[1] "ofn"        "-oTMESO-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/MESO-TP/22507181/MESO-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/MESO-TP/22533659/transformed.cor.cli.txt"

nPatients in clinical file=87, in cluster file=87, common to both=87
[1] "Reduce the number of clustering variables from 82 to 72."
[1] 72 87
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                79 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                79 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               20                67 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               20                67 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                4                83 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                4                83 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                81 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                81 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17                70 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17                70 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               19                68 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               19                68 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               24                63 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               24                63 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               14                73 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               14                73 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7                80 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7                80 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                83 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                83 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               25                62 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               25                62 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               22                65 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               22                65 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                75 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                75 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               14                73 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               14                73 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                84 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                84 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 84 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 84 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                 84 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                 84 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                12                 75 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                12                 75 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                12                 75 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                12                 75 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                18                 69 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                18                 69 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                 69 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                 69 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 82 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 82 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                 77 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                 77 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                 71 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                 71 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                16                 71 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                16                 71 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                 79 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                 79 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                17                 70 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                17                 70 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                 79 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                 79 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 83 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 83 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                14                 73 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                14                 73 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                11                 76 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                11                 76 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                 79 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                 79 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                11                 76 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                11                 76 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 81 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 81 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                7                80 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                7                80 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                81 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                81 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                9                78 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                9                78 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6                81 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6                81 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                82 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                82 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                8                79 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                8                79 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7                80 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7                80 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               33                54 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               33                54 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               34                53 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               34                53 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                83 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                83 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                9                78 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                9                78 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                79 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                79 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               29                58 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               29                58 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13                74 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13                74 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                83 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                83 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               28                59 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               28                59 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               22                65 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               22                65 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                25                 62 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                25                 62 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                19                 68 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                19                 68 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 4                 83 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 4                 83 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 82 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 82 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 83 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 83 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                33                 54 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                33                 54 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                35                 52 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                35                 52 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                11                 76 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                11                 76 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 8                 79 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 8                 79 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                11                 76 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                11                 76 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                23                 64 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                23                 64 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                 80 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                 80 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 9                 78 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 9                 78 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                14                 73 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                14                 73 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 83 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 83 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 7                 80 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 7                 80 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                14                 73 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                14                 73 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                11                 76 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                11                 76 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                67                 20 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                67                 20 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               27                60 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               27                60 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               28                59 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               28                59 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "HISTOLOGICAL_TYPE"                   
[15] "RESIDUAL_TUMOR"                      
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 87 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=70,	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=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RACE excluded in the analysis because there is no case of (both >= 3) in the table below"
              ASIAN   BLACK OR AFRICAN AMERICAN WHITE  
freq.values   "1"     "1"                       "85"   
freq.contrast "86"    "86"                      "2"    
both >= 3     "FALSE" "FALSE"                   "FALSE"
Variable 17:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[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 87 columns, 1 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "HISTOLOGICAL_TYPE"           "RESIDUAL_TUMOR"             
YEARS_TO_BIRTH, nv=36, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
14 26 32 13 
[1] "table(vv)"
vv
T1 T2 T3 T4 
14 26 32 13 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
14 26 32 13 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
14 26 32 13 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
44 10 26  3 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
   44    10    29 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 N3 
44 10 26  3 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
   44    10    29 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=5, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    0  8
  1P GAIN WILD-TYPE 12 65
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                77 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                65 
$`1P GAIN MUTATED`
TCGA-3H-AB3U TCGA-LK-A4O0 TCGA-SH-A7BC TCGA-SH-A7BH TCGA-UD-AAC5 TCGA-UD-AAC6 
       27.16         6.08        23.90         7.99         8.32        14.99 
TCGA-UD-AAC7 TCGA-YS-A95B 
       13.35         1.28 

$`1P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I 
       13.61        48.99         4.67        17.62        38.01        28.27 
TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 
       24.36        17.95         5.52         8.02         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        77.56 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       68.71        19.99         0.66        28.96        13.61         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU 
        9.76        38.40        15.09        14.76        24.07        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
        8.38        27.75        41.46        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY 
       19.43        15.02        32.28        11.77        10.78        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G 
       27.72         6.48        25.94        28.37        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP 
        4.73         4.67         4.37         2.76         8.58         7.50 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       16.41        40.37        32.12        43.04         2.76 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.28              0.66 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            27.16             91.73 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           10.835            17.950 
[1] "1.3 - 27.2 (10.8)" "0.7 - 91.7 (17.9)"
[1] "hr=" "2.3"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         1        1        0        2         3        1
  1P GAIN WILD-TYPE       6        1        1       14        42       15
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 1                 6
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                2                14
  STAGE III               3                42
  STAGE IV                1                15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1P GAIN MUTATED    2  2  3  1
  1P GAIN WILD-TYPE 12 24 29 12
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               2                12
  T2               2                24
  T3               3                29
  T4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  1P GAIN MUTATED    6  0     2
  1P GAIN WILD-TYPE 38 10    27
D1V5, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0                  6                38
  N1                  0                10
  N2+N3               2                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    8  0
  1P GAIN WILD-TYPE 49  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8    0
  1P GAIN WILD-TYPE   49    3
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               8                49
  1               0                 3
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    2  6
  1P GAIN WILD-TYPE 14 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    6
  1P GAIN WILD-TYPE   14   65
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               2                14
  MALE                 6                65
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    4  4
  1P GAIN WILD-TYPE 58 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4    4
  1P GAIN WILD-TYPE   58   20
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                4                58
  YES               4                20
[1] 2 2
[1] FALSE
D1V9, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                16 
       TCGA-3U-A98E        TCGA-UT-A88D        TCGA-3U-A98J        TCGA-SC-A6LM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SC-A6LP        TCGA-SC-A6LR        TCGA-SH-A9CT 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SH-A9CU        TCGA-UT-A88C        TCGA-XT-AASU        TCGA-ZN-A9VO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ZN-A9VP        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  1P GAIN MUTATED                       2                                    0
  1P GAIN WILD-TYPE                    21                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  1P GAIN MUTATED                          5                        1
  1P GAIN WILD-TYPE                       52                        1
D1V10, multiclass
                                      clus
vv                                     1P GAIN MUTATED 1P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              2                21
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           5                52
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  1P GAIN MUTATED    1  0  5  1
  1P GAIN WILD-TYPE 16  3 10 10
D1V11, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               1                16
  R1               0                 3
  R2               5                10
  RX               1                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    1 19
  1Q GAIN WILD-TYPE 11 54
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               20                65 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               19                54 
$`1Q GAIN MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98F TCGA-3U-A98J TCGA-LK-A4NZ 
       29.10        27.16        48.99        17.62        24.36         8.02 
TCGA-LK-A4O0 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-SC-A6LN 
        6.08        14.73        11.51        18.81        23.31        13.61 
TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7PB TCGA-UD-AABZ TCGA-UD-AAC5 
       23.90         7.99        14.76        32.28         6.48         8.32 
TCGA-UD-AAC7 TCGA-YS-A95B 
       13.35         1.28 

$`1Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        11.87        13.61 
TCGA-3U-A98D TCGA-3U-A98H TCGA-3U-A98I TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4O2 
        4.67        38.01        28.27        17.95         5.52         1.87 
TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       12.72        80.84        91.73         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I 
       10.95        24.89        77.56        68.71        19.99         0.66 
TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD TCGA-SH-A9CU 
       28.96         2.56         9.76        38.40        15.09        24.07 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY 
        9.30        19.43        15.02        11.77        10.78        15.42 
TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G 
       27.72        25.94        14.99        28.37        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP 
        4.73         4.67         4.37         2.76         8.58         7.50 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       16.41        40.37        32.12        43.04         2.76 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1.28              0.66 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            48.99             91.73 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           14.745            17.950 
[1] "1.3 - 49.0 (14.7)" "0.7 - 91.7 (17.9)"
[1] "hr=" "1.5"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         1        1        0        5        12        1
  1Q GAIN WILD-TYPE       6        1        1       11        33       15
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 1                 6
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                5                11
  STAGE III              12                33
  STAGE IV                1                15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1Q GAIN MUTATED    2  7 10  1
  1Q GAIN WILD-TYPE 12 19 22 12
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               2                12
  T2               7                19
  T3              10                22
  T4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  1Q GAIN MUTATED   11  3     6
  1Q GAIN WILD-TYPE 33  7    23
D2V5, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0                 11                33
  N1                  3                 7
  N2+N3               6                23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   19  0
  1Q GAIN WILD-TYPE 38  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     19    0
  1Q GAIN WILD-TYPE   38    3
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              19                38
  1               0                 3
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    5 15
  1Q GAIN WILD-TYPE 11 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5   15
  1Q GAIN WILD-TYPE   11   56
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               5                11
  MALE                15                56
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   11  9
  1Q GAIN WILD-TYPE 51 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     11    9
  1Q GAIN WILD-TYPE   51   15
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               11                51
  YES               9                15
[1] 2 2
[1] FALSE
D2V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  1Q GAIN MUTATED                       5                                    0
  1Q GAIN WILD-TYPE                    18                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  1Q GAIN MUTATED                         14                        1
  1Q GAIN WILD-TYPE                       43                        1
D2V10, multiclass
                                      clus
vv                                     1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              5                18
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                          14                43
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  1Q GAIN MUTATED    3  1  5  3
  1Q GAIN WILD-TYPE 14  2 10  8
D2V11, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0               3                14
  R1               1                 2
  R2               5                10
  RX               3                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    0  4
  2P GAIN WILD-TYPE 12 69
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                4                81 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                4                69 
$`2P GAIN MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4O0 TCGA-SH-A9CU 
       29.10        27.16         6.08        24.07 

$`2P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        11.87        13.61 
TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       48.99         4.67        17.62        38.01        28.27        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
       17.95         5.52         8.02         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        77.56        68.71 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       19.99         0.66        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU 
       38.40        23.90        15.09         7.99        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
        8.38        27.75        41.46        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY 
       19.43        15.02        32.28        11.77        10.78        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
       27.72         6.48        25.94         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       28.37        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.37         2.76         8.58         7.50        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             6.08              0.66 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            29.10             91.73 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           25.615            16.410 
[1] "6.1 - 29.1 (25.6)" "0.7 - 91.7 (16.4)"
[1] "hr=" "1"  
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  2P GAIN MUTATED         0        1        0        0         2        1
  2P GAIN WILD-TYPE       7        1        1       16        43       15
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                0                16
  STAGE III               2                43
  STAGE IV                1                15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2P GAIN MUTATED    1  0  2  1
  2P GAIN WILD-TYPE 13 26 30 12
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               1                13
  T2               0                26
  T3               2                30
  T4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  2P GAIN MUTATED    2  0     2
  2P GAIN WILD-TYPE 42 10    27
D3V5, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0                  2                42
  N1                  0                10
  N2+N3               2                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    4  0
  2P GAIN WILD-TYPE 53  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4    0
  2P GAIN WILD-TYPE   53    3
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               4                53
  1               0                 3
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    1  3
  2P GAIN WILD-TYPE 15 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1    3
  2P GAIN WILD-TYPE   15   68
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               1                15
  MALE                 3                68
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    4  0
  2P GAIN WILD-TYPE 58 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4    0
  2P GAIN WILD-TYPE   58   24
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                4                58
  YES               0                24
[1] 2 2
[1] FALSE
D3V9, continuous
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                16 
       TCGA-3U-A98E        TCGA-UT-A88D        TCGA-3U-A98J        TCGA-SC-A6LM 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SC-A6LP        TCGA-SC-A6LR        TCGA-SH-A7BH 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-SH-A9CT        TCGA-UT-A88C        TCGA-XT-AASU        TCGA-ZN-A9VO 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ZN-A9VP        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  2P GAIN MUTATED                       0                                    0
  2P GAIN WILD-TYPE                    23                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  2P GAIN MUTATED                          3                        1
  2P GAIN WILD-TYPE                       54                        1
D3V10, multiclass
                                      clus
vv                                     2P GAIN MUTATED 2P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              0                23
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           3                54
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  2P GAIN MUTATED    1  0  0  1
  2P GAIN WILD-TYPE 16  3 15 10
D3V11, multiclass
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                44 
       TCGA-3U-A98G        TCGA-LK-A4O4        TCGA-SC-AA5Z        TCGA-UD-AAC4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-UT-A88D        TCGA-LK-A4NW        TCGA-LK-A4NY        TCGA-LK-A4NZ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-LK-A4O2        TCGA-LK-A4O5        TCGA-LK-A4O6        TCGA-LK-A4O7 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-MQ-A4KX        TCGA-MQ-A4LC        TCGA-MQ-A4LI        TCGA-MQ-A4LV 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-MQ-A6BN        TCGA-MQ-A6BQ        TCGA-MQ-A6BR        TCGA-MQ-A6BS 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-NQ-A57I        TCGA-NQ-A638        TCGA-SC-A6LM        TCGA-SC-A6LN 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-SC-A6LP        TCGA-SC-A6LQ        TCGA-SC-A6LR        TCGA-SH-A7BC 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-SH-A7BD        TCGA-SH-A7BH        TCGA-UD-AABY        TCGA-UD-AABZ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-UD-AAC1        TCGA-UD-AAC5        TCGA-UD-AAC6        TCGA-UD-AAC7 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-UT-A88C        TCGA-UT-A88E        TCGA-UT-A88G        TCGA-UT-A97Y 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-XT-AASU        TCGA-YS-A95B        TCGA-YS-A95C        TCGA-YS-AA4M 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    0  6
  2Q GAIN WILD-TYPE 12 67
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                79 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                67 
$`2Q GAIN MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4O0 TCGA-MQ-A6BS TCGA-SH-A9CU TCGA-TS-A7OU 
       29.10        27.16         6.08        19.99        24.07        55.07 

$`2Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        11.87        13.61 
TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       48.99         4.67        17.62        38.01        28.27        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
       17.95         5.52         8.02         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        77.56        68.71 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
        0.66        28.96        13.61         2.56         9.76        38.40 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OY TCGA-TS-A7OZ 
       23.90        15.09         7.99        14.76         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       41.46        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       32.28        11.77        10.78        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E 
       25.94         8.32        14.99        13.35        28.37        14.27 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
        2.50         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV 
        8.58         7.50        16.41        40.37        32.12        43.04 
TCGA-ZN-A9VW 
        2.76 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             6.08              0.66 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            55.07             91.73 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           25.615            15.420 
[1] "6.1 - 55.1 (25.6)" "0.7 - 91.7 (15.4)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED         0        1        0        1         2        2
  2Q GAIN WILD-TYPE       7        1        1       15        43       14
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               2                43
  STAGE IV                2                14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2Q GAIN MUTATED    1  1  2  2
  2Q GAIN WILD-TYPE 13 25 30 11
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               1                13
  T2               1                25
  T3               2                30
  T4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  2Q GAIN MUTATED    4  0     2
  2Q GAIN WILD-TYPE 40 10    27
D4V5, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0                  4                40
  N1                  0                10
  N2+N3               2                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    4  0
  2Q GAIN WILD-TYPE 53  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4    0
  2Q GAIN WILD-TYPE   53    3
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               4                53
  1               0                 3
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    1  5
  2Q GAIN WILD-TYPE 15 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1    5
  2Q GAIN WILD-TYPE   15   66
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               1                15
  MALE                 5                66
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    6  0
  2Q GAIN WILD-TYPE 56 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      6    0
  2Q GAIN WILD-TYPE   56   24
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                6                56
  YES               0                24
[1] 2 2
[1] FALSE
D4V9, continuous
[1] "Remove cluster labels:" "2Q GAIN MUTATED"       
clus
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                16 
       TCGA-3U-A98E        TCGA-UT-A88D        TCGA-3U-A98J        TCGA-SC-A6LM 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SC-A6LP        TCGA-SC-A6LR        TCGA-SH-A7BH 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-SH-A9CT        TCGA-UT-A88C        TCGA-XT-AASU        TCGA-ZN-A9VO 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ZN-A9VP        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  2Q GAIN MUTATED                       0                                    0
  2Q GAIN WILD-TYPE                    23                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  2Q GAIN MUTATED                          5                        1
  2Q GAIN WILD-TYPE                       52                        1
D4V10, multiclass
                                      clus
vv                                     2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              0                23
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           5                52
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  2Q GAIN MUTATED    2  0  0  1
  2Q GAIN WILD-TYPE 15  3 15 10
D4V11, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0               2                15
  R1               0                 3
  R2               0                15
  RX               1                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    2 15
  3P GAIN WILD-TYPE 10 58
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17                68 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               15                58 
$`3P GAIN MUTATED`
TCGA-SC-AA5Z TCGA-TS-A8AS TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4O0 
       21.83        26.14        11.87        29.10        27.16         6.08 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A6BS TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BH 
       12.72        14.73        19.99        38.40        23.90         7.99 
TCGA-TS-A7P6 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
        9.30        14.99        13.35        28.37         2.50 

$`3P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-UD-AAC4 
       42.81        12.66        62.99        20.71        31.20        23.64 
TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3T TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F 
       27.06        56.38        13.61        48.99         4.67        17.62 
TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ 
       38.01        28.27        24.36        17.95         5.52         8.02 
TCGA-LK-A4O2 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.87        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        77.56 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       68.71         0.66        28.96        13.61         2.56         9.76 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
       15.09        14.76        24.07        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       41.46        18.51        22.65        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       11.77        10.78        15.42        27.72         6.48        25.94 
TCGA-UD-AAC5 TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
        8.32        14.27         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        2.76         8.58         7.50        16.41        40.37        32.12 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       43.04         2.76 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             2.50              0.66 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            38.40             91.73 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           14.990            17.475 
[1] "2.5 - 38.4 (15.0)" "0.7 - 91.7 (17.5)"
[1] "hr=" "1.3"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         0        2        0        3        11        1
  3P GAIN WILD-TYPE       7        0        1       13        34       15
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                2                 0
  STAGE IB                0                 1
  STAGE II                3                13
  STAGE III              11                34
  STAGE IV                1                15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3P GAIN MUTATED    3  3  9  1
  3P GAIN WILD-TYPE 11 23 23 12
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               3                11
  T2               3                23
  T3               9                23
  T4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  3P GAIN MUTATED    9  1     7
  3P GAIN WILD-TYPE 35  9    22
D5V5, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0                  9                35
  N1                  1                 9
  N2+N3               7                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"
D5V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   14  0
  3P GAIN WILD-TYPE 43  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     14    0
  3P GAIN WILD-TYPE   43    3
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              14                43
  1               0                 3
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    4 13
  3P GAIN WILD-TYPE 12 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4   13
  3P GAIN WILD-TYPE   12   58
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               4                12
  MALE                13                58
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   11  6
  3P GAIN WILD-TYPE 51 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     11    6
  3P GAIN WILD-TYPE   51   18
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               11                51
  YES               6                18
[1] 2 2
[1] FALSE
D5V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  3P GAIN MUTATED                       4                                    0
  3P GAIN WILD-TYPE                    19                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  3P GAIN MUTATED                         12                        1
  3P GAIN WILD-TYPE                       45                        1
D5V10, multiclass
                                      clus
vv                                     3P GAIN MUTATED 3P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              4                19
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                          12                45
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  3P GAIN MUTATED    3  1  6  2
  3P GAIN WILD-TYPE 14  2  9  9
D5V11, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0               3                14
  R1               1                 2
  R2               6                 9
  RX               2                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    2 17
  3Q GAIN WILD-TYPE 10 56
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               19                66 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               17                56 
$`3Q GAIN MUTATED`
TCGA-SC-AA5Z TCGA-TS-A8AS TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4O0 
       21.83        26.14        11.87        29.10        27.16         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A6BS TCGA-SC-A6LR TCGA-SH-A7BC 
        1.87        12.72        14.73        19.99        38.40        23.90 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7P6 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        7.99        14.76         9.30        14.99        13.35        28.37 
TCGA-UT-A88G 
        2.50 

