD-TYPE"    
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 9                  2 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"17Q LOSS MUTATED" "17Q LOSS MUTATED" "17Q LOSS MUTATED" "17Q LOSS MUTATED" 
      TCGA-KL-8345       TCGA-KN-8428       TCGA-KO-8408       TCGA-KO-8409 
"17Q LOSS MUTATED" "17Q LOSS MUTATED" "17Q LOSS MUTATED" "17Q LOSS MUTATED" 
      TCGA-KO-8416 
"17Q LOSS MUTATED" 
D54V10, continuous
[1] "Remove cluster labels:" "17Q LOSS WILD-TYPE"    
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                  2 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"17Q LOSS MUTATED" "17Q LOSS MUTATED" "17Q LOSS MUTATED" "17Q LOSS MUTATED" 
      TCGA-KO-8408       TCGA-KO-8409 
"17Q LOSS MUTATED" "17Q LOSS MUTATED" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       2                         3    43
  17Q LOSS WILD-TYPE     0                         1    15
D54V11, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    2                  0
  BLACK OR AFRICAN AMERICAN                3                  1
  WHITE                                   43                 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"
D54V12, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    3 21
  17Q LOSS WILD-TYPE  1 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3   21
  17Q LOSS WILD-TYPE    1   11
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO               21                 11
[1] 2 2
[1] FALSE

Clustering(55) Variable = 18P LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    6  1
  18P LOSS WILD-TYPE 50  8
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                 58 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                  8 
$`18P LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8336 TCGA-KN-8427 TCGA-KN-8429 
      102.81        90.48        98.96        30.25         0.99        87.12 
TCGA-KO-8414 
       77.85 

$`18P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8330 
       38.07       141.73        23.84       109.22       137.06       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 
       84.89        98.33        96.95        92.55        44.84        86.56 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       28.11        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.74        62.37       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       47.24        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
        3.55        52.27        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       86.10        57.17        61.58        63.95 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.99               2.50 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            102.81             151.96 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             87.12              63.16 
[1] "1.0 - 102.8 (87.1)" "2.5 - 152.0 (63.2)"
[1] "hr=" "1"  
D55V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED         2        3         1        2
  18P LOSS WILD-TYPE      19       22        13        4
D55V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  2                 19
  STAGE II                 3                 22
  STAGE III                1                 13
  STAGE IV                 2                  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                 T1 T2 T3+T4
  18P LOSS MUTATED    2  3     3
  18P LOSS WILD-TYPE 19 22    17
D55V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                   2                 19
  T2                   3                 22
  T3+T4                3                 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"
                    vv
clus                 N0 N1+N2
  18P LOSS MUTATED    6     2
  18P LOSS WILD-TYPE 34     3
D55V5, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                   6                 34
  N1+N2                2                  3
[1] 2 2
[1] FALSE
D55V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    5  0
  18P LOSS WILD-TYPE 29  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      5    0
  18P LOSS WILD-TYPE   29    2
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0                5                 29
  1                0                  2
[1] 2 2
[1] FALSE
D55V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    5  3
  18P LOSS WILD-TYPE 22 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      5    3
  18P LOSS WILD-TYPE   22   36
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                5                 22
  MALE                  3                 36
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
D55V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       1                         0     7
  18P LOSS WILD-TYPE     1                         4    51
D55V11, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    7                 51
[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"
D55V12, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    0  2
  18P LOSS WILD-TYPE  4 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0    2
  18P LOSS WILD-TYPE    4   30
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                2                 30
[1] 2 2
[1] FALSE

Clustering(56) Variable = 18Q LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    7  2
  18Q LOSS WILD-TYPE 49  7
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 9                 56 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                  7 
$`18Q LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8336 TCGA-KN-8424 TCGA-KN-8427 
      102.81        90.48        98.96        30.25        65.19         0.99 
TCGA-KN-8429 TCGA-KO-8404 TCGA-KO-8414 
       87.12        10.68        77.85 