$`3Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-UD-AAC4 
       42.81        12.66        62.99        20.71        31.20        23.64 
TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3T TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F 
       27.06        56.38        13.61        48.99         4.67        17.62 
TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ 
       38.01        28.27        24.36        17.95         5.52         8.02 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        77.56        68.71 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BD 
        0.66        28.96        13.61         2.56         9.76        15.09 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       24.07        55.07         8.38        27.75        41.46        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
       22.65        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UT-A88E 
       15.42        27.72         6.48        25.94         8.32        14.27 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO 
        4.73         4.67         1.28         4.37         2.76         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        40.37        32.12        43.04         2.76 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             1.87              0.66 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            38.40             91.73 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           14.760            17.785 
[1] "1.9 - 38.4 (14.8)" "0.7 - 91.7 (17.8)"
[1] "hr=" "1.4"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED         0        2        0        4        12        1
  3Q GAIN WILD-TYPE       7        0        1       12        33       15
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                2                 0
  STAGE IB                0                 1
  STAGE II                4                12
  STAGE III              12                33
  STAGE IV                1                15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED    3  4 10  1
  3Q GAIN WILD-TYPE 11 22 22 12
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               3                11
  T2               4                22
  T3              10                22
  T4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  3Q GAIN MUTATED   11  1     7
  3Q GAIN WILD-TYPE 33  9    22
D6V5, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0                 11                33
  N1                  1                 9
  N2+N3               7                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"
D6V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   16  0
  3Q GAIN WILD-TYPE 41  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     16    0
  3Q GAIN WILD-TYPE   41    3
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              16                41
  1               0                 3
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    5 14
  3Q GAIN WILD-TYPE 11 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5   14
  3Q GAIN WILD-TYPE   11   57
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               5                11
  MALE                14                57
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   13  6
  3Q GAIN WILD-TYPE 49 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     13    6
  3Q GAIN WILD-TYPE   49   18
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               13                49
  YES               6                18
[1] 2 2
[1] FALSE
D6V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  3Q GAIN MUTATED                       4                                    0
  3Q GAIN WILD-TYPE                    19                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  3Q GAIN MUTATED                         14                        1
  3Q GAIN WILD-TYPE                       43                        1
D6V10, multiclass
                                      clus
vv                                     3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              4                19
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                          14                43
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  3Q GAIN MUTATED    3  1  7  2
  3Q GAIN WILD-TYPE 14  2  8  9
D6V11, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0               3                14
  R1               1                 2
  R2               7                 8
  RX               2                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 5P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    6 17
  5P GAIN WILD-TYPE  6 56
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               23                62 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               17                56 
$`5P GAIN MUTATED`
TCGA-3U-A98E TCGA-SC-AA5Z TCGA-3H-AB3U TCGA-3U-A98D TCGA-3U-A98I TCGA-LK-A4NW 
       62.99        21.83        27.16         4.67        28.27        17.95 
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O7 TCGA-MQ-A4LP TCGA-MQ-A6BR TCGA-MQ-A6BS 
        6.08         1.87        11.51        17.33        68.71        19.99 
TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P1 TCGA-UD-AABZ 
        2.56        38.40         7.99        24.07        18.51         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-YS-A95C TCGA-ZN-A9VO TCGA-ZN-A9VP 
       25.94         8.32         4.37         8.58         7.50 

$`5P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS TCGA-UD-AAC4 
       42.81        12.66        20.71        31.20        26.14        23.64 
TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T TCGA-3H-AB3X 
       27.06        56.38        11.87        29.10        13.61        48.99 
TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O5 
       17.62        38.01        24.36         5.52         8.02        12.72 
TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       14.73        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SC-A6LM 
        3.52        10.95        24.89        77.56         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU 
       13.61         9.76        23.90        15.09        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
        8.38        27.75        41.46        22.65         9.30        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY 
       15.02        32.28        11.77        10.78        15.42        27.72 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       14.99        13.35        28.37        14.27         2.50         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        4.67         1.28         2.76        16.41        40.37        32.12 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       43.04         2.76 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             1.87              0.66 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            68.71             91.73 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           17.330            17.015 
[1] "1.9 - 68.7 (17.3)" "0.7 - 91.7 (17.0)"
[1] "hr=" "1"  
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  5P GAIN MUTATED         2        1        0        4        11        6
  5P GAIN WILD-TYPE       5        1        1       12        34       10
D7V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 2                 5
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                4                12
  STAGE III              11                34
  STAGE IV                6                10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5P GAIN MUTATED    6  6  6  6
  5P GAIN WILD-TYPE  8 20 26  7
D7V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               6                 8
  T2               6                20
  T3               6                26
  T4               6                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  5P GAIN MUTATED   10  2    11
  5P GAIN WILD-TYPE 34  8    18
D7V5, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0                 10                34
  N1                  2                 8
  N2+N3              11                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"
D7V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   19  1
  5P GAIN WILD-TYPE 38  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     19    1
  5P GAIN WILD-TYPE   38    2
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              19                38
  1               1                 2
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    5 19
  5P GAIN WILD-TYPE 11 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      5   19
  5P GAIN WILD-TYPE   11   52
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               5                11
  MALE                19                52
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   16  7
  5P GAIN WILD-TYPE 46 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     16    7
  5P GAIN WILD-TYPE   46   17
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               16                46
  YES               7                17
[1] 2 2
[1] FALSE
D7V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  5P GAIN MUTATED                       5                                    1
  5P GAIN WILD-TYPE                    18                                    4
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  5P GAIN MUTATED                         17                        1
  5P GAIN WILD-TYPE                       40                        1
D7V10, multiclass
                                      clus
vv                                     5P GAIN MUTATED 5P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              5                18
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               1                 4
  EPITHELIOID MESOTHELIOMA                          17                40
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED    5  0  5  6
  5P GAIN WILD-TYPE 12  3 10  5
D7V11, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0               5                12
  R1               0                 3
  R2               5                10
  RX               6                 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"

Clustering(8) Variable = 5Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    5  9
  5Q GAIN WILD-TYPE  7 64
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               14                71 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9                64 
$`5Q GAIN MUTATED`
TCGA-3U-A98E TCGA-SC-AA5Z TCGA-3U-A98D TCGA-LK-A4O0 TCGA-MQ-A6BR TCGA-MQ-A6BS 
       62.99        21.83         4.67         6.08        68.71        19.99 
TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SH-A7BH TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 
        2.56        38.40         7.99         6.48        25.94         8.32 
TCGA-YS-A95C TCGA-ZN-A9VP 
        4.37         7.50 

$`5Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS TCGA-UD-AAC4 
       42.81        12.66        20.71        31.20        26.14        23.64 
TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T TCGA-3H-AB3U 
       27.06        56.38        11.87        29.10        13.61        27.16 
TCGA-3H-AB3X TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW 
       48.99        17.62        38.01        28.27        24.36        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
        5.52         8.02         1.87        12.72        14.73        11.51 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       80.84        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SC-A6LM 
        3.52        10.95        24.89        77.56         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU 
       13.61         9.76        23.90        15.09        14.76        24.07 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E 
       15.42        27.72        14.99        13.35        28.37        14.27 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VO 
        2.50         4.73         4.67         1.28         2.76         8.58 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       16.41        40.37        32.12        43.04         2.76 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             2.56              0.66 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            68.71             91.73 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            8.155            17.620 
[1] "2.6 - 68.7 (8.2)"  "0.7 - 91.7 (17.6)"
[1] "hr=" "1.2"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED         1        1        0        3         7        2
  5Q GAIN WILD-TYPE       6        1        1       13        38       14
D8V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 1                 6
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                3                13
  STAGE III               7                38
  STAGE IV                2                14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5Q GAIN MUTATED    5  5  2  2
  5Q GAIN WILD-TYPE  9 21 30 11
D8V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               5                 9
  T2               5                21
  T3               2                30
  T4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  5Q GAIN MUTATED    6  1     7
  5Q GAIN WILD-TYPE 38  9    22
D8V5, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0                  6                38
  N1                  1                 9
  N2+N3               7                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"
D8V6, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   11  0
  5Q GAIN WILD-TYPE 46  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11    0
  5Q GAIN WILD-TYPE   46    3
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              11                46
  1               0                 3
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    4 10
  5Q GAIN WILD-TYPE 12 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4   10
  5Q GAIN WILD-TYPE   12   61
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               4                12
  MALE                10                61
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    9  5
  5Q GAIN WILD-TYPE 53 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      9    5
  5Q GAIN WILD-TYPE   53   19
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                9                53
  YES               5                19
[1] 2 2
[1] FALSE
D8V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  5Q GAIN MUTATED                       3                                    0
  5Q GAIN WILD-TYPE                    20                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  5Q GAIN MUTATED                         10                        1
  5Q GAIN WILD-TYPE                       47                        1
D8V10, multiclass
                                      clus
vv                                     5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              3                20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                          10                47
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  5Q GAIN MUTATED    3  0  4  4
  5Q GAIN WILD-TYPE 14  3 11  7
D8V11, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0               3                14
  R1               0                 3
  R2               4                11
  RX               4                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = 6P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    3  4
  6P GAIN WILD-TYPE  9 69
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7                78 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                69 
$`6P GAIN MUTATED`
TCGA-3U-A98E TCGA-SC-AA5Z TCGA-3H-AB3M TCGA-MQ-A6BS TCGA-SC-A6LR TCGA-SH-A9CU 
       62.99        21.83        29.10        19.99        38.40        24.07 
TCGA-UD-AAC6 
       14.99 

$`6P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS TCGA-UD-AAC4 
       42.81        12.66        20.71        31.20        26.14        23.64 
TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X 
       27.06        56.38        11.87        13.61        27.16        48.99 
TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW 
        4.67        17.62        38.01        28.27        24.36        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        77.56        68.71 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BC 
        0.66        28.96        13.61         2.56         9.76        23.90 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
       15.09         7.99        14.76        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       41.46        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       32.28        11.77        10.78        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G 
       25.94         8.32        13.35        28.37        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO 
        4.73         4.67         1.28         4.37         2.76         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        40.37        32.12        43.04         2.76 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            14.99              0.66 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            62.99             91.73 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           24.070            15.255 
[1] "15.0 - 63.0 (24.1)" "0.7 - 91.7 (15.3)" 
[1] "hr=" "2.3"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         0        0        0        2         2        3
  6P GAIN WILD-TYPE       7        2        1       14        43       13
D9V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                2                14
  STAGE III               2                43
  STAGE IV                3                13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6P GAIN MUTATED    1  2  1  3
  6P GAIN WILD-TYPE 13 24 31 10
D9V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               1                13
  T2               2                24
  T3               1                31
  T4               3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  6P GAIN MUTATED    2  0     5
  6P GAIN WILD-TYPE 42 10    24
D9V5, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0                  2                42
  N1                  0                10
  N2+N3               5                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    6  0
  6P GAIN WILD-TYPE 51  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6    0
  6P GAIN WILD-TYPE   51    3
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               6                51
  1               0                 3
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    2  5
  6P GAIN WILD-TYPE 14 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    5
  6P GAIN WILD-TYPE   14   66
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               2                14
  MALE                 5                66
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    4  3
  6P GAIN WILD-TYPE 58 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4    3
  6P GAIN WILD-TYPE   58   21
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                4                58
  YES               3                21
[1] 2 2
[1] FALSE
D9V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  6P GAIN MUTATED                       1                                    0
  6P GAIN WILD-TYPE                    22                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  6P GAIN MUTATED                          6                        0
  6P GAIN WILD-TYPE                       51                        2
D9V10, multiclass
                                      clus
vv                                     6P GAIN MUTATED 6P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              1                22
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           6                51
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  6P GAIN MUTATED    1  0  3  1
  6P GAIN WILD-TYPE 16  3 12 10
D9V11, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0               1                16
  R1               0                 3
  R2               3                12
  RX               1                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = 6Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    1  3
  6Q GAIN WILD-TYPE 11 70
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                81 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                70 
$`6Q GAIN MUTATED`
TCGA-SC-AA5Z TCGA-MQ-A6BS TCGA-SH-A9CU TCGA-UD-AAC6 
       21.83        19.99        24.07        14.99 

$`6Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       23.64        27.06        56.38        11.87        29.10        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I 
       27.16        48.99         4.67        17.62        38.01        28.27 
TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       24.36        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       77.56        68.71         0.66        28.96        13.61         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
        9.76        38.40        23.90        15.09         7.99        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC7 
       15.42        27.72         6.48        25.94         8.32        13.35 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       28.37        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.37         2.76         8.58         7.50        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            14.99              0.66 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            24.07             91.73 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            20.91             16.41 
[1] "15.0 - 24.1 (20.9)" "0.7 - 91.7 (16.4)" 
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         0        0        0        2         0        2
  6Q GAIN WILD-TYPE       7        2        1       14        45       14
D10V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                2                14
  STAGE III               0                45
  STAGE IV                2                14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6Q GAIN MUTATED    0  2  0  2
  6Q GAIN WILD-TYPE 14 24 32 11
D10V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               0                14
  T2               2                24
  T3               0                32
  T4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  6Q GAIN MUTATED    2  0     2
  6Q GAIN WILD-TYPE 42 10    27
D10V5, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0                  2                42
  N1                  0                10
  N2+N3               2                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    3  0
  6Q GAIN WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    0
  6Q GAIN WILD-TYPE   54    3
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    0  4
  6Q GAIN WILD-TYPE 16 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    4
  6Q GAIN WILD-TYPE   16   67
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               0                16
  MALE                 4                67
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    2  2
  6Q GAIN WILD-TYPE 60 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2    2
  6Q GAIN WILD-TYPE   60   22
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                2                60
  YES               2                22
[1] 2 2
[1] FALSE
D10V9, continuous
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                16 
       TCGA-3U-A98E        TCGA-UT-A88D        TCGA-3U-A98J        TCGA-SC-A6LM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SC-A6LP        TCGA-SC-A6LR        TCGA-SH-A7BH 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-SH-A9CT        TCGA-UT-A88C        TCGA-XT-AASU        TCGA-ZN-A9VO 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ZN-A9VP        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  6Q GAIN MUTATED                       1                                    0
  6Q GAIN WILD-TYPE                    22                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  6Q GAIN MUTATED                          3                        0
  6Q GAIN WILD-TYPE                       54                        2
D10V10, multiclass
                                      clus
vv                                     6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              1                22
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           3                54
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  6Q GAIN MUTATED    1  0  2  1
  6Q GAIN WILD-TYPE 16  3 13 10
D10V11, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0               1                16
  R1               0                 3
  R2               2                13
  RX               1                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = 7P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED    3 21
  7P GAIN WILD-TYPE  9 52
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               24                61 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               21                52 
$`7P GAIN MUTATED`
TCGA-SC-AA5Z TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3U TCGA-3U-A98D TCGA-3U-A98H 
       21.83        11.87        29.10        27.16         4.67        38.01 
TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-MQ-A6BS TCGA-SC-A6LQ TCGA-SC-A6LR 
       17.95         6.08         1.87        19.99         9.76        38.40 
TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A8AF TCGA-UD-AAC1 
       23.90         7.99        24.07        41.46        11.77        25.94 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G TCGA-YS-A95C TCGA-ZN-A9VP 
       14.99        13.35        28.37         2.50         4.37         7.50 

$`7P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3T TCGA-3H-AB3X TCGA-3U-A98F 
       23.64        27.06        56.38        13.61        48.99        17.62 
TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O5 TCGA-LK-A4O6 
       28.27        24.36         5.52         8.02        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        77.56        68.71 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SH-A7BD TCGA-SH-A9CT 
        0.66        28.96        13.61         2.56        15.09        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
       55.07         8.38        27.75        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY 
       19.43        15.02        32.28        10.78        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
        6.48         8.32        14.27         4.73         4.67         1.28 
TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV 
        2.76         8.58        16.41        40.37        32.12        43.04 
TCGA-ZN-A9VW 
        2.76 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             1.87              0.66 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            41.46             91.73 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            16.47             17.33 
[1] "1.9 - 41.5 (16.5)" "0.7 - 91.7 (17.3)"
[1] "hr=" "1.3"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  7P GAIN MUTATED         0        1        0        4        16        4
  7P GAIN WILD-TYPE       7        1        1       12        29       12
D11V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                4                12
  STAGE III              16                29
  STAGE IV                4                12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED    3  7 10  4
  7P GAIN WILD-TYPE 11 19 22  9
D11V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               3                11
  T2               7                19
  T3              10                22
  T4               4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  7P GAIN MUTATED    9  0    15
  7P GAIN WILD-TYPE 35 10    14
D11V5, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0                  9                35
  N1                  0                10
  N2+N3              15                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"
D11V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   21  0
  7P GAIN WILD-TYPE 36  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     21    0
  7P GAIN WILD-TYPE   36    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              21                36
  1               0                 3
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    5 20
  7P GAIN WILD-TYPE 11 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5   20
  7P GAIN WILD-TYPE   11   51
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               5                11
  MALE                20                51
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   17  7
  7P GAIN WILD-TYPE 45 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     17    7
  7P GAIN WILD-TYPE   45   17
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               17                45
  YES               7                17
[1] 2 2
[1] FALSE
D11V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  7P GAIN MUTATED                       5                                    1
  7P GAIN WILD-TYPE                    18                                    4
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  7P GAIN MUTATED                         18                        1
  7P GAIN WILD-TYPE                       39                        1
D11V10, multiclass
                                      clus
vv                                     7P GAIN MUTATED 7P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              5                18
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               1                 4
  EPITHELIOID MESOTHELIOMA                          18                39
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED    6  0  8  3
  7P GAIN WILD-TYPE 11  3  7  8
D11V11, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0               6                11
  R1               0                 3
  R2               8                 7
  RX               3                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = 7Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED    3 19
  7Q GAIN WILD-TYPE  9 54
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               22                63 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               19                54 
$`7Q GAIN MUTATED`
TCGA-SC-AA5Z TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3U TCGA-3U-A98D TCGA-3U-A98H 
       21.83        11.87        29.10        27.16         4.67        38.01 
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-MQ-A6BS TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC 
       17.95         1.87        19.99         9.76        38.40        23.90 
TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A8AF TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UD-AAC7 
        7.99        24.07        11.77        25.94        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88G TCGA-YS-A95C TCGA-ZN-A9VP 
       28.37         2.50         4.37         7.50 

$`7Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3T TCGA-3H-AB3X TCGA-3U-A98F 
       23.64        27.06        56.38        13.61        48.99        17.62 
TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O5 
       28.27        24.36         5.52         8.02         6.08        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        77.56 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SH-A7BD 
       68.71         0.66        28.96        13.61         2.56        15.09 
TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       14.76        55.07         8.38        27.75        41.46        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI 
       22.65         9.30        19.43        15.02        32.28        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UT-A88E TCGA-UT-A97Y 
       15.42        27.72         6.48         8.32        14.27         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.67         1.28         2.76         8.58        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             1.87              0.66 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            38.40             91.73 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            16.47             17.33 
[1] "1.9 - 38.4 (16.5)" "0.7 - 91.7 (17.3)"
[1] "hr=" "1.3"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED         0        0        0        3        15        4
  7Q GAIN WILD-TYPE       7        2        1       13        30       12
D12V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                3                13
  STAGE III              15                30
  STAGE IV                4                12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7Q GAIN MUTATED    2  6  9  4
  7Q GAIN WILD-TYPE 12 20 23  9
D12V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               2                12
  T2               6                20
  T3               9                23
  T4               4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  7Q GAIN MUTATED    7  0    15
  7Q GAIN WILD-TYPE 37 10    14
D12V5, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0                  7                37
  N1                  0                10
  N2+N3              15                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"
D12V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   19  0
  7Q GAIN WILD-TYPE 38  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     19    0
  7Q GAIN WILD-TYPE   38    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              19                38
  1               0                 3
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    5 17
  7Q GAIN WILD-TYPE 11 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5   17
  7Q GAIN WILD-TYPE   11   54
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               5                11
  MALE                17                54
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   15  7
  7Q GAIN WILD-TYPE 47 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     15    7
  7Q GAIN WILD-TYPE   47   17
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               15                47
  YES               7                17
[1] 2 2
[1] FALSE
D12V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  7Q GAIN MUTATED                       5                                    1
  7Q GAIN WILD-TYPE                    18                                    4
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  7Q GAIN MUTATED                         16                        0
  7Q GAIN WILD-TYPE                       41                        2
D12V10, multiclass
                                      clus
vv                                     7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              5                18
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               1                 4
  EPITHELIOID MESOTHELIOMA                          16                41
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  7Q GAIN MUTATED    4  0  8  3
  7Q GAIN WILD-TYPE 13  3  7  8
D12V11, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0               4                13
  R1               0                 3
  R2               8                 7
  RX               3                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 8P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    2 10
  8P GAIN WILD-TYPE 10 63
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                73 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               10                63 
$`8P GAIN MUTATED`
TCGA-3H-AB3U TCGA-LK-A4NW TCGA-MQ-A4LM TCGA-SC-A6LR TCGA-SH-A7BH TCGA-TS-A7P0 
       27.16        17.95         5.19        38.40         7.99        41.46 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G TCGA-XT-AASU TCGA-ZN-A9VP TCGA-ZN-A9VW 
       13.35        28.37         2.50         4.67         7.50         2.76 

$`8P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I 
       13.61        48.99         4.67        17.62        38.01        28.27 
TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       24.36         5.52         8.02         6.08         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        77.56        68.71 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       19.99         0.66        28.96        13.61         2.56         9.76 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       23.90        15.09        14.76        24.07        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       27.75        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       32.28        11.77        10.78        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88E TCGA-UT-A97Y TCGA-YS-A95B 
       25.94         8.32        14.99        14.27         4.73         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        4.37         2.76         8.58        16.41        40.37        32.12 
TCGA-ZN-A9VV 
       43.04 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             2.50              0.66 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            41.46             91.73 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            10.67             17.62 
[1] "2.5 - 41.5 (10.7)" "0.7 - 91.7 (17.6)"
[1] "hr=" "1.3"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         0        0        0        1         9        2
  8P GAIN WILD-TYPE       7        2        1       15        36       14
D13V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               9                36
  STAGE IV                2                14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8P GAIN MUTATED    1  1  8  2
  8P GAIN WILD-TYPE 13 25 24 11
D13V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               1                13
  T2               1                25
  T3               8                24
  T4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  8P GAIN MUTATED    7  0     4
  8P GAIN WILD-TYPE 37 10    25
D13V5, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0                  7                37
  N1                  0                10
  N2+N3               4                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"
D13V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    8  0
  8P GAIN WILD-TYPE 49  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      8    0
  8P GAIN WILD-TYPE   49    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               8                49
  1               0                 3
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    1 11
  8P GAIN WILD-TYPE 15 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   11
  8P GAIN WILD-TYPE   15   60
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               1                15
  MALE                11                60
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    9  3
  8P GAIN WILD-TYPE 53 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9    3
  8P GAIN WILD-TYPE   53   21
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                9                53
  YES               3                21
[1] 2 2
[1] FALSE
D13V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  8P GAIN MUTATED                       5                                    1
  8P GAIN WILD-TYPE                    18                                    4
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  8P GAIN MUTATED                          6                        0
  8P GAIN WILD-TYPE                       51                        2
D13V10, multiclass
                                      clus
vv                                     8P GAIN MUTATED 8P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              5                18
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               1                 4
  EPITHELIOID MESOTHELIOMA                           6                51
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  8P GAIN MUTATED    2  0  3  2
  8P GAIN WILD-TYPE 15  3 12  9
D13V11, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0               2                15
  R1               0                 3
  R2               3                12
  RX               2                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 8Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED    3 11
  8Q GAIN WILD-TYPE  9 62
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               14                71 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               11                62 
$`8Q GAIN MUTATED`
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98J TCGA-LK-A4NW TCGA-MQ-A4LM TCGA-NQ-A57I 
       27.16        48.99        24.36        17.95         5.19         0.66 
TCGA-SC-A6LR TCGA-SH-A7BH TCGA-TS-A7P0 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       38.40         7.99        41.46        13.35        28.37         2.50 
TCGA-XT-AASU TCGA-ZN-A9VO 
        4.67         8.58 

$`8Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-LK-A4NY 
       13.61         4.67        17.62        38.01        28.27         5.52 
TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
        8.02         6.08         1.87        12.72        14.73        11.51 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV 
       80.84        91.73        18.81        23.31        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM 
       10.95        24.89        77.56        68.71        19.99        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT 
       13.61         2.56         9.76        23.90        15.09        14.76 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 
       24.07        55.07         8.38        27.75        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 
       15.42        27.72         6.48        25.94         8.32        14.99 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VP 
       14.27         4.73         1.28         4.37         2.76         7.50 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       16.41        40.37        32.12        43.04         2.76 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.66              1.28 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            48.99             91.73 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            15.65             17.33 
[1] "0.7 - 49.0 (15.6)" "1.3 - 91.7 (17.3)"
[1] "hr=" "1"  
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         0        0        1        1        10        2
  8Q GAIN WILD-TYPE       7        2        0       15        35       14
D14V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                1                 0
  STAGE II                1                15
  STAGE III              10                35
  STAGE IV                2                14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED    2  1  9  2
  8Q GAIN WILD-TYPE 12 25 23 11
D14V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               2                12
  T2               1                25
  T3               9                23
  T4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  8Q GAIN MUTATED    7  0     5
  8Q GAIN WILD-TYPE 37 10    24
D14V5, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0                  7                37
  N1                  0                10
  N2+N3               5                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   10  1
  8Q GAIN WILD-TYPE 47  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     10    1
  8Q GAIN WILD-TYPE   47    2
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              10                47
  1               1                 2
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    1 13
  8Q GAIN WILD-TYPE 15 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   13
  8Q GAIN WILD-TYPE   15   58
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               1                15
  MALE                13                58
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    9  5
  8Q GAIN WILD-TYPE 53 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      9    5
  8Q GAIN WILD-TYPE   53   19
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                9                53
  YES               5                19
[1] 2 2
[1] FALSE
D14V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  8Q GAIN MUTATED                       5                                    1
  8Q GAIN WILD-TYPE                    18                                    4
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  8Q GAIN MUTATED                          8                        0
  8Q GAIN WILD-TYPE                       49                        2
D14V10, multiclass
                                      clus
vv                                     8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              5                18
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               1                 4
  EPITHELIOID MESOTHELIOMA                           8                49
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  8Q GAIN MUTATED    2  0  4  2
  8Q GAIN WILD-TYPE 15  3 11  9
D14V11, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0               2                15
  R1               0                 3
  R2               4                11
  RX               2                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 9Q GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    0  3
  9Q GAIN WILD-TYPE 12 70
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                82 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                70 
$`9Q GAIN MUTATED`
TCGA-TS-A8AF TCGA-UD-AAC5 TCGA-ZN-A9VW 
       11.77         8.32         2.76 

$`9Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H 
       13.61        27.16        48.99         4.67        17.62        38.01 
TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 
       28.27        24.36        17.95         5.52         8.02         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        1.87        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
       24.89        77.56        68.71        19.99         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD 
       13.61         2.56         9.76        38.40        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
        7.99        14.76        24.07        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       41.46        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       32.28        10.78        15.42        27.72         6.48        25.94 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       14.99        13.35        28.37        14.27         2.50         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP 
        4.67         1.28         4.37         2.76         8.58         7.50 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV 
       16.41        40.37        32.12        43.04 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             2.76              0.66 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            11.77             91.73 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            8.320            17.785 
[1] "2.8 - 11.8 (8.3)"  "0.7 - 91.7 (17.8)"
[1] "hr=" "4.8"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         1        0        0        0         1        1
  9Q GAIN WILD-TYPE       6        2        1       16        44       15
D15V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 1                 6
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                0                16
  STAGE III               1                44
  STAGE IV                1                15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9Q GAIN MUTATED    1  1  0  1
  9Q GAIN WILD-TYPE 13 25 32 12
D15V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               1                13
  T2               1                25
  T3               0                32
  T4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  9Q GAIN MUTATED    2  0     1
  9Q GAIN WILD-TYPE 42 10    28
D15V5, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0                  2                42
  N1                  0                10
  N2+N3               1                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    1  0
  9Q GAIN WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1    0
  9Q GAIN WILD-TYPE   56    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               1                56
  1               0                 3
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    0  3
  9Q GAIN WILD-TYPE 16 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    3
  9Q GAIN WILD-TYPE   16   68
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               0                16
  MALE                 3                68
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    2  1
  9Q GAIN WILD-TYPE 60 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    1
  9Q GAIN WILD-TYPE   60   23
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                2                60
  YES               1                23
[1] 2 2
[1] FALSE
D15V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  9Q GAIN MUTATED                       1                                    0
  9Q GAIN WILD-TYPE                    22                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  9Q GAIN MUTATED                          2                        0
  9Q GAIN WILD-TYPE                       55                        2
D15V10, multiclass
                                      clus
vv                                     9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              1                22
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           2                55
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  9Q GAIN MUTATED    0  0  0  1
  9Q GAIN WILD-TYPE 17  3 15 10
D15V11, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                45 
       TCGA-3U-A98G        TCGA-LK-A4O4        TCGA-SC-AA5Z        TCGA-UD-AAC4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-UT-A88D        TCGA-LK-A4NW        TCGA-LK-A4NY        TCGA-LK-A4NZ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-LK-A4O0        TCGA-LK-A4O2        TCGA-LK-A4O5        TCGA-LK-A4O6 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-LK-A4O7        TCGA-MQ-A4KX        TCGA-MQ-A4LC        TCGA-MQ-A4LI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-MQ-A4LV        TCGA-MQ-A6BN        TCGA-MQ-A6BQ        TCGA-MQ-A6BR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-MQ-A6BS        TCGA-NQ-A57I        TCGA-NQ-A638        TCGA-SC-A6LM 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SC-A6LP        TCGA-SC-A6LQ        TCGA-SC-A6LR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-SH-A7BC        TCGA-SH-A7BD        TCGA-SH-A7BH        TCGA-SH-A9CU 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-UD-AABY        TCGA-UD-AABZ        TCGA-UD-AAC1        TCGA-UD-AAC6 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-UD-AAC7        TCGA-UT-A88C        TCGA-UT-A88E        TCGA-UT-A88G 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-UT-A97Y        TCGA-XT-AASU        TCGA-YS-A95B        TCGA-YS-A95C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-YS-AA4M 
"9Q GAIN WILD-TYPE" 

Clustering(16) Variable = 10P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    1  2
  10P GAIN WILD-TYPE 11 71
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 82 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 71 
$`10P GAIN MUTATED`
TCGA-SC-AA5Z TCGA-LK-A4O0 TCGA-MQ-A6BN 
       21.83         6.08        24.89 

$`10P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       23.64        27.06        56.38        11.87        29.10        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I 
       27.16        48.99         4.67        17.62        38.01        28.27 
TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 
       24.36        17.95         5.52         8.02         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BQ TCGA-MQ-A6BR 
        5.19        17.33         3.52        10.95        77.56        68.71 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       19.99         0.66        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
       38.40        23.90        15.09         7.99        14.76        24.07 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 
       15.42        27.72         6.48        25.94         8.32        14.99 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       13.35        28.37        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ 
        1.28         4.37         2.76         8.58         7.50        16.41 
TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       40.37        32.12        43.04         2.76 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              6.08               0.66 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             24.89              91.73 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             21.83              16.87 
[1] "6.1 - 24.9 (21.8)" "0.7 - 91.7 (16.9)"
[1] "hr=" "1"  
D16V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         0        1        0        0         1        1
  10P GAIN WILD-TYPE       7        1        1       16        44       15
D16V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 0                 16
  STAGE III                1                 44
  STAGE IV                 1                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10P GAIN MUTATED    1  1  0  1
  10P GAIN WILD-TYPE 13 25 32 12
D16V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                1                 13
  T2                1                 25
  T3                0                 32
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  10P GAIN MUTATED    1  1     1
  10P GAIN WILD-TYPE 43  9    28
D16V5, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                   1                 43
  N1                   1                  9
  N2+N3                1                 28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    2  0
  10P GAIN WILD-TYPE 55  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    0
  10P GAIN WILD-TYPE   55    3
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                2                 55
  1                0                  3
[1] 2 2
[1] FALSE
D16V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    1  2
  10P GAIN WILD-TYPE 15 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    2
  10P GAIN WILD-TYPE   15   69
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                1                 15
  MALE                  2                 69
[1] 2 2
[1] FALSE
D16V8, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    2  1
  10P GAIN WILD-TYPE 60 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    1
  10P GAIN WILD-TYPE   60   23
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 2                 60
  YES                1                 23
[1] 2 2
[1] FALSE
D16V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  10P GAIN MUTATED                       0                                    0
  10P GAIN WILD-TYPE                    23                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  10P GAIN MUTATED                          2                        1
  10P GAIN WILD-TYPE                       55                        1
D16V10, multiclass
                                      clus
vv                                     10P GAIN MUTATED 10P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               0                 23
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            2                 55
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  10P GAIN MUTATED    2  0  1  0
  10P GAIN WILD-TYPE 15  3 14 11
D16V11, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0                2                 15
  R1                0                  3
  R2                1                 14
  RX                0                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 10Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED    1  2
  10Q GAIN WILD-TYPE 11 71
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                 82 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 71 
$`10Q GAIN MUTATED`
TCGA-SC-AA5Z TCGA-LK-A4O0 TCGA-MQ-A6BN 
       21.83         6.08        24.89 

$`10Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       23.64        27.06        56.38        11.87        29.10        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I 
       27.16        48.99         4.67        17.62        38.01        28.27 
TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 
       24.36        17.95         5.52         8.02         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BQ TCGA-MQ-A6BR 
        5.19        17.33         3.52        10.95        77.56        68.71 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       19.99         0.66        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
       38.40        23.90        15.09         7.99        14.76        24.07 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 
       15.42        27.72         6.48        25.94         8.32        14.99 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       13.35        28.37        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ 
        1.28         4.37         2.76         8.58         7.50        16.41 
TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       40.37        32.12        43.04         2.76 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              6.08               0.66 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             24.89              91.73 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             21.83              16.87 
[1] "6.1 - 24.9 (21.8)" "0.7 - 91.7 (16.9)"
[1] "hr=" "1"  
D17V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         0        1        0        0         1        1
  10Q GAIN WILD-TYPE       7        1        1       16        44       15
D17V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 0                 16
  STAGE III                1                 44
  STAGE IV                 1                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10Q GAIN MUTATED    1  1  0  1
  10Q GAIN WILD-TYPE 13 25 32 12
D17V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                1                 13
  T2                1                 25
  T3                0                 32
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  10Q GAIN MUTATED    1  1     1
  10Q GAIN WILD-TYPE 43  9    28
D17V5, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                   1                 43
  N1                   1                  9
  N2+N3                1                 28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    2  0
  10Q GAIN WILD-TYPE 55  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    0
  10Q GAIN WILD-TYPE   55    3
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                2                 55
  1                0                  3
[1] 2 2
[1] FALSE
D17V7, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    1  2
  10Q GAIN WILD-TYPE 15 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    2
  10Q GAIN WILD-TYPE   15   69
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                1                 15
  MALE                  2                 69
[1] 2 2
[1] FALSE
D17V8, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    2  1
  10Q GAIN WILD-TYPE 60 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    1
  10Q GAIN WILD-TYPE   60   23
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 2                 60
  YES                1                 23
[1] 2 2
[1] FALSE
D17V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  10Q GAIN MUTATED                       0                                    0
  10Q GAIN WILD-TYPE                    23                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  10Q GAIN MUTATED                          2                        1
  10Q GAIN WILD-TYPE                       55                        1
D17V10, multiclass
                                      clus
vv                                     10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               0                 23
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            2                 55
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  10Q GAIN MUTATED    2  0  1  0
  10Q GAIN WILD-TYPE 15  3 14 11
D17V11, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0                2                 15
  R1                0                  3
  R2                1                 14
  RX                0                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 11P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    3  8
  11P GAIN WILD-TYPE  9 65
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                11                 74 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                 65 
$`11P GAIN MUTATED`
TCGA-SC-AA5Z TCGA-3H-AB3L TCGA-3H-AB3U TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LQ 
       21.83        11.87        27.16        68.71        19.99         9.76 
TCGA-SC-A6LR TCGA-SH-A9CU TCGA-TS-A7P6 TCGA-TS-A8AF TCGA-UD-AAC7 
       38.40        24.07         9.30        11.77        13.35 

$`11P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3T TCGA-3H-AB3X 
       23.64        27.06        56.38        29.10        13.61        48.99 
TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW 
        4.67        17.62        38.01        28.27        24.36        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I 
       17.33         3.52        10.95        24.89        77.56         0.66 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       28.96        13.61         2.56        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       14.76        55.07         8.38        27.75        41.46        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AY 
       22.65        19.43        15.02        32.28        10.78        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C 
       27.72         6.48        25.94         8.32        14.99        28.37 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       14.27         2.50         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        2.76         8.58         7.50        16.41        40.37        32.12 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       43.04         2.76 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              9.30               0.66 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             68.71              91.73 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             19.99              16.87 
[1] "9.3 - 68.7 (20.0)" "0.7 - 91.7 (16.9)"
[1] "hr=" "1.2"
D18V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         0        0        0        3         7        2
  11P GAIN WILD-TYPE       7        2        1       13        38       14
D18V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 3                 13
  STAGE III                7                 38
  STAGE IV                 2                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11P GAIN MUTATED    2  4  3  2
  11P GAIN WILD-TYPE 12 22 29 11
D18V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                2                 12
  T2                4                 22
  T3                3                 29
  T4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  11P GAIN MUTATED    3  1     7
  11P GAIN WILD-TYPE 41  9    22
D18V5, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                   3                 41
  N1                   1                  9
  N2+N3                7                 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"
D18V6, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    8  0
  11P GAIN WILD-TYPE 49  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      8    0
  11P GAIN WILD-TYPE   49    3
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                8                 49
  1                0                  3
[1] 2 2
[1] FALSE
D18V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    2 10
  11P GAIN WILD-TYPE 14 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   10
  11P GAIN WILD-TYPE   14   61
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 14
  MALE                 10                 61
[1] 2 2
[1] FALSE
D18V8, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    6  5
  11P GAIN WILD-TYPE 56 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6    5
  11P GAIN WILD-TYPE   56   19
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 6                 56
  YES                5                 19
[1] 2 2
[1] FALSE
D18V9, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 15 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SH-A7BH         TCGA-SH-A9CT         TCGA-UT-A88C 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-XT-AASU         TCGA-ZN-A9VO         TCGA-ZN-A9VP 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ZN-A9VQ         TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  11P GAIN MUTATED                       0                                    0
  11P GAIN WILD-TYPE                    23                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  11P GAIN MUTATED                         12                        0
  11P GAIN WILD-TYPE                       45                        2
D18V10, multiclass
                                      clus
vv                                     11P GAIN MUTATED 11P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               0                 23
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                           12                 45
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  11P GAIN MUTATED    3  0  3  2
  11P GAIN WILD-TYPE 14  3 12  9
D18V11, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                3                 14
  R1                0                  3
  R2                3                 12
  RX                2                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = 11Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    4  7
  11Q GAIN WILD-TYPE  8 66
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                11                 74 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                 66 
$`11Q GAIN MUTATED`
TCGA-SC-AA5Z TCGA-3H-AB3L TCGA-3H-AB3U TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LR 
       21.83        11.87        27.16        68.71        19.99        38.40 
TCGA-SH-A9CU TCGA-TS-A7P6 TCGA-TS-A8AF TCGA-UD-AAC7 TCGA-ZN-A9VP 
       24.07         9.30        11.77        13.35         7.50 

$`11Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3T TCGA-3H-AB3X 
       23.64        27.06        56.38        29.10        13.61        48.99 
TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW 
        4.67        17.62        38.01        28.27        24.36        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I 
       17.33         3.52        10.95        24.89        77.56         0.66 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD 
       28.96        13.61         2.56         9.76        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
        7.99        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI 
       18.51        22.65        19.43        15.02        32.28        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 
       15.42        27.72         6.48        25.94         8.32        14.99 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       28.37        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        4.37         2.76         8.58        16.41        40.37        32.12 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       43.04         2.76 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              7.50               0.66 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             68.71              91.73 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             19.99              16.87 
[1] "7.5 - 68.7 (20.0)" "0.7 - 91.7 (16.9)"
[1] "hr=" "1.4"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         0        0        0        3         7        2
  11Q GAIN WILD-TYPE       7        2        1       13        38       14
D19V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 3                 13
  STAGE III                7                 38
  STAGE IV                 2                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11Q GAIN MUTATED    2  4  3  2
  11Q GAIN WILD-TYPE 12 22 29 11
D19V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                2                 12
  T2                4                 22
  T3                3                 29
  T4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  11Q GAIN MUTATED    3  1     7
  11Q GAIN WILD-TYPE 41  9    22
D19V5, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                   3                 41
  N1                   1                  9
  N2+N3                7                 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"
D19V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    7  0
  11Q GAIN WILD-TYPE 50  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      7    0
  11Q GAIN WILD-TYPE   50    3
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                7                 50
  1                0                  3
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    1 11
  11Q GAIN WILD-TYPE 15 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   11
  11Q GAIN WILD-TYPE   15   60
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                1                 15
  MALE                 11                 60
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    7  4
  11Q GAIN WILD-TYPE 55 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      7    4
  11Q GAIN WILD-TYPE   55   20
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 7                 55
  YES                4                 20
[1] 2 2
[1] FALSE
D19V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  11Q GAIN MUTATED                       0                                    0
  11Q GAIN WILD-TYPE                    23                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  11Q GAIN MUTATED                         12                        0
  11Q GAIN WILD-TYPE                       45                        2
D19V10, multiclass
                                      clus
vv                                     11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               0                 23
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                           12                 45
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  11Q GAIN MUTATED    2  0  3  2
  11Q GAIN WILD-TYPE 15  3 12  9
D19V11, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                2                 15
  R1                0                  3
  R2                3                 12
  RX                2                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = 12P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    0 18
  12P GAIN WILD-TYPE 12 55
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                18                 67 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                18                 55 
$`12P GAIN MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       29.10        27.16        17.95         6.08        12.72        80.84 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A9CU TCGA-TS-A7P6 TCGA-TS-A7P7 
       19.99         0.66        23.90        24.07         9.30        19.43 
TCGA-TS-A8AF TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       11.77         8.32        14.99        13.35        28.37         2.50 

$`12P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        11.87        13.61 
TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       48.99         4.67        17.62        38.01        28.27        24.36 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LC 
        5.52         8.02         1.87        14.73        11.51        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       24.89        77.56        68.71        28.96        13.61         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU 
        9.76        38.40        15.09         7.99        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P8 
        8.38        27.75        41.46        18.51        22.65        15.02 
TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       32.28        10.78        15.42        27.72         6.48        25.94 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
       14.27         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV 
        8.58         7.50        16.41        40.37        32.12        43.04 
TCGA-ZN-A9VW 
        2.76 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.66               1.28 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             80.84              91.73 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             16.47              17.33 
[1] "0.7 - 80.8 (16.5)" "1.3 - 91.7 (17.3)"
[1] "hr=" "1.4"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  12P GAIN MUTATED         2        1        1        3         9        2
  12P GAIN WILD-TYPE       5        1        0       13        36       14
D20V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  2                  5
  STAGE IA                 1                  1
  STAGE IB                 1                  0
  STAGE II                 3                 13
  STAGE III                9                 36
  STAGE IV                 2                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12P GAIN MUTATED    4  4  8  2
  12P GAIN WILD-TYPE 10 22 24 11
D20V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                4                 10
  T2                4                 22
  T3                8                 24
  T4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  12P GAIN MUTATED    9  0     8
  12P GAIN WILD-TYPE 35 10    21
D20V5, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                   9                 35
  N1                   0                 10
  N2+N3                8                 21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   13  0
  12P GAIN WILD-TYPE 44  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     13    0
  12P GAIN WILD-TYPE   44    3
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               13                 44
  1                0                  3
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    2 16
  12P GAIN WILD-TYPE 14 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   16
  12P GAIN WILD-TYPE   14   55
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                2                 14
  MALE                 16                 55
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   13  5
  12P GAIN WILD-TYPE 49 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     13    5
  12P GAIN WILD-TYPE   49   19
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                13                 49
  YES                5                 19
[1] 2 2
[1] FALSE
D20V9, continuous
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                 15 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A7BH         TCGA-SH-A9CT 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-XT-AASU         TCGA-ZN-A9VO         TCGA-ZN-A9VP 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ZN-A9VQ         TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  12P GAIN MUTATED                       3                                    1
  12P GAIN WILD-TYPE                    20                                    4
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  12P GAIN MUTATED                         13                        1
  12P GAIN WILD-TYPE                       44                        1
D20V10, multiclass
                                      clus
vv                                     12P GAIN MUTATED 12P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               3                 20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                1                  4
  EPITHELIOID MESOTHELIOMA                           13                 44
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  12P GAIN MUTATED    4  1  4  4
  12P GAIN WILD-TYPE 13  2 11  7
D20V11, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0                4                 13
  R1                1                  2
  R2                4                 11
  RX                4                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = 12Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    0 18
  12Q GAIN WILD-TYPE 12 55
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                 67 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                 55 
$`12Q GAIN MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       29.10        27.16        17.95         6.08        12.72        80.84 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A9CU TCGA-TS-A7P6 TCGA-TS-A7P7 
       19.99         0.66        23.90        24.07         9.30        19.43 
TCGA-TS-A8AF TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       11.77         8.32        14.99        13.35        28.37         2.50 