$`18Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8330 
       38.07       141.73        23.84       109.22       137.06       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 
       84.89        98.33        96.95        92.55        44.84        86.56 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       28.11        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.74        62.37       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       47.24        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
       23.47        87.91        25.48        25.91       104.52         3.55 
TCGA-KN-8428 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 
       16.67        80.38        87.78       103.27        86.10        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.95 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.99               2.50 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            102.81             151.96 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             77.85              63.16 
[1] "1.0 - 102.8 (77.8)" "2.5 - 152.0 (63.2)"
[1] "hr=" "1.8"
D56V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED         3        3         1        3
  18Q LOSS WILD-TYPE      18       22        13        3
D56V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  3                 18
  STAGE II                 3                 22
  STAGE III                1                 13
  STAGE IV                 3                  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                 T1 T2 T3+T4
  18Q LOSS MUTATED    3  3     4
  18Q LOSS WILD-TYPE 18 22    16
D56V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                   3                 18
  T2                   3                 22
  T3+T4                4                 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"
                    vv
clus                 N0 N1+N2
  18Q LOSS MUTATED    7     2
  18Q LOSS WILD-TYPE 33     3
D56V5, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                   7                 33
  N1+N2                2                  3
[1] 2 2
[1] FALSE
D56V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    5  0
  18Q LOSS WILD-TYPE 29  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5    0
  18Q LOSS WILD-TYPE   29    2
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0                5                 29
  1                0                  2
[1] 2 2
[1] FALSE
D56V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    6  4
  18Q LOSS WILD-TYPE 21 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      6    4
  18Q LOSS WILD-TYPE   21   35
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                6                 21
  MALE                  4                 35
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
D56V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       1                         0     9
  18Q LOSS WILD-TYPE     1                         4    49
D56V11, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    9                 49
[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"
D56V12, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    0  3
  18Q LOSS WILD-TYPE  4 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      0    3
  18Q LOSS WILD-TYPE    4   29
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                3                 29
[1] 2 2
[1] FALSE

Clustering(57) Variable = 19Q LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    2  1
  19Q LOSS WILD-TYPE 54  8
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 62 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                  8 
$`19Q LOSS MUTATED`
TCGA-KL-8341 TCGA-KN-8427 TCGA-KO-8415 
       24.79         0.99        57.17 

$`19Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       25.91        65.19       104.52         3.55        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.95 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.99               2.50 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             57.17             151.96 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            24.790             68.975 
[1] "1.0 - 57.2 (24.8)"  "2.5 - 152.0 (69.0)"
[1] "hr=" "5"  
D57V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         1        0         0        2
  19Q LOSS WILD-TYPE      20       25        14        4
D57V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  1                 20
  STAGE II                 0                 25
  STAGE III                0                 14
  STAGE IV                 2                  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                 T1 T2 T3+T4
  19Q LOSS MUTATED    1  0     2
  19Q LOSS WILD-TYPE 20 25    18
D57V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                   1                 20
  T2                   0                 25
  T3+T4                2                 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"
                    vv
clus                 N0 N1+N2
  19Q LOSS MUTATED    1     2
  19Q LOSS WILD-TYPE 39     3
D57V5, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                   1                 39
  N1+N2                2                  3
[1] 2 2
[1] FALSE
D57V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  0
  19Q LOSS WILD-TYPE 32  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    0
  19Q LOSS WILD-TYPE   32    2
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                2                 32
  1                0                  2
[1] 2 2
[1] FALSE
D57V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    1  2
  19Q LOSS WILD-TYPE 26 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    2
  19Q LOSS WILD-TYPE   26   37
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                1                 26
  MALE                  2                 37
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 10 
        TCGA-KL-8324         TCGA-KL-8330         TCGA-KL-8335 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8428 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-KN-8433         TCGA-KO-8408         TCGA-KO-8409 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-KO-8416 
"19Q LOSS WILD-TYPE" 
D57V10, continuous
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8345 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8433         TCGA-KO-8408 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-KO-8409 
"19Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         0     2
  19Q LOSS WILD-TYPE     1                         4    56
D57V11, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    2                 56
[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"
D57V12, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    1  0
  19Q LOSS WILD-TYPE  3 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    0
  19Q LOSS WILD-TYPE    3   32
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO                0                 32
[1] 2 2
[1] FALSE

Clustering(58) Variable = 20P LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    3  1
  20P LOSS WILD-TYPE 53  8
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                 61 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                  8 
$`20P LOSS MUTATED`
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 TCGA-KN-8434 
       92.55        30.25        86.56        59.08 