$`12Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        11.87        13.61 
TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       48.99         4.67        17.62        38.01        28.27        24.36 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LC 
        5.52         8.02         1.87        14.73        11.51        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       24.89        77.56        68.71        28.96        13.61         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU 
        9.76        38.40        15.09         7.99        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P8 
        8.38        27.75        41.46        18.51        22.65        15.02 
TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       32.28        10.78        15.42        27.72         6.48        25.94 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
       14.27         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV 
        8.58         7.50        16.41        40.37        32.12        43.04 
TCGA-ZN-A9VW 
        2.76 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.66               1.28 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             80.84              91.73 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             16.47              17.33 
[1] "0.7 - 80.8 (16.5)" "1.3 - 91.7 (17.3)"
[1] "hr=" "1.4"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED         2        1        1        3         9        2
  12Q GAIN WILD-TYPE       5        1        0       13        36       14
D21V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  2                  5
  STAGE IA                 1                  1
  STAGE IB                 1                  0
  STAGE II                 3                 13
  STAGE III                9                 36
  STAGE IV                 2                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12Q GAIN MUTATED    4  4  8  2
  12Q GAIN WILD-TYPE 10 22 24 11
D21V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                4                 10
  T2                4                 22
  T3                8                 24
  T4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  12Q GAIN MUTATED    9  0     8
  12Q GAIN WILD-TYPE 35 10    21
D21V5, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                   9                 35
  N1                   0                 10
  N2+N3                8                 21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   13  0
  12Q GAIN WILD-TYPE 44  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     13    0
  12Q GAIN WILD-TYPE   44    3
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               13                 44
  1                0                  3
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    2 16
  12Q GAIN WILD-TYPE 14 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   16
  12Q GAIN WILD-TYPE   14   55
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                2                 14
  MALE                 16                 55
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   13  5
  12Q GAIN WILD-TYPE 49 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     13    5
  12Q GAIN WILD-TYPE   49   19
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                13                 49
  YES                5                 19
[1] 2 2
[1] FALSE
D21V9, continuous
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 15 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A7BH         TCGA-SH-A9CT 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-XT-AASU         TCGA-ZN-A9VO         TCGA-ZN-A9VP 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ZN-A9VQ         TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  12Q GAIN MUTATED                       3                                    1
  12Q GAIN WILD-TYPE                    20                                    4
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  12Q GAIN MUTATED                         13                        1
  12Q GAIN WILD-TYPE                       44                        1
D21V10, multiclass
                                      clus
vv                                     12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               3                 20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                1                  4
  EPITHELIOID MESOTHELIOMA                           13                 44
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  12Q GAIN MUTATED    4  1  4  4
  12Q GAIN WILD-TYPE 13  2 11  7
D21V11, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0                4                 13
  R1                1                  2
  R2                4                 11
  RX                4                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 13Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    1  4
  13Q GAIN WILD-TYPE 11 69
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 80 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 4                 69 
$`13Q GAIN MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3X TCGA-3U-A98D TCGA-TS-A7P0 TCGA-TS-A8AF 
       29.10        48.99         4.67        41.46        11.77 

$`13Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        11.87        13.61 
TCGA-3H-AB3U TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW 
       27.16        17.62        38.01        28.27        24.36        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        77.56        68.71 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       19.99         0.66        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
       38.40        23.90        15.09         7.99        14.76        24.07 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
       55.07         8.38        27.75        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY 
       19.43        15.02        32.28        10.78        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        6.48        25.94         8.32        14.99        13.35        28.37 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       14.27         2.50         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        2.76         8.58         7.50        16.41        40.37        32.12 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       43.04         2.76 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              4.67               0.66 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             48.99              91.73 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             29.10              16.87 
[1] "4.7 - 49.0 (29.1)" "0.7 - 91.7 (16.9)"
[1] "hr=" "1.5"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED         0        0        0        0         5        0
  13Q GAIN WILD-TYPE       7        2        1       16        40       16
D22V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 0                 16
  STAGE III                5                 40
  STAGE IV                 0                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  13Q GAIN MUTATED    0  2  3  0
  13Q GAIN WILD-TYPE 14 24 29 13
D22V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                0                 14
  T2                2                 24
  T3                3                 29
  T4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  13Q GAIN MUTATED    2  0     3
  13Q GAIN WILD-TYPE 42 10    26
D22V5, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0                   2                 42
  N1                   0                 10
  N2+N3                3                 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"
D22V6, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    3  0
  13Q GAIN WILD-TYPE 54  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    0
  13Q GAIN WILD-TYPE   54    3
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                3                 54
  1                0                  3
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    1  4
  13Q GAIN WILD-TYPE 15 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1    4
  13Q GAIN WILD-TYPE   15   67
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                1                 15
  MALE                  4                 67
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    4  1
  13Q GAIN WILD-TYPE 58 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    1
  13Q GAIN WILD-TYPE   58   23
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 4                 58
  YES                1                 23
[1] 2 2
[1] FALSE
D22V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  13Q GAIN MUTATED                       1                                    0
  13Q GAIN WILD-TYPE                    22                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  13Q GAIN MUTATED                          4                        0
  13Q GAIN WILD-TYPE                       53                        2
D22V10, multiclass
                                      clus
vv                                     13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               1                 22
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            4                 53
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  13Q GAIN MUTATED    0  0  0  0
  13Q GAIN WILD-TYPE 17  3 15 11
D22V11, multiclass

Clustering(23) Variable = 15Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    2  8
  15Q GAIN WILD-TYPE 10 65
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                 75 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                 65 
$`15Q GAIN MUTATED`
TCGA-3H-AB3M TCGA-LK-A4NY TCGA-SC-A6LN TCGA-SC-A6LR TCGA-TS-A7P0 TCGA-UD-AAC5 
       29.10         5.52        13.61        38.40        41.46         8.32 
TCGA-UT-A88E TCGA-UT-A88G TCGA-YS-A95B TCGA-ZN-A9VP 
       14.27         2.50         1.28         7.50 

$`15Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        11.87        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I 
       27.16        48.99         4.67        17.62        38.01        28.27 
TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       24.36        17.95         8.02         6.08         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        77.56 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ 
       68.71        19.99         0.66        28.96         2.56         9.76 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU 
       23.90        15.09         7.99        14.76        24.07        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
        8.38        27.75        18.51        22.65         9.30        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY 
       15.02        32.28        11.77        10.78        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A97Y 
        6.48        25.94        14.99        13.35        28.37         4.73 
TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.67         4.37         2.76         8.58        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.28               0.66 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             41.46              91.73 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            10.965             17.950 
[1] "1.3 - 41.5 (11.0)" "0.7 - 91.7 (17.9)"
[1] "hr=" "1.2"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED         2        0        0        0         7        1
  15Q GAIN WILD-TYPE       5        2        1       16        38       15
D23V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  2                  5
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 0                 16
  STAGE III                7                 38
  STAGE IV                 1                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  15Q GAIN MUTATED    3  1  5  1
  15Q GAIN WILD-TYPE 11 25 27 12
D23V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                3                 11
  T2                1                 25
  T3                5                 27
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  15Q GAIN MUTATED    5  0     5
  15Q GAIN WILD-TYPE 39 10    24
D23V5, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                   5                 39
  N1                   0                 10
  N2+N3                5                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    8  0
  15Q GAIN WILD-TYPE 49  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      8    0
  15Q GAIN WILD-TYPE   49    3
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                8                 49
  1                0                  3
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    3  7
  15Q GAIN WILD-TYPE 13 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    7
  15Q GAIN WILD-TYPE   13   64
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 13
  MALE                  7                 64
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    7  3
  15Q GAIN WILD-TYPE 55 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      7    3
  15Q GAIN WILD-TYPE   55   21
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 7                 55
  YES                3                 21
[1] 2 2
[1] FALSE
D23V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  15Q GAIN MUTATED                       3                                    0
  15Q GAIN WILD-TYPE                    20                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  15Q GAIN MUTATED                          7                        0
  15Q GAIN WILD-TYPE                       50                        2
D23V10, multiclass
                                      clus
vv                                     15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               3                 20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            7                 50
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  15Q GAIN MUTATED    2  0  2  3
  15Q GAIN WILD-TYPE 15  3 13  8
D23V11, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                2                 15
  R1                0                  3
  R2                2                 13
  RX                3                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = 16P GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    2 14
  16P GAIN WILD-TYPE 10 59
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                 69 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                14                 59 
$`16P GAIN MUTATED`
TCGA-SC-AA5Z TCGA-3H-AB3U TCGA-3U-A98J TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-NQ-A57I 
       21.83        27.16        24.36        18.81        23.31         0.66 
TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A7P6 
       38.40        23.90         7.99        24.07        41.46         9.30 
TCGA-TS-A8AF TCGA-UD-AAC7 TCGA-UT-A88C TCGA-YS-A95C 
       11.77        13.35        28.37         4.37 

$`16P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       23.64        27.06        56.38        11.87        29.10        13.61 
TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-LK-A4NW 
       48.99         4.67        17.62        38.01        28.27        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       11.51        80.84        91.73         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM 
       10.95        24.89        77.56        68.71        19.99        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU 
       13.61         2.56         9.76        15.09        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 
        8.38        27.75        18.51        22.65        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       32.28        10.78        15.42        27.72         6.48        25.94 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
        8.32        14.99        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        1.28         2.76         8.58         7.50        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.66               1.28 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             41.46              91.73 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             22.57              15.42 
[1] "0.7 - 41.5 (22.6)" "1.3 - 91.7 (15.4)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  16P GAIN MUTATED         0        0        1        2        11        2
  16P GAIN WILD-TYPE       7        2        0       14        34       14
D24V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 2                 14
  STAGE III               11                 34
  STAGE IV                 2                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  16P GAIN MUTATED    3  4  7  2
  16P GAIN WILD-TYPE 11 22 25 11
D24V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                3                 11
  T2                4                 22
  T3                7                 25
  T4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  16P GAIN MUTATED    5  1     9
  16P GAIN WILD-TYPE 39  9    20
D24V5, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                   5                 39
  N1                   1                  9
  N2+N3                9                 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"
D24V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   12  0
  16P GAIN WILD-TYPE 45  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     12    0
  16P GAIN WILD-TYPE   45    3
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               12                 45
  1                0                  3
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    2 14
  16P GAIN WILD-TYPE 14 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2   14
  16P GAIN WILD-TYPE   14   57
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                2                 14
  MALE                 14                 57
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   10  6
  16P GAIN WILD-TYPE 52 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     10    6
  16P GAIN WILD-TYPE   52   18
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                10                 52
  YES                6                 18
[1] 2 2
[1] FALSE
D24V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  16P GAIN MUTATED                       2                                    0
  16P GAIN WILD-TYPE                    21                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  16P GAIN MUTATED                         14                        0
  16P GAIN WILD-TYPE                       43                        2
D24V10, multiclass
                                      clus
vv                                     16P GAIN MUTATED 16P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               2                 21
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                           14                 43
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  16P GAIN MUTATED    2  1  6  1
  16P GAIN WILD-TYPE 15  2  9 10
D24V11, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0                2                 15
  R1                1                  2
  R2                6                  9
  RX                1                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 16Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    2 14
  16Q GAIN WILD-TYPE 10 59
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                16                 69 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                14                 59 
$`16Q GAIN MUTATED`
TCGA-SC-AA5Z TCGA-3H-AB3U TCGA-3U-A98J TCGA-LK-A4O2 TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       21.83        27.16        24.36         1.87        18.81        23.31 
TCGA-NQ-A57I TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P0 
        0.66        38.40        23.90         7.99        24.07        41.46 
TCGA-TS-A7P6 TCGA-TS-A8AF TCGA-UD-AAC7 TCGA-UT-A88C 
        9.30        11.77        13.35        28.37 

$`16Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       23.64        27.06        56.38        11.87        29.10        13.61 
TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-LK-A4NW 
       48.99         4.67        17.62        38.01        28.27        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
        5.52         8.02         6.08        12.72        14.73        11.51 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       80.84        91.73         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN 
       24.89        77.56        68.71        19.99        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY 
        2.56         9.76        15.09        14.76        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       27.75        18.51        22.65        19.43        15.02        32.28 
TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 
       10.78        15.42        27.72         6.48        25.94         8.32 
TCGA-UD-AAC6 TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       14.99        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.37         2.76         8.58         7.50        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.66               1.28 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             41.46              91.73 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             22.57              15.42 
[1] "0.7 - 41.5 (22.6)" "1.3 - 91.7 (15.4)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED         0        0        1        2        11        2
  16Q GAIN WILD-TYPE       7        2        0       14        34       14
D25V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 2                 14
  STAGE III               11                 34
  STAGE IV                 2                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  16Q GAIN MUTATED    2  4  8  2
  16Q GAIN WILD-TYPE 12 22 24 11
D25V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                2                 12
  T2                4                 22
  T3                8                 24
  T4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  16Q GAIN MUTATED    6  1     8
  16Q GAIN WILD-TYPE 38  9    21
D25V5, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                   6                 38
  N1                   1                  9
  N2+N3                8                 21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   12  0
  16Q GAIN WILD-TYPE 45  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     12    0
  16Q GAIN WILD-TYPE   45    3
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               12                 45
  1                0                  3
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3 13
  16Q GAIN WILD-TYPE 13 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3   13
  16Q GAIN WILD-TYPE   13   58
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                 13
  MALE                 13                 58
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   10  6
  16Q GAIN WILD-TYPE 52 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     10    6
  16Q GAIN WILD-TYPE   52   18
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                10                 52
  YES                6                 18
[1] 2 2
[1] FALSE
D25V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  16Q GAIN MUTATED                       2                                    0
  16Q GAIN WILD-TYPE                    21                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  16Q GAIN MUTATED                         14                        0
  16Q GAIN WILD-TYPE                       43                        2
D25V10, multiclass
                                      clus
vv                                     16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               2                 21
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                           14                 43
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  16Q GAIN MUTATED    1  1  7  1
  16Q GAIN WILD-TYPE 16  2  8 10
D25V11, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                1                 16
  R1                1                  2
  R2                7                  8
  RX                1                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = 17P GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    0  8
  17P GAIN WILD-TYPE 12 65
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                 77 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                 65 
$`17P GAIN MUTATED`
TCGA-3H-AB3K TCGA-3H-AB3U TCGA-3U-A98I TCGA-LK-A4O0 TCGA-SH-A7BC TCGA-TS-A7P6 
       56.38        27.16        28.27         6.08        23.90         9.30 
TCGA-UD-AAC6 TCGA-UT-A88E 
       14.99        14.27 

$`17P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       26.14        23.64        27.06        11.87        29.10        13.61 
TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NW 
       48.99         4.67        17.62        38.01        24.36        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
        5.52         8.02         1.87        12.72        14.73        11.51 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       80.84        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
        3.52        10.95        24.89        77.56        68.71        19.99 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
        0.66        28.96        13.61         2.56         9.76        38.40 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       15.09         7.99        14.76        24.07        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 
       27.75        41.46        18.51        22.65        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       32.28        11.77        10.78        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G TCGA-UT-A97Y 
       25.94         8.32        13.35        28.37         2.50         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP 
        4.67         1.28         4.37         2.76         8.58         7.50 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       16.41        40.37        32.12        43.04         2.76 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              6.08               0.66 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             56.38              91.73 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            19.445             17.330 
[1] "6.1 - 56.4 (19.4)" "0.7 - 91.7 (17.3)"
[1] "hr=" "1.1"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  17P GAIN MUTATED         1        1        0        2         3        1
  17P GAIN WILD-TYPE       6        1        1       14        42       15
D26V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 2                 14
  STAGE III                3                 42
  STAGE IV                 1                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17P GAIN MUTATED    2  2  3  1
  17P GAIN WILD-TYPE 12 24 29 12
D26V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                2                 12
  T2                2                 24
  T3                3                 29
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  17P GAIN MUTATED    5  0     3
  17P GAIN WILD-TYPE 39 10    26
D26V5, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                   5                 39
  N1                   0                 10
  N2+N3                3                 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"
D26V6, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    7  0
  17P GAIN WILD-TYPE 50  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      7    0
  17P GAIN WILD-TYPE   50    3
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                7                 50
  1                0                  3
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    0  8
  17P GAIN WILD-TYPE 16 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    8
  17P GAIN WILD-TYPE   16   63
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                0                 16
  MALE                  8                 63
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    5  3
  17P GAIN WILD-TYPE 57 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    3
  17P GAIN WILD-TYPE   57   21
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 5                 57
  YES                3                 21
[1] 2 2
[1] FALSE
D26V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  17P GAIN MUTATED                       2                                    1
  17P GAIN WILD-TYPE                    21                                    4
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  17P GAIN MUTATED                          4                        1
  17P GAIN WILD-TYPE                       53                        1
D26V10, multiclass
                                      clus
vv                                     17P GAIN MUTATED 17P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               2                 21
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                1                  4
  EPITHELIOID MESOTHELIOMA                            4                 53
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  17P GAIN MUTATED    1  0  2  1
  17P GAIN WILD-TYPE 16  3 13 10
D26V11, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                1                 16
  R1                0                  3
  R2                2                 13
  RX                1                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = 17Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    1 15
  17Q GAIN WILD-TYPE 11 58
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                 69 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                15                 58 
$`17Q GAIN MUTATED`
TCGA-UD-AAC4 TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3U TCGA-3U-A98I TCGA-LK-A4NW 
       23.64        56.38        29.10        27.16        28.27        17.95 
TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-MQ-A6BS TCGA-SC-A6LR TCGA-SH-A7BC TCGA-TS-A7P6 
        5.52         6.08        19.99        38.40        23.90         9.30 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E 
       14.99        13.35        28.37        14.27 

$`17Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UT-A88D TCGA-3H-AB3L TCGA-3H-AB3T TCGA-3H-AB3X TCGA-3U-A98D 
       26.14        27.06        11.87        13.61        48.99         4.67 
TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 
       17.62        38.01        24.36         8.02         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        77.56 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       68.71         0.66        28.96        13.61         2.56         9.76 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       15.09         7.99        14.76        24.07        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 
       27.75        41.46        18.51        22.65        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       32.28        11.77        10.78        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       25.94         8.32         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.37         2.76         8.58         7.50        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              5.52               0.66 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             56.38              91.73 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            21.815             15.420 
[1] "5.5 - 56.4 (21.8)" "0.7 - 91.7 (15.4)"
[1] "hr=" "1"  
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED         1        1        0        5         8        2
  17Q GAIN WILD-TYPE       6        1        1       11        37       14
D27V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 5                 11
  STAGE III                8                 37
  STAGE IV                 2                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17Q GAIN MUTATED    3  6  6  2
  17Q GAIN WILD-TYPE 11 20 26 11
D27V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                3                 11
  T2                6                 20
  T3                6                 26
  T4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  17Q GAIN MUTATED    8  0     8
  17Q GAIN WILD-TYPE 36 10    21
D27V5, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                   8                 36
  N1                   0                 10
  N2+N3                8                 21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   15  0
  17Q GAIN WILD-TYPE 42  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     15    0
  17Q GAIN WILD-TYPE   42    3
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               15                 42
  1                0                  3
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    2 15
  17Q GAIN WILD-TYPE 14 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2   15
  17Q GAIN WILD-TYPE   14   56
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                2                 14
  MALE                 15                 56
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   10  6
  17Q GAIN WILD-TYPE 52 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     10    6
  17Q GAIN WILD-TYPE   52   18
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                10                 52
  YES                6                 18
[1] 2 2
[1] FALSE
D27V9, continuous
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 15 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-SH-A7BH         TCGA-SH-A9CT         TCGA-SH-A9CU 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-XT-AASU         TCGA-ZN-A9VO         TCGA-ZN-A9VP 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ZN-A9VQ         TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  17Q GAIN MUTATED                       3                                    3
  17Q GAIN WILD-TYPE                    20                                    2
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  17Q GAIN MUTATED                         10                        1
  17Q GAIN WILD-TYPE                       47                        1
D27V10, multiclass
                                      clus
vv                                     17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               3                 20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                3                  2
  EPITHELIOID MESOTHELIOMA                           10                 47
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  17Q GAIN MUTATED    5  0  5  2
  17Q GAIN WILD-TYPE 12  3 10  9
D27V11, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0                5                 12
  R1                0                  3
  R2                5                 10
  RX                2                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = 18P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    0  8
  18P GAIN WILD-TYPE 12 65
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                 77 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                 65 
$`18P GAIN MUTATED`
TCGA-3H-AB3M TCGA-3U-A98D TCGA-LK-A4O0 TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P0 
       29.10         4.67         6.08         7.99        24.07        41.46 
TCGA-TS-A8AF TCGA-UD-AAC7 
       11.77        13.35 