$`20P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8337 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        28.11        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       28.80        54.74        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       28.80        47.24        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      104.52         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
        2.50        11.21       115.00        42.35       100.87        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68        74.93        79.04        92.71        16.67        80.38 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       87.78       103.27        86.10        77.85        57.17        61.58 
TCGA-KO-8417 
       63.95 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             30.25               0.99 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             92.55             151.96 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             72.82              65.19 
[1] "30.2 - 92.5 (72.8)" "1.0 - 152.0 (65.2)"
[1] "hr=" "1.6"
D58V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         0        1         2        1
  20P LOSS WILD-TYPE      21       24        12        5
D58V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  0                 21
  STAGE II                 1                 24
  STAGE III                2                 12
  STAGE IV                 1                  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                 T1 T2 T3+T4
  20P LOSS MUTATED    0  1     3
  20P LOSS WILD-TYPE 21 24    17
D58V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                   0                 21
  T2                   1                 24
  T3+T4                3                 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"
                    vv
clus                 N0 N1+N2
  20P LOSS MUTATED    2     1
  20P LOSS WILD-TYPE 38     4
D58V5, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                   2                 38
  N1+N2                1                  4
[1] 2 2
[1] FALSE
D58V6, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    3  0
  20P LOSS WILD-TYPE 31  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    0
  20P LOSS WILD-TYPE   31    2
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                3                 31
  1                0                  2
[1] 2 2
[1] FALSE
D58V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    2  2
  20P LOSS WILD-TYPE 25 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2    2
  20P LOSS WILD-TYPE   25   37
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                2                 25
  MALE                  2                 37
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 10 
        TCGA-KL-8324         TCGA-KL-8330         TCGA-KL-8341 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8428 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8433         TCGA-KO-8408         TCGA-KO-8409 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8416 
"20P LOSS WILD-TYPE" 
D58V10, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8341         TCGA-KL-8345 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8433         TCGA-KO-8408 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8409 
"20P LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         0     4
  20P LOSS WILD-TYPE     2                         4    54
D58V11, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    4                 54
[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"
D58V12, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    0  1
  20P LOSS WILD-TYPE  4 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    1
  20P LOSS WILD-TYPE    4   31
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                1                 31
[1] 2 2
[1] FALSE

Clustering(59) Variable = 20Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    2  1
  20Q LOSS WILD-TYPE 54  8
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 62 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                  8 
$`20Q LOSS MUTATED`
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 
       92.55        30.25        86.56 

$`20Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8337 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        28.11        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       28.80        54.74        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       28.80        47.24        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      104.52         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        59.08       115.00        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78       103.27        86.10        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.95 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             30.25               0.99 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             92.55             151.96 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             86.56              64.57 
[1] "30.2 - 92.5 (86.6)" "1.0 - 152.0 (64.6)"
[1] "hr=" "2.2"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q LOSS MUTATED         0        0         2        1
  20Q LOSS WILD-TYPE      21       25        12        5
D59V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  0                 21
  STAGE II                 0                 25
  STAGE III                2                 12
  STAGE IV                 1                  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                 T1 T2 T3+T4
  20Q LOSS MUTATED    0  0     3
  20Q LOSS WILD-TYPE 21 25    17
D59V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                   0                 21
  T2                   0                 25
  T3+T4                3                 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"
                    vv
clus                 N0 N1+N2
  20Q LOSS MUTATED    2     1
  20Q LOSS WILD-TYPE 38     4
D59V5, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                   2                 38
  N1+N2                1                  4
[1] 2 2
[1] FALSE
D59V6, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    3  0
  20Q LOSS WILD-TYPE 31  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    0
  20Q LOSS WILD-TYPE   31    2
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                3                 31
  1                0                  2
[1] 2 2
[1] FALSE
D59V7, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  2
  20Q LOSS WILD-TYPE 26 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    2
  20Q LOSS WILD-TYPE   26   37
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                 26
  MALE                  2                 37
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 10 
        TCGA-KL-8324         TCGA-KL-8330         TCGA-KL-8341 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8428 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8433         TCGA-KO-8408         TCGA-KO-8409 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8416 
"20Q LOSS WILD-TYPE" 
D59V10, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8341         TCGA-KL-8345 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8433         TCGA-KO-8408 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8409 
"20Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         0     3
  20Q LOSS WILD-TYPE     2                         4    55
D59V11, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    3                 55
[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"
D59V12, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    0  0
  20Q LOSS WILD-TYPE  4 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    0
  20Q LOSS WILD-TYPE    4   32

Clustering(60) Variable = 21Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   26  8
  21Q LOSS WILD-TYPE 30  1
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                34                 31 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                  1 
$`21Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8328 TCGA-KL-8330 TCGA-KL-8331 
       38.07       141.73        23.84       102.81       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       84.89        96.95        30.25        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8443 TCGA-KM-8476 
       24.79        71.41        28.80        62.37        49.97       123.12 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       25.48        65.19       104.52         0.99        52.27        87.12 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8408 TCGA-KO-8409 
        2.50        59.08        76.90        79.04        16.67        80.38 
TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
      103.27        77.85        57.17        61.58 