$`18P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        11.87        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       27.16        48.99        17.62        38.01        28.27        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
       17.95         5.52         8.02         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        77.56        68.71 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       19.99         0.66        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY 
       38.40        23.90        15.09        14.76        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       27.75        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       32.28        10.78        15.42        27.72         6.48        25.94 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
        8.32        14.99        28.37        14.27         2.50         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP 
        4.67         1.28         4.37         2.76         8.58         7.50 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       16.41        40.37        32.12        43.04         2.76 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              4.67               0.66 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             41.46              91.73 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             12.56              17.62 
[1] "4.7 - 41.5 (12.6)" "0.7 - 91.7 (17.6)"
[1] "hr=" "1.5"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         0        1        0        1         5        1
  18P GAIN WILD-TYPE       7        1        1       15        40       15
D28V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 1                 15
  STAGE III                5                 40
  STAGE IV                 1                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18P GAIN MUTATED    1  3  3  1
  18P GAIN WILD-TYPE 13 23 29 12
D28V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                1                 13
  T2                3                 23
  T3                3                 29
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  18P GAIN MUTATED    4  0     4
  18P GAIN WILD-TYPE 40 10    25
D28V5, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                   4                 40
  N1                   0                 10
  N2+N3                4                 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"
D28V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    6  0
  18P GAIN WILD-TYPE 51  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6    0
  18P GAIN WILD-TYPE   51    3
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                6                 51
  1                0                  3
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    2  6
  18P GAIN WILD-TYPE 14 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    6
  18P GAIN WILD-TYPE   14   65
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                2                 14
  MALE                  6                 65
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    7  1
  18P GAIN WILD-TYPE 55 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7    1
  18P GAIN WILD-TYPE   55   23
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 7                 55
  YES                1                 23
[1] 2 2
[1] FALSE
D28V9, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 15 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A9CT         TCGA-UT-A88C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-XT-AASU         TCGA-ZN-A9VO         TCGA-ZN-A9VP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ZN-A9VQ         TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  18P GAIN MUTATED                       2                                    0
  18P GAIN WILD-TYPE                    21                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  18P GAIN MUTATED                          5                        1
  18P GAIN WILD-TYPE                       52                        1
D28V10, multiclass
                                      clus
vv                                     18P GAIN MUTATED 18P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               2                 21
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            5                 52
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  18P GAIN MUTATED    1  0  2  1
  18P GAIN WILD-TYPE 16  3 13 10
D28V11, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                1                 16
  R1                0                  3
  R2                2                 13
  RX                1                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = 18Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    0  4
  18Q GAIN WILD-TYPE 12 69
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 81 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 69 
$`18Q GAIN MUTATED`
TCGA-LK-A4O0 TCGA-SH-A7BH TCGA-SH-A9CU TCGA-UD-AAC7 
        6.08         7.99        24.07        13.35 

$`18Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H 
       13.61        27.16        48.99         4.67        17.62        38.01 
TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 
       28.27        24.36        17.95         5.52         8.02         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       77.56        68.71        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT 
        2.56         9.76        38.40        23.90        15.09        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 
       15.42        27.72         6.48        25.94         8.32        14.99 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       28.37        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.37         2.76         8.58         7.50        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              6.08               0.66 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             24.07              91.73 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             10.67              17.62 
[1] "6.1 - 24.1 (10.7)" "0.7 - 91.7 (17.6)"
[1] "hr=" "2.3"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED         0        1        0        1         1        1
  18Q GAIN WILD-TYPE       7        1        1       15        44       15
D29V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 1                 15
  STAGE III                1                 44
  STAGE IV                 1                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18Q GAIN MUTATED    1  1  1  1
  18Q GAIN WILD-TYPE 13 25 31 12
D29V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                1                 13
  T2                1                 25
  T3                1                 31
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  18Q GAIN MUTATED    3  0     1
  18Q GAIN WILD-TYPE 41 10    28
D29V5, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                   3                 41
  N1                   0                 10
  N2+N3                1                 28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4  0
  18Q GAIN WILD-TYPE 53  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    0
  18Q GAIN WILD-TYPE   53    3
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                4                 53
  1                0                  3
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    1  3
  18Q GAIN WILD-TYPE 15 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    3
  18Q GAIN WILD-TYPE   15   68
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 15
  MALE                  3                 68
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    3  1
  18Q GAIN WILD-TYPE 59 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    1
  18Q GAIN WILD-TYPE   59   23
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 3                 59
  YES                1                 23
[1] 2 2
[1] FALSE
D29V9, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 15 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A9CT         TCGA-UT-A88C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-XT-AASU         TCGA-ZN-A9VO         TCGA-ZN-A9VP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ZN-A9VQ         TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  18Q GAIN MUTATED                       1                                    0
  18Q GAIN WILD-TYPE                    22                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  18Q GAIN MUTATED                          2                        1
  18Q GAIN WILD-TYPE                       55                        1
D29V10, multiclass
                                      clus
vv                                     18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               1                 22
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            2                 55
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  18Q GAIN MUTATED    1  0  2  1
  18Q GAIN WILD-TYPE 16  3 13 10
D29V11, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                1                 16
  R1                0                  3
  R2                2                 13
  RX                1                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = 19P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    2 11
  19P GAIN WILD-TYPE 10 62
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                13                 72 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                11                 62 
$`19P GAIN MUTATED`
TCGA-3H-AB3S TCGA-UD-AAC4 TCGA-3H-AB3M TCGA-3H-AB3X TCGA-3U-A98I TCGA-LK-A4O0 
       12.66        23.64        29.10        48.99        28.27         6.08 
TCGA-MQ-A4LP TCGA-SC-A6LR TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A8AF TCGA-UD-AAC5 
       17.33        38.40         7.99        24.07        11.77         8.32 
TCGA-UD-AAC7 
       13.35 

$`19P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-TS-A8AS 
       42.81        62.99        20.71        31.20        21.83        26.14 
TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3U-A98D 
       27.06        56.38        11.87        13.61        27.16         4.67 
TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ 
       17.62        38.01        24.36        17.95         5.52         8.02 
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        1.87        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       18.81        23.31         5.19         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       77.56        68.71        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU 
        2.56         9.76        23.90        15.09        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
        8.38        27.75        41.46        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY 
       19.43        15.02        32.28        10.78        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G 
        6.48        25.94        14.99        28.37        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO 
        4.73         4.67         1.28         4.37         2.76         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        40.37        32.12        43.04         2.76 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              6.08               0.66 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             48.99              91.73 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            17.330             17.015 
[1] "6.1 - 49.0 (17.3)" "0.7 - 91.7 (17.0)"
[1] "hr=" "1"  
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  19P GAIN MUTATED         1        1        0        3         7        2
  19P GAIN WILD-TYPE       6        1        1       13        38       14
D30V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 3                 13
  STAGE III                7                 38
  STAGE IV                 2                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19P GAIN MUTATED    3  5  4  2
  19P GAIN WILD-TYPE 11 21 28 11
D30V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                3                 11
  T2                5                 21
  T3                4                 28
  T4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  19P GAIN MUTATED    7  0     6
  19P GAIN WILD-TYPE 37 10    23
D30V5, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                   7                 37
  N1                   0                 10
  N2+N3                6                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   13  0
  19P GAIN WILD-TYPE 44  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     13    0
  19P GAIN WILD-TYPE   44    3
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               13                 44
  1                0                  3
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    2 12
  19P GAIN WILD-TYPE 14 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2   12
  19P GAIN WILD-TYPE   14   59
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                2                 14
  MALE                 12                 59
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    8  5
  19P GAIN WILD-TYPE 54 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      8    5
  19P GAIN WILD-TYPE   54   19
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 8                 54
  YES                5                 19
[1] 2 2
[1] FALSE
D30V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  19P GAIN MUTATED                       3                                    1
  19P GAIN WILD-TYPE                    20                                    4
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  19P GAIN MUTATED                          9                        1
  19P GAIN WILD-TYPE                       48                        1
D30V10, multiclass
                                      clus
vv                                     19P GAIN MUTATED 19P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               3                 20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                1                  4
  EPITHELIOID MESOTHELIOMA                            9                 48
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  19P GAIN MUTATED    2  0  4  2
  19P GAIN WILD-TYPE 15  3 11  9
D30V11, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                2                 15
  R1                0                  3
  R2                4                 11
  RX                2                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = 19Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    1  9
  19Q GAIN WILD-TYPE 11 64
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                 75 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                 64 
$`19Q GAIN MUTATED`
TCGA-UD-AAC4 TCGA-3U-A98I TCGA-LK-A4O0 TCGA-MQ-A4LP TCGA-SH-A7BH TCGA-SH-A9CU 
       23.64        28.27         6.08        17.33         7.99        24.07 
TCGA-TS-A8AF TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-ZN-A9VU 
       11.77         8.32        13.35        32.12 

$`19Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       26.14        27.06        56.38        11.87        29.10        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98J 
       27.16        48.99         4.67        17.62        38.01        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
       17.95         5.52         8.02         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
        3.52        10.95        24.89        77.56        68.71        19.99 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
        0.66        28.96        13.61         2.56         9.76        38.40 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
       23.90        15.09        14.76        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       41.46        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       32.28        10.78        15.42        27.72         6.48        25.94 
TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       14.99        28.37        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ 
        1.28         4.37         2.76         8.58         7.50        16.41 
TCGA-ZN-A9VS TCGA-ZN-A9VV TCGA-ZN-A9VW 
       40.37        43.04         2.76 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              6.08               0.66 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             32.12              91.73 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             15.34              17.62 
[1] "6.1 - 32.1 (15.3)" "0.7 - 91.7 (17.6)"
[1] "hr=" "1.3"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED         1        1        0        3         4        2
  19Q GAIN WILD-TYPE       6        1        1       13        41       14
D31V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 3                 13
  STAGE III                4                 41
  STAGE IV                 2                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19Q GAIN MUTATED    2  5  2  2
  19Q GAIN WILD-TYPE 12 21 30 11
D31V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                2                 12
  T2                5                 21
  T3                2                 30
  T4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  19Q GAIN MUTATED    6  0     4
  19Q GAIN WILD-TYPE 38 10    25
D31V5, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                   6                 38
  N1                   0                 10
  N2+N3                4                 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"
D31V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    9  0
  19Q GAIN WILD-TYPE 48  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      9    0
  19Q GAIN WILD-TYPE   48    3
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                9                 48
  1                0                  3
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    1 10
  19Q GAIN WILD-TYPE 15 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   10
  19Q GAIN WILD-TYPE   15   61
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                1                 15
  MALE                 10                 61
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    8  2
  19Q GAIN WILD-TYPE 54 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      8    2
  19Q GAIN WILD-TYPE   54   22
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 8                 54
  YES                2                 22
[1] 2 2
[1] FALSE
D31V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  19Q GAIN MUTATED                       3                                    1
  19Q GAIN WILD-TYPE                    20                                    4
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  19Q GAIN MUTATED                          6                        1
  19Q GAIN WILD-TYPE                       51                        1
D31V10, multiclass
                                      clus
vv                                     19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               3                 20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                1                  4
  EPITHELIOID MESOTHELIOMA                            6                 51
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  19Q GAIN MUTATED    2  0  3  2
  19Q GAIN WILD-TYPE 15  3 12  9
D31V11, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0                2                 15
  R1                0                  3
  R2                3                 12
  RX                2                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = 20P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    1  7
  20P GAIN WILD-TYPE 11 66
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                 77 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 7                 66 
$`20P GAIN MUTATED`
TCGA-SC-AA5Z TCGA-3H-AB3U TCGA-LK-A4NY TCGA-MQ-A6BL TCGA-NQ-A57I TCGA-SH-A9CU 
       21.83        27.16         5.52        10.95         0.66        24.07 
TCGA-UD-AAC7 TCGA-UT-A88G 
       13.35         2.50 

$`20P GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       23.64        27.06        56.38        11.87        29.10        13.61 
TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       48.99         4.67        17.62        38.01        28.27        24.36 
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
       17.95         8.02         6.08         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
       17.33         3.52        24.89        77.56        68.71        19.99 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC 
       28.96        13.61         2.56         9.76        38.40        23.90 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
       15.09         7.99        14.76        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       41.46        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       32.28        11.77        10.78        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A97Y 
       25.94         8.32        14.99        28.37        14.27         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP 
        4.67         1.28         4.37         2.76         8.58         7.50 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       16.41        40.37        32.12        43.04         2.76 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.66               1.28 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             27.16              91.73 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             12.15              17.62 
[1] "0.7 - 27.2 (12.1)" "1.3 - 91.7 (17.6)"
[1] "hr=" "1.8"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  20P GAIN MUTATED         0        0        1        2         3        2
  20P GAIN WILD-TYPE       7        2        0       14        42       14
D32V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 2                 14
  STAGE III                3                 42
  STAGE IV                 2                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20P GAIN MUTATED    1  2  3  2
  20P GAIN WILD-TYPE 13 24 29 11
D32V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                1                 13
  T2                2                 24
  T3                3                 29
  T4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  20P GAIN MUTATED    5  0     2
  20P GAIN WILD-TYPE 39 10    27
D32V5, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                   5                 39
  N1                   0                 10
  N2+N3                2                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    7  0
  20P GAIN WILD-TYPE 50  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7    0
  20P GAIN WILD-TYPE   50    3
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0                7                 50
  1                0                  3
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    1  7
  20P GAIN WILD-TYPE 15 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1    7
  20P GAIN WILD-TYPE   15   64
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                1                 15
  MALE                  7                 64
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    6  2
  20P GAIN WILD-TYPE 56 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      6    2
  20P GAIN WILD-TYPE   56   22
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 6                 56
  YES                2                 22
[1] 2 2
[1] FALSE
D32V9, continuous
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                 16 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A7BH         TCGA-SH-A9CT 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-UT-A88C         TCGA-XT-AASU         TCGA-ZN-A9VO 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ZN-A9VP         TCGA-ZN-A9VQ         TCGA-ZN-A9VS 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ZN-A9VU 
"20P GAIN WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  20P GAIN MUTATED                       4                                    0
  20P GAIN WILD-TYPE                    19                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  20P GAIN MUTATED                          4                        0
  20P GAIN WILD-TYPE                       53                        2
D32V10, multiclass
                                      clus
vv                                     20P GAIN MUTATED 20P GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               4                 19
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            4                 53
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  20P GAIN MUTATED    1  0  3  2
  20P GAIN WILD-TYPE 16  3 12  9
D32V11, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0                1                 16
  R1                0                  3
  R2                3                 12
  RX                2                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = 20Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED    1 10
  20Q GAIN WILD-TYPE 11 63
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                11                 74 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                 63 
$`20Q GAIN MUTATED`
TCGA-SC-AA5Z TCGA-3H-AB3U TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A9CU 
       21.83        27.16        10.95        19.99         0.66        24.07 
TCGA-TS-A7P0 TCGA-TS-A7P7 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G 
       41.46        19.43        13.35        28.37         2.50 

$`20Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       23.64        27.06        56.38        11.87        29.10        13.61 
TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       48.99         4.67        17.62        38.01        28.27        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       17.95         5.52         8.02         6.08         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
        5.19        17.33         3.52        24.89        77.56        68.71 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC 
       28.96        13.61         2.56         9.76        38.40        23.90 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
       15.09         7.99        14.76        55.07         8.38        27.75 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF 
       18.51        22.65         9.30        15.02        32.28        11.77 
TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 
       10.78        15.42        27.72         6.48        25.94         8.32 
TCGA-UD-AAC6 TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       14.99        14.27         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        2.76         8.58         7.50        16.41        40.37        32.12 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       43.04         2.76 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.66               1.28 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             41.46              91.73 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            19.990             15.915 
[1] "0.7 - 41.5 (20.0)" "1.3 - 91.7 (15.9)"
[1] "hr=" "1.2"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED         0        0        1        3         5        2
  20Q GAIN WILD-TYPE       7        2        0       13        40       14
D33V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 3                 13
  STAGE III                5                 40
  STAGE IV                 2                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20Q GAIN MUTATED    1  3  5  2
  20Q GAIN WILD-TYPE 13 23 27 11
D33V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                1                 13
  T2                3                 23
  T3                5                 27
  T4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  20Q GAIN MUTATED    6  0     4
  20Q GAIN WILD-TYPE 38 10    25
D33V5, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                   6                 38
  N1                   0                 10
  N2+N3                4                 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"
D33V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    7  0
  20Q GAIN WILD-TYPE 50  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      7    0
  20Q GAIN WILD-TYPE   50    3
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0                7                 50
  1                0                  3
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    0 11
  20Q GAIN WILD-TYPE 16 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0   11
  20Q GAIN WILD-TYPE   16   60
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                0                 16
  MALE                 11                 60
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    8  3
  20Q GAIN WILD-TYPE 54 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8    3
  20Q GAIN WILD-TYPE   54   21
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 8                 54
  YES                3                 21
[1] 2 2
[1] FALSE
D33V9, continuous
[1] "Remove cluster labels:" "20Q GAIN MUTATED"      
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 2                 15 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A7BH         TCGA-SH-A9CT 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-XT-AASU         TCGA-ZN-A9VO         TCGA-ZN-A9VP 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ZN-A9VQ         TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  20Q GAIN MUTATED                       3                                    0
  20Q GAIN WILD-TYPE                    20                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  20Q GAIN MUTATED                          8                        0
  20Q GAIN WILD-TYPE                       49                        2
D33V10, multiclass
                                      clus
vv                                     20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               3                 20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            8                 49
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  20Q GAIN MUTATED    2  0  3  2
  20Q GAIN WILD-TYPE 15  3 12  9
D33V11, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0                2                 15
  R1                0                  3
  R2                3                 12
  RX                2                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = 21Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    0  6
  21Q GAIN WILD-TYPE 12 67
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 79 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 67 
$`21Q GAIN MUTATED`
TCGA-3U-A98J TCGA-SH-A7BH TCGA-SH-A9CU TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88G 
       24.36         7.99        24.07         6.48        13.35         2.50 

$`21Q GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H 
       13.61        27.16        48.99         4.67        17.62        38.01 
TCGA-3U-A98I TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       28.27        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       77.56        68.71        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT 
        2.56         9.76        38.40        23.90        15.09        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C 
       15.42        27.72        25.94         8.32        14.99        28.37 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
       14.27         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV 
        8.58         7.50        16.41        40.37        32.12        43.04 
TCGA-ZN-A9VW 
        2.76 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              2.50               0.66 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             24.36              91.73 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             10.67              17.62 
[1] "2.5 - 24.4 (10.7)" "0.7 - 91.7 (17.6)"
[1] "hr=" "2.2"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED         0        0        0        2         3        1
  21Q GAIN WILD-TYPE       7        2        1       14        42       15
D34V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 2                 14
  STAGE III                3                 42
  STAGE IV                 1                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  21Q GAIN MUTATED    0  2  3  1
  21Q GAIN WILD-TYPE 14 24 29 12
D34V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                0                 14
  T2                2                 24
  T3                3                 29
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  21Q GAIN MUTATED    4  0     2
  21Q GAIN WILD-TYPE 40 10    27
D34V5, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                   4                 40
  N1                   0                 10
  N2+N3                2                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    6  0
  21Q GAIN WILD-TYPE 51  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      6    0
  21Q GAIN WILD-TYPE   51    3
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                6                 51
  1                0                  3
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    1  5
  21Q GAIN WILD-TYPE 15 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    5
  21Q GAIN WILD-TYPE   15   66
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                1                 15
  MALE                  5                 66
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    4  2
  21Q GAIN WILD-TYPE 58 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4    2
  21Q GAIN WILD-TYPE   58   22
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 4                 58
  YES                2                 22
[1] 2 2
[1] FALSE
D34V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  21Q GAIN MUTATED                       2                                    0
  21Q GAIN WILD-TYPE                    21                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  21Q GAIN MUTATED                          4                        0
  21Q GAIN WILD-TYPE                       53                        2
D34V10, multiclass
                                      clus
vv                                     21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                               2                 21
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            4                 53
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  21Q GAIN MUTATED    0  0  2  3
  21Q GAIN WILD-TYPE 17  3 13  8
D34V11, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0                0                 17
  R1                0                  3
  R2                2                 13
  RX                3                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = XP GAIN MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                0  1
  XP GAIN MUTATED    2  5
  XP GAIN WILD-TYPE 10 68
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                7                78 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                5                68 
$`XP GAIN MUTATED`
TCGA-SC-AA5Z TCGA-3H-AB3U TCGA-SC-A6LR TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UT-A88G 
       21.83        27.16        38.40        25.94        14.99         2.50 
TCGA-YS-A95B 
        1.28 