$`21Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8333 TCGA-KL-8335 TCGA-KL-8337 
      109.22       137.06        90.48        98.33        92.55        44.84 
TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       73.91        54.74       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
       47.24        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8435 TCGA-KN-8436 
       25.91         3.55        19.33        11.21       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8413 
      100.87        10.68        74.93        92.71        87.78        86.10 
TCGA-KO-8417 
       63.95 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.99               3.55 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            141.73             151.96 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            65.865             63.950 
[1] "1.0 - 141.7 (65.9)" "3.5 - 152.0 (64.0)"
[1] "hr=" "6.9"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED        10       13         8        4
  21Q LOSS WILD-TYPE      11       12         6        2
D60V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                 10                 11
  STAGE II                13                 12
  STAGE III                8                  6
  STAGE IV                 4                  2
[1] 4 2
[1] TRUE
[1] "dimension 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   10 13    12
  21Q LOSS WILD-TYPE 11 12     8
D60V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                  10                 11
  T2                  13                 12
  T3+T4               12                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  21Q LOSS MUTATED   22     5
  21Q LOSS WILD-TYPE 18     0
D60V5, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                  22                 18
  N1+N2                5                  0
[1] 2 2
[1] FALSE
D60V6, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   21  1
  21Q LOSS WILD-TYPE 13  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     21    1
  21Q LOSS WILD-TYPE   13    1
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               21                 13
  1                1                  1
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   15 20
  21Q LOSS WILD-TYPE 12 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     15   20
  21Q LOSS WILD-TYPE   12   19
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               15                 12
  MALE                 20                 19
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
D60V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       1                         1    33
  21Q LOSS WILD-TYPE     1                         3    25
D60V11, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   33                 25
[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"
D60V12, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    1 15
  21Q LOSS WILD-TYPE  3 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   15
  21Q LOSS WILD-TYPE    3   17
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               15                 17
[1] 2 2
[1] FALSE

Clustering(61) Variable = 22Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    5  2
  22Q LOSS WILD-TYPE 51  7
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 7                 58 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                  7 
$`22Q LOSS MUTATED`
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8336 TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8422 
      108.62        98.96        30.25        28.11       151.96        25.48 
TCGA-KO-8415 
       57.17 

$`22Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 
       90.48        84.89        98.33        96.95        92.55        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       54.74        62.37        23.28        44.91        28.80        47.24 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       87.91        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
       86.10        77.85        61.58        63.95 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             25.48               0.99 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            151.96             141.73 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            57.170             65.865 
[1] "25.5 - 152.0 (57.2)" "1.0 - 141.7 (65.9)" 
[1] "hr=" "2.3"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED         3        3         0        2
  22Q LOSS WILD-TYPE      18       22        14        4
D61V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  3                 18
  STAGE II                 3                 22
  STAGE III                0                 14
  STAGE IV                 2                  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                 T1 T2 T3+T4
  22Q LOSS MUTATED    3  3     2
  22Q LOSS WILD-TYPE 18 22    18
D61V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                   3                 18
  T2                   3                 22
  T3+T4                2                 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"
                    vv
clus                 N0 N1+N2
  22Q LOSS MUTATED    6     2
  22Q LOSS WILD-TYPE 34     3
D61V5, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                   6                 34
  N1+N2                2                  3
[1] 2 2
[1] FALSE
D61V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    4  1
  22Q LOSS WILD-TYPE 30  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4    1
  22Q LOSS WILD-TYPE   30    1
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0                4                 30
  1                1                  1
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    6  2
  22Q LOSS WILD-TYPE 21 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6    2
  22Q LOSS WILD-TYPE   21   37
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                6                 21
  MALE                  2                 37
[1] 2 2
[1] FALSE
D61V8, continuous
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 10 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KO-8411 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8413 
"22Q LOSS WILD-TYPE" 
D61V9, continuous
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 10 
        TCGA-KL-8324         TCGA-KL-8335         TCGA-KL-8341 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8428 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8433         TCGA-KO-8408         TCGA-KO-8409 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8416 
"22Q LOSS WILD-TYPE" 
D61V10, continuous
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8335         TCGA-KL-8341         TCGA-KL-8345 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8433         TCGA-KO-8408 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8409 
"22Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       0                         1     7
  22Q LOSS WILD-TYPE     2                         3    51
D61V11, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                    7                 51
[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"
D61V12, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    1  3
  22Q LOSS WILD-TYPE  3 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1    3
  22Q LOSS WILD-TYPE    3   29
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO                3                 29
[1] 2 2
[1] FALSE

Clustering(62) Variable = XP LOSS MUTATION ANALYSIS
D62V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED   32  6
  XP LOSS WILD-TYPE 24  3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               38                27 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                6                 3 
$`XP LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07        23.84       102.81        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 
       86.56        28.11        66.54        73.91        71.41        54.74 
TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
       44.91        47.24       123.12       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       65.19        87.12        19.33         2.50        59.08       115.00 
TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8415 
       76.90        79.04        92.71        16.67       103.27        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.95 

$`XP LOSS WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8344 TCGA-KL-8346 
      141.73       109.22       137.06        24.79        28.80        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 
      151.96        23.28        28.80        49.97        51.06        31.33 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       23.47        25.91       104.52         3.55         0.99        52.27 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 
       11.21        42.35       100.87        10.68        74.93        80.38 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       87.78        86.10        77.85 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             2.50              0.99 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           129.37            151.96 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            72.66             51.06 
[1] "2.5 - 129.4 (72.7)" "1.0 - 152.0 (51.1)"
[1] "hr=" "1.1"
D62V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP LOSS MUTATED        10       16        10        2
  XP LOSS WILD-TYPE      11        9         4        4
D62V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                10                11
  STAGE II               16                 9
  STAGE III              10                 4
  STAGE IV                2                 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                T1 T2 T3+T4
  XP LOSS MUTATED   10 16    12
  XP LOSS WILD-TYPE 11  9     8
D62V4, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  T1                 10                11
  T2                 16                 9
  T3+T4              12                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  XP LOSS MUTATED   24     3
  XP LOSS WILD-TYPE 16     2
D62V5, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  N0                 24                16
  N1+N2               3                 2
[1] 2 2
[1] FALSE
D62V6, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   23  1
  XP LOSS WILD-TYPE 11  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     23    1
  XP LOSS WILD-TYPE   11    1
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              23                11
  1               1                 1
[1] 2 2
[1] FALSE
D62V7, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   19 19
  XP LOSS WILD-TYPE  8 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     19   19
  XP LOSS WILD-TYPE    8   20
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              19                 8
  MALE                19                20
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
D62V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       1                         3    32
  XP LOSS WILD-TYPE     1                         1    26
D62V11, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               3                 1
  WHITE                                  32                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    2 15
  XP LOSS WILD-TYPE  2 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2   15
  XP LOSS WILD-TYPE    2   17
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              15                17
[1] 2 2
[1] FALSE

Clustering(63) Variable = XQ LOSS MUTATION ANALYSIS
D63V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   32  7
  XQ LOSS WILD-TYPE 24  2
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               39                26 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7                 2 
$`XQ LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07        23.84       102.81        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 
       86.56        28.11        66.54        73.91        71.41        54.74 
TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
       44.91        47.24       123.12       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8435 
       65.19        87.12        19.33         2.50        11.21       115.00 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 
       76.90        10.68        79.04        92.71        16.67       103.27 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       57.17        61.58        63.95 

$`XQ LOSS WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8344 TCGA-KL-8346 
      141.73       109.22       137.06        24.79        28.80        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 
      151.96        23.28        28.80        49.97        51.06        31.33 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       23.47        25.91       104.52         3.55         0.99        52.27 
TCGA-KN-8434 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 
       59.08        42.35       100.87        74.93        80.38        87.78 
TCGA-KO-8413 TCGA-KO-8414 
       86.10        77.85 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             2.50              0.99 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           129.37            151.96 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           71.410            55.675 
[1] "2.5 - 129.4 (71.4)" "1.0 - 152.0 (55.7)"
[1] "hr=" "2.1"
D63V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED        10       15        11        3
  XQ LOSS WILD-TYPE      11       10         3        3
D63V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                10                11
  STAGE II               15                10
  STAGE III              11                 3
  STAGE IV                3                 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                T1 T2 T3+T4
  XQ LOSS MUTATED   10 15    14
  XQ LOSS WILD-TYPE 11 10     6
D63V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1                 10                11
  T2                 15                10
  T3+T4              14                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  XQ LOSS MUTATED   24     3
  XQ LOSS WILD-TYPE 16     2
D63V5, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0                 24                16
  N1+N2               3                 2
[1] 2 2
[1] FALSE
D63V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   23  1
  XQ LOSS WILD-TYPE 11  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     23    1
  XQ LOSS WILD-TYPE   11    1
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              23                11
  1               1                 1
[1] 2 2
[1] FALSE
D63V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   19 20
  XQ LOSS WILD-TYPE  8 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     19   20
  XQ LOSS WILD-TYPE    8   19
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              19                 8
  MALE                20                19
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, continuous
D63V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       1                         3    33
  XQ LOSS WILD-TYPE     1                         1    25
D63V11, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               3                 1
  WHITE                                  33                25
[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"
D63V12, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    2 16
  XQ LOSS WILD-TYPE  2 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   16
  XQ LOSS WILD-TYPE    2   16
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              16                16
[1] 2 2
[1] FALSE