$`XP GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       23.64        27.06        56.38        11.87        29.10        13.61 
TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       48.99         4.67        17.62        38.01        28.27        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       17.95         5.52         8.02         6.08         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        77.56 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       68.71        19.99         0.66        28.96        13.61         2.56 
TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
        9.76        23.90        15.09         7.99        14.76        24.07 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88C 
       15.42        27.72         6.48         8.32        13.35        28.37 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO 
       14.27         4.73         4.67         4.37         2.76         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        40.37        32.12        43.04         2.76 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             1.28              0.66 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            38.40             91.73 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            21.83             16.87 
[1] "1.3 - 38.4 (21.8)" "0.7 - 91.7 (16.9)"
[1] "hr=" "1.1"
D35V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  XP GAIN MUTATED         0        0        0        1         4        2
  XP GAIN WILD-TYPE       7        2        1       15        41       14
D35V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               4                41
  STAGE IV                2                14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XP GAIN MUTATED    1  2  2  2
  XP GAIN WILD-TYPE 13 24 30 11
D35V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               1                13
  T2               2                24
  T3               2                30
  T4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  XP GAIN MUTATED    3  0     4
  XP GAIN WILD-TYPE 41 10    25
D35V5, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  N0                  3                41
  N1                  0                10
  N2+N3               4                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"
D35V6, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    7  0
  XP GAIN WILD-TYPE 50  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      7    0
  XP GAIN WILD-TYPE   50    3
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0               7                50
  1               0                 3
[1] 2 2
[1] FALSE
D35V7, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    2  5
  XP GAIN WILD-TYPE 14 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2    5
  XP GAIN WILD-TYPE   14   66
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               2                14
  MALE                 5                66
[1] 2 2
[1] FALSE
D35V8, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    4  3
  XP GAIN WILD-TYPE 58 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      4    3
  XP GAIN WILD-TYPE   58   21
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                4                58
  YES               3                21
[1] 2 2
[1] FALSE
D35V9, continuous
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                16 
       TCGA-3U-A98E        TCGA-UT-A88D        TCGA-3U-A98J        TCGA-SC-A6LM 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SC-A6LP        TCGA-SH-A7BH        TCGA-SH-A9CT 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-SH-A9CU        TCGA-UT-A88C        TCGA-XT-AASU        TCGA-ZN-A9VO 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-ZN-A9VP        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  XP GAIN MUTATED                       2                                    0
  XP GAIN WILD-TYPE                    21                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  XP GAIN MUTATED                          5                        0
  XP GAIN WILD-TYPE                       52                        2
D35V10, multiclass
                                      clus
vv                                     XP GAIN MUTATED XP GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              2                21
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           5                52
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  XP GAIN MUTATED    0  0  5  1
  XP GAIN WILD-TYPE 17  3 10 10
D35V11, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0               0                17
  R1               0                 3
  R2               5                10
  RX               1                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = XQ GAIN MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    2  4
  XQ GAIN WILD-TYPE 10 69
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                79 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                69 
$`XQ GAIN MUTATED`
TCGA-SC-AA5Z TCGA-3H-AB3U TCGA-SC-A6LR TCGA-UD-AAC1 TCGA-UT-A88G TCGA-YS-A95B 
       21.83        27.16        38.40        25.94         2.50         1.28 

$`XQ GAIN WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       23.64        27.06        56.38        11.87        29.10        13.61 
TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       48.99         4.67        17.62        38.01        28.27        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       17.95         5.52         8.02         6.08         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        77.56 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       68.71        19.99         0.66        28.96        13.61         2.56 
TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
        9.76        23.90        15.09         7.99        14.76        24.07 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
       15.42        27.72         6.48         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M 
       28.37        14.27         4.73         4.67         4.37         2.76 
TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV 
        8.58         7.50        16.41        40.37        32.12        43.04 
TCGA-ZN-A9VW 
        2.76 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             1.28              0.66 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            38.40             91.73 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           23.885            16.410 
[1] "1.3 - 38.4 (23.9)" "0.7 - 91.7 (16.4)"
[1] "hr=" "1.2"
D36V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED         0        0        0        0         4        2
  XQ GAIN WILD-TYPE       7        2        1       16        41       14
D36V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                0                16
  STAGE III               4                41
  STAGE IV                2                14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XQ GAIN MUTATED    1  1  2  2
  XQ GAIN WILD-TYPE 13 25 30 11
D36V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               1                13
  T2               1                25
  T3               2                30
  T4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  XQ GAIN MUTATED    2  0     4
  XQ GAIN WILD-TYPE 42 10    25
D36V5, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0                  2                42
  N1                  0                10
  N2+N3               4                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"
D36V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    6  0
  XQ GAIN WILD-TYPE 51  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6    0
  XQ GAIN WILD-TYPE   51    3
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               6                51
  1               0                 3
[1] 2 2
[1] FALSE
D36V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2  4
  XQ GAIN WILD-TYPE 14 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    4
  XQ GAIN WILD-TYPE   14   67
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               2                14
  MALE                 4                67
[1] 2 2
[1] FALSE
D36V8, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    4  2
  XQ GAIN WILD-TYPE 58 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4    2
  XQ GAIN WILD-TYPE   58   22
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                4                58
  YES               2                22
[1] 2 2
[1] FALSE
D36V9, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                16 
       TCGA-3U-A98E        TCGA-UT-A88D        TCGA-3U-A98J        TCGA-SC-A6LM 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SC-A6LP        TCGA-SH-A7BH        TCGA-SH-A9CT 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-SH-A9CU        TCGA-UT-A88C        TCGA-XT-AASU        TCGA-ZN-A9VO 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ZN-A9VP        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  XQ GAIN MUTATED                       1                                    0
  XQ GAIN WILD-TYPE                    22                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  XQ GAIN MUTATED                          5                        0
  XQ GAIN WILD-TYPE                       52                        2
D36V10, multiclass
                                      clus
vv                                     XQ GAIN MUTATED XQ GAIN WILD-TYPE
  BIPHASIC MESOTHELIOMA                              1                22
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           5                52
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  XQ GAIN MUTATED    0  0  4  1
  XQ GAIN WILD-TYPE 17  3 11 10
D36V11, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0               0                17
  R1               0                 3
  R2               4                11
  RX               1                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = 1P LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    0  9
  1P LOSS WILD-TYPE 12 64
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                9                76 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                9                64 
$`1P LOSS MUTATED`
TCGA-3H-AB3M TCGA-3U-A98F TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A6BL 
       29.10        17.62        14.73        11.51        18.81        10.95 
TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-TS-A7P6 
       19.99        13.61         9.30 

$`1P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        11.87        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       27.16        48.99         4.67        38.01        28.27        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       17.95         5.52         8.02         6.08         1.87        12.72 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       80.84        91.73        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP 
       24.89        77.56        68.71         0.66        28.96         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
        9.76        38.40        23.90        15.09         7.99        14.76 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       24.07        55.07         8.38        27.75        41.46        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
       22.65        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 
       15.42        27.72         6.48        25.94         8.32        14.99 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       13.35        28.37        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ 
        1.28         4.37         2.76         8.58         7.50        16.41 
TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       40.37        32.12        43.04         2.76 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             9.30              0.66 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            29.10             91.73 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            14.73             17.64 
[1] "9.3 - 29.1 (14.7)" "0.7 - 91.7 (17.6)"
[1] "hr=" "1.7"
D37V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  1P LOSS MUTATED         0        0        0        3         6        0
  1P LOSS WILD-TYPE       7        2        1       13        39       16
D37V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                3                13
  STAGE III               6                39
  STAGE IV                0                16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1P LOSS MUTATED    0  4  5  0
  1P LOSS WILD-TYPE 14 22 27 13
D37V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               0                14
  T2               4                22
  T3               5                27
  T4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  1P LOSS MUTATED    4  2     3
  1P LOSS WILD-TYPE 40  8    26
D37V5, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0                  4                40
  N1                  2                 8
  N2+N3               3                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"
D37V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    7  0
  1P LOSS WILD-TYPE 50  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      7    0
  1P LOSS WILD-TYPE   50    3
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0               7                50
  1               0                 3
[1] 2 2
[1] FALSE
D37V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    3  6
  1P LOSS WILD-TYPE 13 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    6
  1P LOSS WILD-TYPE   13   65
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               3                13
  MALE                 6                65
[1] 2 2
[1] FALSE
D37V8, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    6  3
  1P LOSS WILD-TYPE 56 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6    3
  1P LOSS WILD-TYPE   56   21
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                6                56
  YES               3                21
[1] 2 2
[1] FALSE
D37V9, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                16 
       TCGA-3U-A98E        TCGA-UT-A88D        TCGA-3U-A98J        TCGA-SC-A6LM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-SC-A6LP        TCGA-SC-A6LR        TCGA-SH-A7BH        TCGA-SH-A9CT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-SH-A9CU        TCGA-UT-A88C        TCGA-XT-AASU        TCGA-ZN-A9VO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ZN-A9VP        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  1P LOSS MUTATED                       4                                    0
  1P LOSS WILD-TYPE                    19                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  1P LOSS MUTATED                          5                        0
  1P LOSS WILD-TYPE                       52                        2
D37V10, multiclass
                                      clus
vv                                     1P LOSS MUTATED 1P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              4                19
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           5                52
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  1P LOSS MUTATED    3  1  0  1
  1P LOSS WILD-TYPE 14  2 15 10
D37V11, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0               3                14
  R1               1                 2
  R2               0                15
  RX               1                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = 2P LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    0  6
  2P LOSS WILD-TYPE 12 67
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6                79 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6                67 
$`2P LOSS MUTATED`
TCGA-3U-A98D TCGA-3U-A98I TCGA-3U-A98J TCGA-MQ-A4LI TCGA-SH-A7BH TCGA-UT-A88G 
        4.67        28.27        24.36        18.81         7.99         2.50 

$`2P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98F TCGA-3U-A98H TCGA-LK-A4NW 
       13.61        27.16        48.99        17.62        38.01        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       11.51        80.84        91.73        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
        3.52        10.95        24.89        77.56        68.71        19.99 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
        0.66        28.96        13.61         2.56         9.76        38.40 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       23.90        15.09        14.76        24.07        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
       27.75        41.46        18.51        22.65         9.30        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY 
       15.02        32.28        11.77        10.78        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        6.48        25.94         8.32        14.99        13.35        28.37 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
       14.27         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV 
        8.58         7.50        16.41        40.37        32.12        43.04 
TCGA-ZN-A9VW 
        2.76 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.50              0.66 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            28.27             91.73 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            13.40             17.33 
[1] "2.5 - 28.3 (13.4)" "0.7 - 91.7 (17.3)"
[1] "hr=" "1.8"
D38V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  2P LOSS MUTATED         0        0        0        1         4        1
  2P LOSS WILD-TYPE       7        2        1       15        41       15
D38V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               4                41
  STAGE IV                1                15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2P LOSS MUTATED    0  2  3  1
  2P LOSS WILD-TYPE 14 24 29 12
D38V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               0                14
  T2               2                24
  T3               3                29
  T4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  2P LOSS MUTATED    3  0     3
  2P LOSS WILD-TYPE 41 10    26
D38V5, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0                  3                41
  N1                  0                10
  N2+N3               3                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"
D38V6, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    6  0
  2P LOSS WILD-TYPE 51  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    0
  2P LOSS WILD-TYPE   51    3
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               6                51
  1               0                 3
[1] 2 2
[1] FALSE
D38V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    2  4
  2P LOSS WILD-TYPE 14 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    4
  2P LOSS WILD-TYPE   14   67
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               2                14
  MALE                 4                67
[1] 2 2
[1] FALSE
D38V8, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    6  0
  2P LOSS WILD-TYPE 56 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    0
  2P LOSS WILD-TYPE   56   24
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                6                56
  YES               0                24
[1] 2 2
[1] FALSE
D38V9, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                15 
       TCGA-3U-A98E        TCGA-UT-A88D        TCGA-SC-A6LM        TCGA-SC-A6LN 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SC-A6LP        TCGA-SC-A6LR        TCGA-SH-A9CT        TCGA-SH-A9CU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UT-A88C        TCGA-XT-AASU        TCGA-ZN-A9VO        TCGA-ZN-A9VP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  2P LOSS MUTATED                       4                                    0
  2P LOSS WILD-TYPE                    19                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  2P LOSS MUTATED                          2                        0
  2P LOSS WILD-TYPE                       55                        2
D38V10, multiclass
                                      clus
vv                                     2P LOSS MUTATED 2P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              4                19
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           2                55
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  2P LOSS MUTATED    0  1  1  1
  2P LOSS WILD-TYPE 17  2 14 10
D38V11, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               0                17
  R1               1                 2
  R2               1                14
  RX               1                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = 2Q LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    0  5
  2Q LOSS WILD-TYPE 12 68
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                80 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                68 
$`2Q LOSS MUTATED`
TCGA-3U-A98D TCGA-3U-A98I TCGA-LK-A4O2 TCGA-MQ-A4LI TCGA-SH-A7BH 
        4.67        28.27         1.87        18.81         7.99 

$`2Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98J 
       13.61        27.16        48.99        17.62        38.01        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-LK-A4O6 
       17.95         5.52         8.02         6.08        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       11.51        80.84        91.73        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
        3.52        10.95        24.89        77.56        68.71        19.99 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
        0.66        28.96        13.61         2.56         9.76        38.40 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       23.90        15.09        14.76        24.07        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
       27.75        41.46        18.51        22.65         9.30        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY 
       15.02        32.28        11.77        10.78        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        6.48        25.94         8.32        14.99        13.35        28.37 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       14.27         2.50         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        2.76         8.58         7.50        16.41        40.37        32.12 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       43.04         2.76 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             1.87              0.66 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            28.27             91.73 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            7.990            17.475 
[1] "1.9 - 28.3 (8.0)"  "0.7 - 91.7 (17.5)"
[1] "hr=" "2.1"
D39V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED         0        0        0        1         3        1
  2Q LOSS WILD-TYPE       7        2        1       15        42       15
D39V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               3                42
  STAGE IV                1                15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2Q LOSS MUTATED    0  2  2  1
  2Q LOSS WILD-TYPE 14 24 30 12
D39V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               0                14
  T2               2                24
  T3               2                30
  T4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  2Q LOSS MUTATED    3  0     2
  2Q LOSS WILD-TYPE 41 10    27
D39V5, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0                  3                41
  N1                  0                10
  N2+N3               2                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    5  0
  2Q LOSS WILD-TYPE 52  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    0
  2Q LOSS WILD-TYPE   52    3
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               5                52
  1               0                 3
[1] 2 2
[1] FALSE
D39V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    3  2
  2Q LOSS WILD-TYPE 13 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3    2
  2Q LOSS WILD-TYPE   13   69
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               3                13
  MALE                 2                69
[1] 2 2
[1] FALSE
D39V8, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    5  0
  2Q LOSS WILD-TYPE 57 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    0
  2Q LOSS WILD-TYPE   57   24
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                5                57
  YES               0                24
[1] 2 2
[1] FALSE
D39V9, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                16 
       TCGA-3U-A98E        TCGA-UT-A88D        TCGA-3U-A98J        TCGA-SC-A6LM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SC-A6LP        TCGA-SC-A6LR        TCGA-SH-A9CT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SH-A9CU        TCGA-UT-A88C        TCGA-XT-AASU        TCGA-ZN-A9VO 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ZN-A9VP        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  2Q LOSS MUTATED                       3                                    0
  2Q LOSS WILD-TYPE                    20                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  2Q LOSS MUTATED                          2                        0
  2Q LOSS WILD-TYPE                       55                        2
D39V10, multiclass
                                      clus
vv                                     2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              3                20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           2                55
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  2Q LOSS MUTATED    0  1  2  0
  2Q LOSS WILD-TYPE 17  2 13 11
D39V11, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               0                17
  R1               1                 2
  R2               2                13
  RX               0                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = 3P LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    1  7
  3P LOSS WILD-TYPE 11 66
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                8                77 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                7                66 
$`3P LOSS MUTATED`
TCGA-3U-A98F TCGA-3U-A98I TCGA-LK-A4O7 TCGA-NQ-A57I TCGA-SH-A9CU TCGA-TS-A8AF 
       17.62        28.27        11.51         0.66        24.07        11.77 
TCGA-UD-AABZ TCGA-ZN-A9VP 
        6.48         7.50 

$`3P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98H TCGA-3U-A98J 
       13.61        27.16        48.99         4.67        38.01        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       17.95         5.52         8.02         6.08         1.87        12.72 
TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       14.73        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        77.56        68.71 
TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
       19.99        28.96        13.61         2.56         9.76        38.40 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY 
       23.90        15.09         7.99        14.76        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
       27.75        41.46        18.51        22.65         9.30        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AAC1 
       15.02        32.28        10.78        15.42        27.72        25.94 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G 
        8.32        14.99        13.35        28.37        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO 
        4.73         4.67         1.28         4.37         2.76         8.58 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       16.41        40.37        32.12        43.04         2.76 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.66              1.28 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            28.27             91.73 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            11.64             17.95 
[1] "0.7 - 28.3 (11.6)" "1.3 - 91.7 (17.9)"
[1] "hr=" "1.8"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         0        0        1        1         4        2
  3P LOSS WILD-TYPE       7        2        0       15        41       14
D40V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                1                 0
  STAGE II                1                15
  STAGE III               4                41
  STAGE IV                2                14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3P LOSS MUTATED    1  2  3  2
  3P LOSS WILD-TYPE 13 24 29 11
D40V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               1                13
  T2               2                24
  T3               3                29
  T4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  3P LOSS MUTATED    2  1     4
  3P LOSS WILD-TYPE 42  9    25
D40V5, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0                  2                42
  N1                  1                 9
  N2+N3               4                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"
D40V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    5  0
  3P LOSS WILD-TYPE 52  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    0
  3P LOSS WILD-TYPE   52    3
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               5                52
  1               0                 3
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    0  8
  3P LOSS WILD-TYPE 16 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    8
  3P LOSS WILD-TYPE   16   63
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               0                16
  MALE                 8                63
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    5  3
  3P LOSS WILD-TYPE 57 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    3
  3P LOSS WILD-TYPE   57   21
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                5                57
  YES               3                21
[1] 2 2
[1] FALSE
D40V9, continuous
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                15 
       TCGA-3U-A98E        TCGA-UT-A88D        TCGA-3U-A98J        TCGA-SC-A6LM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SC-A6LP        TCGA-SC-A6LR        TCGA-SH-A7BH 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-SH-A9CT        TCGA-UT-A88C        TCGA-XT-AASU        TCGA-ZN-A9VO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  3P LOSS MUTATED                       3                                    0
  3P LOSS WILD-TYPE                    20                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  3P LOSS MUTATED                          5                        0
  3P LOSS WILD-TYPE                       52                        2
D40V10, multiclass
                                      clus
vv                                     3P LOSS MUTATED 3P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              3                20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           5                52
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  3P LOSS MUTATED    1  0  1  2
  3P LOSS WILD-TYPE 16  3 14  9
D40V11, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               1                16
  R1               0                 3
  R2               1                14
  RX               2                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = 3Q LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    0  7
  3Q LOSS WILD-TYPE 12 66
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7                78 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7                66 
$`3Q LOSS MUTATED`
TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98I TCGA-LK-A4O7 TCGA-NQ-A57I TCGA-SH-A9CU 
        4.67        17.62        28.27        11.51         0.66        24.07 
TCGA-TS-A8AF 
       11.77 

$`3Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NW 
       13.61        27.16        48.99        38.01        24.36        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08         1.87        12.72        14.73 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       80.84        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
        3.52        10.95        24.89        77.56        68.71        19.99 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC 
       28.96        13.61         2.56         9.76        38.40        23.90 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
       15.09         7.99        14.76        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       41.46        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       32.28        10.78        15.42        27.72         6.48        25.94 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G 
        8.32        14.99        13.35        28.37        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO 
        4.73         4.67         1.28         4.37         2.76         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        40.37        32.12        43.04         2.76 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.66              1.28 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            28.27             91.73 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            11.77             17.64 
[1] "0.7 - 28.3 (11.8)" "1.3 - 91.7 (17.6)"
[1] "hr=" "1.9"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         0        0        1        0         4        2
  3Q LOSS WILD-TYPE       7        2        0       16        41       14
D41V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                1                 0
  STAGE II                0                16
  STAGE III               4                41
  STAGE IV                2                14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3Q LOSS MUTATED    1  2  2  2
  3Q LOSS WILD-TYPE 13 24 30 11
D41V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               1                13
  T2               2                24
  T3               2                30
  T4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  3Q LOSS MUTATED    1  1     4
  3Q LOSS WILD-TYPE 43  9    25
D41V5, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0                  1                43
  N1                  1                 9
  N2+N3               4                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"
D41V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    5  0
  3Q LOSS WILD-TYPE 52  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    0
  3Q LOSS WILD-TYPE   52    3
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               5                52
  1               0                 3
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    0  7
  3Q LOSS WILD-TYPE 16 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    7
  3Q LOSS WILD-TYPE   16   64
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               0                16
  MALE                 7                64
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    5  2
  3Q LOSS WILD-TYPE 57 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    2
  3Q LOSS WILD-TYPE   57   22
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                5                57
  YES               2                22
[1] 2 2
[1] FALSE
D41V9, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                16 
       TCGA-3U-A98E        TCGA-UT-A88D        TCGA-3U-A98J        TCGA-SC-A6LM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SC-A6LP        TCGA-SC-A6LR        TCGA-SH-A7BH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SH-A9CT        TCGA-UT-A88C        TCGA-XT-AASU        TCGA-ZN-A9VO 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ZN-A9VP        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  3Q LOSS MUTATED                       4                                    0
  3Q LOSS WILD-TYPE                    19                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  3Q LOSS MUTATED                          3                        0
  3Q LOSS WILD-TYPE                       54                        2
D41V10, multiclass
                                      clus
vv                                     3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              4                19
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           3                54
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  3Q LOSS MUTATED    1  0  1  1
  3Q LOSS WILD-TYPE 16  3 14 10
D41V11, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               1                16
  R1               0                 3
  R2               1                14
  RX               1                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = 4P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    3 29
  4P LOSS WILD-TYPE  9 44
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               32                53 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               29                44 
$`4P LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98I 
       11.87        29.10        48.99         4.67        17.62        28.27 
TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LM 
        6.08        12.72        14.73        11.51        18.81         5.19 
TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BC 
       17.33        10.95        68.71        19.99        13.61        23.90 
TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A8AI 
        7.99        24.07         8.38        41.46         9.30        10.78 
TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G 
        6.48         8.32        14.99        13.35        14.27         2.50 
TCGA-UT-A97Y TCGA-ZN-A9VS 
        4.73        40.37 

$`4P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3T TCGA-3H-AB3U 
       26.14        23.64        27.06        56.38        13.61        27.16 
TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 
       38.01        24.36        17.95         5.52         8.02         1.87 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       80.84        91.73        23.31         3.52        24.89        77.56 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD 
        0.66        28.96         2.56         9.76        38.40        15.09 
TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 
       14.76        55.07        27.75        18.51        22.65        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AAC1 
       15.02        32.28        11.77        15.42        27.72        25.94 
TCGA-UT-A88C TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO 
       28.37         4.67         1.28         4.37         2.76         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        32.12        43.04         2.76 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             2.50              0.66 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            68.71             91.73 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            13.48             21.83 
[1] "2.5 - 68.7 (13.5)" "0.7 - 91.7 (21.8)"
[1] "hr=" "1.6"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         3        1        0        7        18        4
  4P LOSS WILD-TYPE       4        1        1        9        27       12
D42V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 3                 4
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                7                 9
  STAGE III              18                27
  STAGE IV                4                12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  4P LOSS MUTATED    5  9 15  3
  4P LOSS WILD-TYPE  9 17 17 10
D42V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               5                 9
  T2               9                17
  T3              15                17
  T4               3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  4P LOSS MUTATED   19  4     9
  4P LOSS WILD-TYPE 25  6    20
D42V5, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0                 19                25
  N1                  4                 6
  N2+N3               9                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"
D42V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   26  0
  4P LOSS WILD-TYPE 31  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     26    0
  4P LOSS WILD-TYPE   31    3
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              26                31
  1               0                 3
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    7 26
  4P LOSS WILD-TYPE  9 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      7   26
  4P LOSS WILD-TYPE    9   45
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               7                 9
  MALE                26                45
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   22 10
  4P LOSS WILD-TYPE 40 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     22   10
  4P LOSS WILD-TYPE   40   14
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               22                40
  YES              10                14
[1] 2 2
[1] FALSE
D42V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  4P LOSS MUTATED                      11                                    0
  4P LOSS WILD-TYPE                    12                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  4P LOSS MUTATED                         21                        1
  4P LOSS WILD-TYPE                       36                        1
D42V10, multiclass
                                      clus
vv                                     4P LOSS MUTATED 4P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                             11                12
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                          21                36
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED    5  2  4  8
  4P LOSS WILD-TYPE 12  1 11  3
D42V11, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0               5                12
  R1               2                 1
  R2               4                11
  RX               8                 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"

Clustering(43) Variable = 4Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    3 31
  4Q LOSS WILD-TYPE  9 42
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               34                51 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               31                42 
$`4Q LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F 
       11.87        29.10        13.61        48.99         4.67        17.62 
TCGA-3U-A98I TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI 
       28.27         6.08        12.72        14.73        11.51        18.81 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-SC-A6LN TCGA-SH-A7BC 
        5.19        17.33        10.95        68.71        13.61        23.90 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
        7.99        14.76        24.07         8.38        27.75        41.46 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC5 
        9.30        19.43        10.78        15.42         6.48         8.32 
TCGA-UD-AAC7 TCGA-UT-A88G TCGA-UT-A97Y TCGA-ZN-A9VS 
       13.35         2.50         4.73        40.37 

$`4Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3U TCGA-3U-A98H 
       26.14        23.64        27.06        56.38        27.16        38.01 
TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-MQ-A4KX 
       24.36        17.95         5.52         8.02         1.87        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS 
       91.73        23.31         3.52        24.89        77.56        19.99 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD 
        0.66        28.96         2.56         9.76        38.40        15.09 
TCGA-TS-A7OU TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF 
       55.07        18.51        22.65        15.02        32.28        11.77 
TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E TCGA-XT-AASU 
       27.72        25.94        14.99        28.37        14.27         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ 
        1.28         4.37         2.76         8.58         7.50        16.41 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             2.50              0.66 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            68.71             91.73 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            13.61             21.83 
[1] "2.5 - 68.7 (13.6)" "0.7 - 91.7 (21.8)"
[1] "hr=" "1.6"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         3        1        0        5        21        4
  4Q LOSS WILD-TYPE       4        1        1       11        24       12
D43V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 3                 4
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                5                11
  STAGE III              21                24
  STAGE IV                4                12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  4Q LOSS MUTATED    5  7 18  3
  4Q LOSS WILD-TYPE  9 19 14 10
D43V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               5                 9
  T2               7                19
  T3              18                14
  T4               3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  4Q LOSS MUTATED   18  6    10
  4Q LOSS WILD-TYPE 26  4    19
D43V5, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0                 18                26
  N1                  6                 4
  N2+N3              10                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"
D43V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   25  0
  4Q LOSS WILD-TYPE 32  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     25    0
  4Q LOSS WILD-TYPE   32    3
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              25                32
  1               0                 3
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    8 26
  4Q LOSS WILD-TYPE  8 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8   26
  4Q LOSS WILD-TYPE    8   45
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               8                 8
  MALE                26                45
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   24 10
  4Q LOSS WILD-TYPE 38 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     24   10
  4Q LOSS WILD-TYPE   38   14
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               24                38
  YES              10                14
[1] 2 2
[1] FALSE
D43V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  4Q LOSS MUTATED                      11                                    0
  4Q LOSS WILD-TYPE                    12                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  4Q LOSS MUTATED                         22                        1
  4Q LOSS WILD-TYPE                       35                        1
D43V10, multiclass
                                      clus
vv                                     4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                             11                12
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                          22                35
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED    3  2  3  7
  4Q LOSS WILD-TYPE 14  1 12  4
D43V11, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0               3                14
  R1               2                 1
  R2               3                12
  RX               7                 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"

Clustering(44) Variable = 5P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    0  4
  5P LOSS WILD-TYPE 12 69
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                81 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                69 
$`5P LOSS MUTATED`
TCGA-3U-A98F TCGA-MQ-A4LV TCGA-SC-A6LQ TCGA-UD-AAC7 
       17.62         3.52         9.76        13.35 

$`5P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98H TCGA-3U-A98I 
       13.61        27.16        48.99         4.67        38.01        28.27 
TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       24.36        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       23.31         5.19        17.33        10.95        24.89        77.56 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       68.71        19.99         0.66        28.96        13.61         2.56 
TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
       38.40        23.90        15.09         7.99        14.76        24.07 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 
       15.42        27.72         6.48        25.94         8.32        14.99 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       28.37        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.37         2.76         8.58         7.50        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             3.52              0.66 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            17.62             91.73 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           11.555            17.950 
[1] "3.5 - 17.6 (11.6)" "0.7 - 91.7 (17.9)"
[1] "hr=" "2.9"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         0        0        0        1         3        0
  5P LOSS WILD-TYPE       7        2        1       15        42       16
D44V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               3                42
  STAGE IV                0                16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5P LOSS MUTATED    0  1  3  0
  5P LOSS WILD-TYPE 14 25 29 13
D44V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               0                14
  T2               1                25
  T3               3                29
  T4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  5P LOSS MUTATED    3  0     1
  5P LOSS WILD-TYPE 41 10    28
D44V5, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0                  3                41
  N1                  0                10
  N2+N3               1                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    4  0
  5P LOSS WILD-TYPE 53  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    0
  5P LOSS WILD-TYPE   53    3
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               4                53
  1               0                 3
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    1  3
  5P LOSS WILD-TYPE 15 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    3
  5P LOSS WILD-TYPE   15   68
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               1                15
  MALE                 3                68
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    1  3
  5P LOSS WILD-TYPE 61 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    3
  5P LOSS WILD-TYPE   61   21
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                1                61
  YES               3                21
[1] 2 2
[1] FALSE
D44V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  5P LOSS MUTATED                       2                                    0
  5P LOSS WILD-TYPE                    21                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  5P LOSS MUTATED                          2                        0
  5P LOSS WILD-TYPE                       55                        2
D44V10, multiclass
                                      clus
vv                                     5P LOSS MUTATED 5P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              2                21
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           2                55
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  5P LOSS MUTATED    2  0  1  0
  5P LOSS WILD-TYPE 15  3 14 11
D44V11, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0               2                15
  R1               0                 3
  R2               1                14
  RX               0                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = 5Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    0  9
  5Q LOSS WILD-TYPE 12 64
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                9                76 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                9                64 
$`5Q LOSS MUTATED`
TCGA-3H-AB3L TCGA-3U-A98F TCGA-MQ-A4LV TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SH-A9CU 
       11.87        17.62         3.52        13.61         9.76        24.07 
TCGA-TS-A7P1 TCGA-TS-A8AF TCGA-UD-AAC7 
       18.51        11.77        13.35 

$`5Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        29.10        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       27.16        48.99         4.67        38.01        28.27        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       17.95         5.52         8.02         6.08         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
        5.19        17.33        10.95        24.89        77.56        68.71 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SH-A7BC 
       19.99         0.66        28.96         2.56        38.40        23.90 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
       15.09         7.99        14.76        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       41.46        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 
       10.78        15.42        27.72         6.48        25.94         8.32 
TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       14.99        28.37        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ 
        1.28         4.37         2.76         8.58         7.50        16.41 
TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       40.37        32.12        43.04         2.76 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             3.52              0.66 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            24.07             91.73 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            13.35             18.38 
[1] "3.5 - 24.1 (13.3)" "0.7 - 91.7 (18.4)"
[1] "hr=" "2.3"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         1        0        0        1         6        1
  5Q LOSS WILD-TYPE       6        2        1       15        39       15
D45V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 1                 6
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               6                39
  STAGE IV                1                15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    1  3  3  1
  5Q LOSS WILD-TYPE 13 23 29 12
D45V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               1                13
  T2               3                23
  T3               3                29
  T4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  5Q LOSS MUTATED    4  0     5
  5Q LOSS WILD-TYPE 40 10    24
D45V5, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0                  4                40
  N1                  0                10
  N2+N3               5                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    7  0
  5Q LOSS WILD-TYPE 50  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7    0
  5Q LOSS WILD-TYPE   50    3
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               7                50
  1               0                 3
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    1  8
  5Q LOSS WILD-TYPE 15 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    8
  5Q LOSS WILD-TYPE   15   63
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               1                15
  MALE                 8                63
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    5  4
  5Q LOSS WILD-TYPE 57 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5    4
  5Q LOSS WILD-TYPE   57   20
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                5                57
  YES               4                20
[1] 2 2
[1] FALSE
D45V9, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                15 
       TCGA-3U-A98E        TCGA-UT-A88D        TCGA-3U-A98J        TCGA-SC-A6LM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SC-A6LP        TCGA-SC-A6LR        TCGA-SH-A7BH        TCGA-SH-A9CT 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-UT-A88C        TCGA-XT-AASU        TCGA-ZN-A9VO        TCGA-ZN-A9VP 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  5Q LOSS MUTATED                       3                                    0
  5Q LOSS WILD-TYPE                    20                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  5Q LOSS MUTATED                          6                        0
  5Q LOSS WILD-TYPE                       51                        2
D45V10, multiclass
                                      clus
vv                                     5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              3                20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           6                51
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  5Q LOSS MUTATED    3  0  1  1
  5Q LOSS WILD-TYPE 14  3 14 10
D45V11, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0               3                14
  R1               0                 3
  R2               1                14
  RX               1                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = 6P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    0  8
  6P LOSS WILD-TYPE 12 65
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                77 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                65 
$`6P LOSS MUTATED`
TCGA-TS-A8AS TCGA-LK-A4O0 TCGA-LK-A4O7 TCGA-MQ-A6BL TCGA-NQ-A57I TCGA-TS-A7P0 
       26.14         6.08        11.51        10.95         0.66        41.46 
TCGA-TS-A7P6 TCGA-UT-A88G 
        9.30         2.50 

$`6P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       23.64        27.06        56.38        11.87        29.10        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I 
       27.16        48.99         4.67        17.62        38.01        28.27 
TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 
       24.36        17.95         5.52         8.02         1.87        12.72 
TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       14.73        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
       17.33         3.52        24.89        77.56        68.71        19.99 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC 
       28.96        13.61         2.56         9.76        38.40        23.90 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       15.09         7.99        14.76        24.07        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       27.75        18.51        22.65        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       11.77        10.78        15.42        27.72         6.48        25.94 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A97Y 
        8.32        14.99        13.35        28.37        14.27         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP 
        4.67         1.28         4.37         2.76         8.58         7.50 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       16.41        40.37        32.12        43.04         2.76 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.66              1.28 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            41.46             91.73 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           10.125            17.950 
[1] "0.7 - 41.5 (10.1)" "1.3 - 91.7 (17.9)"
[1] "hr=" "2.1"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  6P LOSS MUTATED         0        2        1        1         4        0
  6P LOSS WILD-TYPE       7        0        0       15        41       16
D46V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 0                 7
  STAGE IA                2                 0
  STAGE IB                1                 0
  STAGE II                1                15
  STAGE III               4                41
  STAGE IV                0                16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6P LOSS MUTATED    3  1  4  0
  6P LOSS WILD-TYPE 11 25 28 13
D46V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               3                11
  T2               1                25
  T3               4                28
  T4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  6P LOSS MUTATED    5  1     1
  6P LOSS WILD-TYPE 39  9    28
D46V5, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0                  5                39
  N1                  1                 9
  N2+N3               1                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    4  0
  6P LOSS WILD-TYPE 53  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4    0
  6P LOSS WILD-TYPE   53    3
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0               4                53
  1               0                 3
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    0  8
  6P LOSS WILD-TYPE 16 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    8
  6P LOSS WILD-TYPE   16   63
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               0                16
  MALE                 8                63
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    7  1
  6P LOSS WILD-TYPE 55 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      7    1
  6P LOSS WILD-TYPE   55   23
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                7                55
  YES               1                23
[1] 2 2
[1] FALSE
D46V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  6P LOSS MUTATED                       3                                    0
  6P LOSS WILD-TYPE                    20                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  6P LOSS MUTATED                          4                        1
  6P LOSS WILD-TYPE                       53                        1
D46V10, multiclass
                                      clus
vv                                     6P LOSS MUTATED 6P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              3                20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           4                53
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  6P LOSS MUTATED    2  0  1  1
  6P LOSS WILD-TYPE 15  3 14 10
D46V11, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0               2                15
  R1               0                 3
  R2               1                14
  RX               1                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = 6Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    6 22
  6Q LOSS WILD-TYPE  6 51
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               28                57 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22                51 
$`6Q LOSS MUTATED`
TCGA-3U-A98E TCGA-TS-A8AS TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3U-A98D 
       62.99        26.14        56.38        11.87        29.10         4.67 
TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
        8.02         6.08         1.87        80.84        91.73        18.81 
TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SH-A7BC TCGA-TS-A7P0 
        5.19        10.95        77.56         0.66        23.90        41.46 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AY TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88G 
        9.30        19.43        15.42         8.32        13.35         2.50 
TCGA-ZN-A9VO TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        8.58        16.41        40.37        32.12 

$`6Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-UD-AAC4 
       42.81        12.66        20.71        31.20        21.83        23.64 
TCGA-UT-A88D TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98F TCGA-3U-A98H 
       27.06        13.61        27.16        48.99        17.62        38.01 
TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4O5 TCGA-LK-A4O6 
       28.27        24.36        17.95         5.52        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BR 
       11.51        23.31        17.33         3.52        24.89        68.71 
TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
       19.99        28.96        13.61         2.56         9.76        38.40 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       15.09         7.99        14.76        24.07        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF 
       27.75        18.51        22.65        15.02        32.28        11.77 
TCGA-TS-A8AI TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UT-A88C 
       10.78        27.72         6.48        25.94        14.99        28.37 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
       14.27         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VP TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        43.04         2.76 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.66              1.28 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            91.73             68.71 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           15.915            17.620 
[1] "0.7 - 91.7 (15.9)" "1.3 - 68.7 (17.6)"
[1] "hr=" "1.4"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED         3        2        1        9        12        2
  6Q LOSS WILD-TYPE       4        0        0        7        33       14
D47V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 3                 4
  STAGE IA                2                 0
  STAGE IB                1                 0
  STAGE II                9                 7
  STAGE III              12                33
  STAGE IV                2                14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6Q LOSS MUTATED    6 10 10  2
  6Q LOSS WILD-TYPE  8 16 22 11
D47V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               6                 8
  T2              10                16
  T3              10                22
  T4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  6Q LOSS MUTATED   18  1     8
  6Q LOSS WILD-TYPE 26  9    21
D47V5, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0                 18                26
  N1                  1                 9
  N2+N3               8                21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   18  1
  6Q LOSS WILD-TYPE 39  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     18    1
  6Q LOSS WILD-TYPE   39    2
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              18                39
  1               1                 2
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    5 24
  6Q LOSS WILD-TYPE 11 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5   24
  6Q LOSS WILD-TYPE   11   47
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               5                11
  MALE                24                47
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   22  6
  6Q LOSS WILD-TYPE 40 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     22    6
  6Q LOSS WILD-TYPE   40   18
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               22                40
  YES               6                18
[1] 2 2
[1] FALSE
D47V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  6Q LOSS MUTATED                       6                                    1
  6Q LOSS WILD-TYPE                    17                                    4
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  6Q LOSS MUTATED                         21                        1
  6Q LOSS WILD-TYPE                       36                        1
D47V10, multiclass
                                      clus
vv                                     6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              6                17
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               1                 4
  EPITHELIOID MESOTHELIOMA                          21                36
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  6Q LOSS MUTATED    4  2  5  2
  6Q LOSS WILD-TYPE 13  1 10  9
D47V11, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0               4                13
  R1               2                 1
  R2               5                10
  RX               2                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = 8P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    2 11
  8P LOSS WILD-TYPE 10 62
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13                72 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               11                62 
$`8P LOSS MUTATED`
TCGA-3H-AB3K TCGA-3U-A98D TCGA-3U-A98J TCGA-LK-A4O0 TCGA-MQ-A4LC TCGA-MQ-A4LI 
       56.38         4.67        24.36         6.08        91.73        18.81 
TCGA-MQ-A6BQ TCGA-SC-A6LQ TCGA-SH-A9CU TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-UD-AAC5 
       77.56         9.76        24.07        27.75        18.51         8.32 
TCGA-ZN-A9VO 
        8.58 

$`8P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       26.14        23.64        27.06        11.87        29.10        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-LK-A4NW 
       27.16        48.99        17.62        38.01        28.27        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
        5.52         8.02         1.87        12.72        14.73        11.51 
TCGA-MQ-A4KX TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       80.84        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       24.89        68.71        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
        2.56        38.40        23.90        15.09         7.99        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
       55.07         8.38        41.46        22.65         9.30        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY 
       15.02        32.28        11.77        10.78        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E 
        6.48        25.94        14.99        13.35        28.37        14.27 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
        2.50         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        40.37        32.12        43.04         2.76 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             4.67              0.66 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            91.73             80.84 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           18.810            15.915 
[1] "4.7 - 91.7 (18.8)" "0.7 - 80.8 (15.9)"
[1] "hr=" "1.4"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         2        1        0        4         4        2
  8P LOSS WILD-TYPE       5        1        1       12        41       14
D48V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 2                 5
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                4                12
  STAGE III               4                41
  STAGE IV                2                14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8P LOSS MUTATED    3  5  3  2
  8P LOSS WILD-TYPE 11 21 29 11
D48V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               3                11
  T2               5                21
  T3               3                29
  T4               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  8P LOSS MUTATED    7  1     5
  8P LOSS WILD-TYPE 37  9    24
D48V5, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0                  7                37
  N1                  1                 9
  N2+N3               5                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    9  1
  8P LOSS WILD-TYPE 48  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      9    1
  8P LOSS WILD-TYPE   48    2
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               9                48
  1               1                 2
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    2 11
  8P LOSS WILD-TYPE 14 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2   11
  8P LOSS WILD-TYPE   14   60
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               2                14
  MALE                11                60
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    8  5
  8P LOSS WILD-TYPE 54 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      8    5
  8P LOSS WILD-TYPE   54   19
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                8                54
  YES               5                19
[1] 2 2
[1] FALSE
D48V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  8P LOSS MUTATED                       1                                    1
  8P LOSS WILD-TYPE                    22                                    4
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  8P LOSS MUTATED                         10                        1
  8P LOSS WILD-TYPE                       47                        1
D48V10, multiclass
                                      clus
vv                                     8P LOSS MUTATED 8P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              1                22
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               1                 4
  EPITHELIOID MESOTHELIOMA                          10                47
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED    3  2  0  2
  8P LOSS WILD-TYPE 14  1 15  9
D48V11, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0               3                14
  R1               2                 1
  R2               0                15
  RX               2                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = 8Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    0  4
  8Q LOSS WILD-TYPE 12 69
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                81 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                69 
$`8Q LOSS MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A4LI TCGA-SH-A9CU TCGA-UD-AAC5 
        6.08        18.81        24.07         8.32 

$`8Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H 
       13.61        27.16        48.99         4.67        17.62        38.01 
TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 
       28.27        24.36        17.95         5.52         8.02         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ 
       12.72        14.73        11.51        80.84        91.73        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        77.56 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       68.71        19.99         0.66        28.96        13.61         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
        9.76        38.40        23.90        15.09         7.99        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UD-AAC7 
       15.42        27.72         6.48        25.94        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       28.37        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.37         2.76         8.58         7.50        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             6.08              0.66 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            24.07             91.73 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           13.565            17.330 
[1] "6.1 - 24.1 (13.6)" "0.7 - 91.7 (17.3)"
[1] "hr=" "1.9"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         1        1        0        1         0        1
  8Q LOSS WILD-TYPE       6        1        1       15        45       15
D49V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 1                 6
  STAGE IA                1                 1
  STAGE IB                0                 1
  STAGE II                1                15
  STAGE III               0                45
  STAGE IV                1                15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8Q LOSS MUTATED    2  1  0  1
  8Q LOSS WILD-TYPE 12 25 32 12
D49V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               2                12
  T2               1                25
  T3               0                32
  T4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  8Q LOSS MUTATED    3  0     1
  8Q LOSS WILD-TYPE 41 10    28
D49V5, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0                  3                41
  N1                  0                10
  N2+N3               1                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    4  0
  8Q LOSS WILD-TYPE 53  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      4    0
  8Q LOSS WILD-TYPE   53    3
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               4                53
  1               0                 3
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    1  3
  8Q LOSS WILD-TYPE 15 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    3
  8Q LOSS WILD-TYPE   15   68
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               1                15
  MALE                 3                68
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    3  1
  8Q LOSS WILD-TYPE 59 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    1
  8Q LOSS WILD-TYPE   59   23
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                3                59
  YES               1                23
[1] 2 2
[1] FALSE
D49V9, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                16 
       TCGA-3U-A98E        TCGA-UT-A88D        TCGA-3U-A98J        TCGA-SC-A6LM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SC-A6LN        TCGA-SC-A6LP        TCGA-SC-A6LR        TCGA-SH-A7BH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SH-A9CT        TCGA-UT-A88C        TCGA-XT-AASU        TCGA-ZN-A9VO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ZN-A9VP        TCGA-ZN-A9VQ        TCGA-ZN-A9VS        TCGA-ZN-A9VU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  8Q LOSS MUTATED                       0                                    0
  8Q LOSS WILD-TYPE                    23                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  8Q LOSS MUTATED                          3                        1
  8Q LOSS WILD-TYPE                       54                        1
D49V10, multiclass
                                      clus
vv                                     8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              0                23
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                           3                54
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  8Q LOSS MUTATED    1  1  0  2
  8Q LOSS WILD-TYPE 16  2 15  9
D49V11, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               1                16
  R1               1                 2
  R2               0                15
  RX               2                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = 9P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED    1 26
  9P LOSS WILD-TYPE 11 47
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               27                58 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               26                47 
$`9P LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3T TCGA-3U-A98F TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O7 
       11.87        13.61        17.62         5.52         6.08        11.51 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
        5.19        17.33         3.52        19.99         0.66        28.96 
TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
       13.61        23.90        24.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P6 TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AAC7 
       18.51         9.30        11.77        10.78        15.42        13.35 
TCGA-UT-A88E TCGA-UT-A88G TCGA-ZN-A9VP 
       14.27         2.50         7.50 

$`9P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3U 
       26.14        23.64        27.06        56.38        29.10        27.16 
TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW 
       48.99         4.67        38.01        28.27        24.36        17.95 
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        8.02         1.87        12.72        14.73        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       18.81        23.31        10.95        24.89        77.56        68.71 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
        2.56         9.76        38.40        15.09         7.99        14.76 
TCGA-TS-A7OU TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-UD-AABY 
       55.07        22.65        19.43        15.02        32.28        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A97Y 
        6.48        25.94         8.32        14.99        28.37         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VQ 
        4.67         1.28         4.37         2.76         8.58        16.41 
TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       40.37        32.12        43.04         2.76 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.66              1.28 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            41.46             91.73 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            13.35             22.24 
[1] "0.7 - 41.5 (13.3)" "1.3 - 91.7 (22.2)"
[1] "hr=" "2.4"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         3        1        1        3        16        4
  9P LOSS WILD-TYPE       4        1        0       13        29       12
D50V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 3                 4
  STAGE IA                1                 1
  STAGE IB                1                 0
  STAGE II                3                13
  STAGE III              16                29
  STAGE IV                4                12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9P LOSS MUTATED    5  5 14  3
  9P LOSS WILD-TYPE  9 21 18 10
D50V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               5                 9
  T2               5                21
  T3              14                18
  T4               3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  9P LOSS MUTATED   13  4     8
  9P LOSS WILD-TYPE 31  6    21
D50V5, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0                 13                31
  N1                  4                 6
  N2+N3               8                21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   17  0
  9P LOSS WILD-TYPE 40  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     17    0
  9P LOSS WILD-TYPE   40    3
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              17                40
  1               0                 3
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    3 25
  9P LOSS WILD-TYPE 13 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      3   25
  9P LOSS WILD-TYPE   13   46
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               3                13
  MALE                25                46
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   20  7
  9P LOSS WILD-TYPE 42 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     20    7
  9P LOSS WILD-TYPE   42   17
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               20                42
  YES               7                17
[1] 2 2
[1] FALSE
D50V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  9P LOSS MUTATED                       9                                    0
  9P LOSS WILD-TYPE                    14                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  9P LOSS MUTATED                         18                        1
  9P LOSS WILD-TYPE                       39                        1
D50V10, multiclass
                                      clus
vv                                     9P LOSS MUTATED 9P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              9                14
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                          18                39
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  9P LOSS MUTATED    7  0  4  3
  9P LOSS WILD-TYPE 10  3 11  8
D50V11, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0               7                10
  R1               0                 3
  R2               4                11
  RX               3                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 9Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    2 19
  9Q LOSS WILD-TYPE 10 54
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               21                64 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               19                54 
$`9Q LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3T TCGA-3U-A98F TCGA-LK-A4O0 TCGA-MQ-A4LI TCGA-MQ-A4LM 
       11.87        13.61        17.62         6.08        18.81         5.19 
TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BC TCGA-SH-A9CT 
        3.52        19.99         0.66        28.96        23.90        14.76 
TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A8AI TCGA-UD-AAC7 TCGA-UT-A88E 
       24.07         8.38        41.46        10.78        13.35        14.27 
TCGA-UT-A88G TCGA-ZN-A9VO TCGA-ZN-A9VP 
        2.50         8.58         7.50 

$`9Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3U 
       26.14        23.64        27.06        56.38        29.10        27.16 
TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW 
       48.99         4.67        38.01        28.27        24.36        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
        5.52         8.02         1.87        12.72        14.73        11.51 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN 
       80.84        91.73        23.31        17.33        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
       77.56        68.71        13.61         2.56         9.76        38.40 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-TS-A7OU TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 
       15.09         7.99        55.07        27.75        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AY 
        9.30        19.43        15.02        32.28        11.77        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C 
       27.72         6.48        25.94         8.32        14.99        28.37 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ 
        4.73         4.67         1.28         4.37         2.76        16.41 
TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       40.37        32.12        43.04         2.76 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.66              1.28 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            41.46             91.73 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            13.35             20.07 
[1] "0.7 - 41.5 (13.3)" "1.3 - 91.7 (20.1)"
[1] "hr=" "2"  
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         2        1        1        5         8        5
  9Q LOSS WILD-TYPE       5        1        0       11        37       11
D51V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 2                 5
  STAGE IA                1                 1
  STAGE IB                1                 0
  STAGE II                5                11
  STAGE III               8                37
  STAGE IV                5                11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9Q LOSS MUTATED    4  5  8  4
  9Q LOSS WILD-TYPE 10 21 24  9
D51V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               4                10
  T2               5                21
  T3               8                24
  T4               4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  9Q LOSS MUTATED   12  1     6
  9Q LOSS WILD-TYPE 32  9    23
D51V5, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0                 12                32
  N1                  1                 9
  N2+N3               6                23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   15  1
  9Q LOSS WILD-TYPE 42  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     15    1
  9Q LOSS WILD-TYPE   42    2
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              15                42
  1               1                 2
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    2 20
  9Q LOSS WILD-TYPE 14 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2   20
  9Q LOSS WILD-TYPE   14   51
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               2                14
  MALE                20                51
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   15  6
  9Q LOSS WILD-TYPE 47 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     15    6
  9Q LOSS WILD-TYPE   47   18
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               15                47
  YES               6                18
[1] 2 2
[1] FALSE
D51V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  9Q LOSS MUTATED                       6                                    0
  9Q LOSS WILD-TYPE                    17                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  9Q LOSS MUTATED                         15                        1
  9Q LOSS WILD-TYPE                       42                        1
D51V10, multiclass
                                      clus
vv                                     9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              6                17
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                          15                42
  SARCOMATOID MESOTHELIOMA                           1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  9Q LOSS MUTATED    4  1  4  3
  9Q LOSS WILD-TYPE 13  2 11  8
D51V11, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0               4                13
  R1               1                 2
  R2               4                11
  RX               3                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = 10P LOSS MUTATION ANALYSIS
D52V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    1 23
  10P LOSS WILD-TYPE 11 50
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                24                 61 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                23                 50 
$`10P LOSS MUTATED`
TCGA-3H-AB3L TCGA-3U-A98D TCGA-3U-A98I TCGA-LK-A4O7 TCGA-MQ-A4LP TCGA-MQ-A6BS 
       11.87         4.67        28.27        11.51        17.33        19.99 
TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P0 
        0.66        23.90        15.09         7.99        24.07        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A8AI TCGA-UD-AABY TCGA-UD-AAC5 
       18.51         9.30        15.02        10.78        27.72         8.32 
TCGA-UD-AAC7 TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-ZN-A9VQ TCGA-ZN-A9VW 
       13.35         2.50         4.73         4.67        16.41         2.76 

$`10P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        29.10        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NW 
       27.16        48.99        17.62        38.01        24.36        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08         1.87        12.72        14.73 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV 
       80.84        91.73        18.81        23.31         5.19         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN 
       10.95        24.89        77.56        68.71        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY 
        2.56         9.76        38.40        14.76        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AY 
       27.75        22.65        19.43        32.28        11.77        15.42 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E TCGA-YS-A95B 
        6.48        25.94        14.99        28.37        14.27         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VS TCGA-ZN-A9VU 
        4.37         2.76         8.58         7.50        40.37        32.12 
TCGA-ZN-A9VV 
       43.04 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.66               1.28 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             41.46              91.73 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             12.61              20.71 
[1] "0.7 - 41.5 (12.6)" "1.3 - 91.7 (20.7)"
[1] "hr=" "2.2"
D52V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         4        0        1        3        12        5
  10P LOSS WILD-TYPE       3        2        0       13        33       11
D52V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  4                  3
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 3                 13
  STAGE III               12                 33
  STAGE IV                 5                 11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10P LOSS MUTATED    5  5  9  4
  10P LOSS WILD-TYPE  9 21 23  9
D52V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                5                  9
  T2                5                 21
  T3                9                 23
  T4                4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  10P LOSS MUTATED   13  3     6
  10P LOSS WILD-TYPE 31  7    23
D52V5, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                  13                 31
  N1                   3                  7
  N2+N3                6                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   14  1
  10P LOSS WILD-TYPE 43  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     14    1
  10P LOSS WILD-TYPE   43    2
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               14                 43
  1                1                  2
[1] 2 2
[1] FALSE
D52V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    2 23
  10P LOSS WILD-TYPE 14 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   23
  10P LOSS WILD-TYPE   14   48
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                2                 14
  MALE                 23                 48
[1] 2 2
[1] FALSE
D52V8, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   19  5
  10P LOSS WILD-TYPE 43 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     19    5
  10P LOSS WILD-TYPE   43   19
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                19                 43
  YES                5                 19
[1] 2 2
[1] FALSE
D52V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  10P LOSS MUTATED                       9                                    1
  10P LOSS WILD-TYPE                    14                                    4
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  10P LOSS MUTATED                         15                        0
  10P LOSS WILD-TYPE                       42                        2
D52V10, multiclass
                                      clus
vv                                     10P LOSS MUTATED 10P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               9                 14
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                1                  4
  EPITHELIOID MESOTHELIOMA                           15                 42
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  10P LOSS MUTATED    4  0  5  5
  10P LOSS WILD-TYPE 13  3 10  6
D52V11, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0                4                 13
  R1                0                  3
  R2                5                 10
  RX                5                  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"

Clustering(53) Variable = 10Q LOSS MUTATION ANALYSIS
D53V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    2 17
  10Q LOSS WILD-TYPE 10 56
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                19                 66 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                17                 56 
$`10Q LOSS MUTATED`
TCGA-3H-AB3L TCGA-3U-A98D TCGA-LK-A4O7 TCGA-MQ-A4LP TCGA-MQ-A6BS TCGA-NQ-A57I 
       11.87         4.67        11.51        17.33        19.99         0.66 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A8AI 
       15.09         7.99        24.07         9.30        15.02        10.78 
TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88G TCGA-UT-A97Y TCGA-ZN-A9VO TCGA-ZN-A9VQ 
        8.32        13.35         2.50         4.73         8.58        16.41 
TCGA-ZN-A9VW 
        2.76 

$`10Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        29.10        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       27.16        48.99        17.62        38.01        28.27        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       17.95         5.52         8.02         6.08         1.87        12.72 
TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       14.73        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM 
        3.52        10.95        24.89        77.56        68.71        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A9CT 
       13.61         2.56         9.76        38.40        23.90        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       19.43        32.28        11.77        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-A95B 
       25.94        14.99        28.37        14.27         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VP TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV 
        4.37         2.76         7.50        40.37        32.12        43.04 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.66               1.28 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             24.07              91.73 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             10.78              22.24 
[1] "0.7 - 24.1 (10.8)" "1.3 - 91.7 (22.2)"
[1] "hr=" "3.2"
D53V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         3        0        1        2         8        5
  10Q LOSS WILD-TYPE       4        2        0       14        37       11
D53V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  3                  4
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 2                 14
  STAGE III                8                 37
  STAGE IV                 5                 11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10Q LOSS MUTATED    4  4  5  4
  10Q LOSS WILD-TYPE 10 22 27  9
D53V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                4                 10
  T2                4                 22
  T3                5                 27
  T4                4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  10Q LOSS MUTATED   10  3     5
  10Q LOSS WILD-TYPE 34  7    24
D53V5, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                  10                 34
  N1                   3                  7
  N2+N3                5                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   10  2
  10Q LOSS WILD-TYPE 47  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     10    2
  10Q LOSS WILD-TYPE   47    1
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               10                 47
  1                2                  1
[1] 2 2
[1] FALSE
D53V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    2 17
  10Q LOSS WILD-TYPE 14 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2   17
  10Q LOSS WILD-TYPE   14   54
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                2                 14
  MALE                 17                 54
[1] 2 2
[1] FALSE
D53V8, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   14  5
  10Q LOSS WILD-TYPE 48 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     14    5
  10Q LOSS WILD-TYPE   48   19
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                14                 48
  YES                5                 19
[1] 2 2
[1] FALSE
D53V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  10Q LOSS MUTATED                       7                                    0
  10Q LOSS WILD-TYPE                    16                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  10Q LOSS MUTATED                         12                        0
  10Q LOSS WILD-TYPE                       45                        2
D53V10, multiclass
                                      clus
vv                                     10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               7                 16
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                           12                 45
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  10Q LOSS MUTATED    2  0  4  4
  10Q LOSS WILD-TYPE 15  3 11  7
D53V11, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0                2                 15
  R1                0                  3
  R2                4                 11
  RX                4                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 11P LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    0  4
  11P LOSS WILD-TYPE 12 69
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 4                 81 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 4                 69 
$`11P LOSS MUTATED`
TCGA-3H-AB3M TCGA-LK-A4O0 TCGA-NQ-A57I TCGA-SC-A6LN 
       29.10         6.08         0.66        13.61 

$`11P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        11.87        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I 
       27.16        48.99         4.67        17.62        38.01        28.27 
TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 
       24.36        17.95         5.52         8.02         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        77.56 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
       68.71        19.99        28.96         2.56         9.76        38.40 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU 
       23.90        15.09         7.99        14.76        24.07        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
        8.38        27.75        41.46        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY 
       19.43        15.02        32.28        11.77        10.78        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
       27.72         6.48        25.94         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       28.37        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.37         2.76         8.58         7.50        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.66               1.28 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             29.10              91.73 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             9.845             17.620 
[1] "0.7 - 29.1 (9.8)"  "1.3 - 91.7 (17.6)"
[1] "hr=" "1.9"
D54V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         0        1        1        0         2        0
  11P LOSS WILD-TYPE       7        1        0       16        43       16
D54V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 1                  1
  STAGE IB                 1                  0
  STAGE II                 0                 16
  STAGE III                2                 43
  STAGE IV                 0                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11P LOSS MUTATED    2  1  1  0
  11P LOSS WILD-TYPE 12 25 31 13
D54V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                2                 12
  T2                1                 25
  T3                1                 31
  T4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  11P LOSS MUTATED    1  0     2
  11P LOSS WILD-TYPE 43 10    27
D54V5, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                   1                 43
  N1                   0                 10
  N2+N3                2                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    3  0
  11P LOSS WILD-TYPE 54  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3    0
  11P LOSS WILD-TYPE   54    3
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                3                 54
  1                0                  3
[1] 2 2
[1] FALSE
D54V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    1  3
  11P LOSS WILD-TYPE 15 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1    3
  11P LOSS WILD-TYPE   15   68
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                1                 15
  MALE                  3                 68
[1] 2 2
[1] FALSE
D54V8, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    3  1
  11P LOSS WILD-TYPE 59 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3    1
  11P LOSS WILD-TYPE   59   23
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 3                 59
  YES                1                 23
[1] 2 2
[1] FALSE
D54V9, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 16 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LP         TCGA-SC-A6LR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-SH-A7BH         TCGA-SH-A9CT         TCGA-SH-A9CU 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-UT-A88C         TCGA-XT-AASU         TCGA-ZN-A9VO 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ZN-A9VP         TCGA-ZN-A9VQ         TCGA-ZN-A9VS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ZN-A9VU 
"11P LOSS WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  11P LOSS MUTATED                       2                                    0
  11P LOSS WILD-TYPE                    21                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  11P LOSS MUTATED                          1                        1
  11P LOSS WILD-TYPE                       56                        1
D54V10, multiclass
                                      clus
vv                                     11P LOSS MUTATED 11P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               2                 21
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            1                 56
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  11P LOSS MUTATED    2  0  1  0
  11P LOSS WILD-TYPE 15  3 14 11
D54V11, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0                2                 15
  R1                0                  3
  R2                1                 14
  RX                0                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = 11Q LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    0  5
  11Q LOSS WILD-TYPE 12 68
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 80 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 68 
$`11Q LOSS MUTATED`
TCGA-3H-AB3M TCGA-LK-A4O0 TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-NQ-A57I 
       29.10         6.08         5.19         3.52         0.66 

$`11Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        11.87        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I 
       27.16        48.99         4.67        17.62        38.01        28.27 
TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 
       24.36        17.95         5.52         8.02         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
       17.33        10.95        24.89        77.56        68.71        19.99 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC 
       28.96        13.61         2.56         9.76        38.40        23.90 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       15.09         7.99        14.76        24.07        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
       27.75        41.46        18.51        22.65         9.30        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY 
       15.02        32.28        11.77        10.78        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        6.48        25.94         8.32        14.99        13.35        28.37 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       14.27         2.50         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        2.76         8.58         7.50        16.41        40.37        32.12 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       43.04         2.76 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.66               1.28 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             29.10              91.73 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             5.190             17.785 
[1] "0.7 - 29.1 (5.2)"  "1.3 - 91.7 (17.8)"
[1] "hr=" "2.7"
D55V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         0        1        1        0         3        0
  11Q LOSS WILD-TYPE       7        1        0       16        42       16
D55V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 1                  1
  STAGE IB                 1                  0
  STAGE II                 0                 16
  STAGE III                3                 42
  STAGE IV                 0                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED    2  0  3  0
  11Q LOSS WILD-TYPE 12 26 29 13
D55V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                2                 12
  T2                0                 26
  T3                3                 29
  T4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  11Q LOSS MUTATED    3  0     1
  11Q LOSS WILD-TYPE 41 10    28
D55V5, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                   3                 41
  N1                   0                 10
  N2+N3                1                 28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    4  0
  11Q LOSS WILD-TYPE 53  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4    0
  11Q LOSS WILD-TYPE   53    3
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                4                 53
  1                0                  3
[1] 2 2
[1] FALSE
D55V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    1  4
  11Q LOSS WILD-TYPE 15 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1    4
  11Q LOSS WILD-TYPE   15   67
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                1                 15
  MALE                  4                 67
[1] 2 2
[1] FALSE
D55V8, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    5  0
  11Q LOSS WILD-TYPE 57 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      5    0
  11Q LOSS WILD-TYPE   57   24
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 5                 57
  YES                0                 24
[1] 2 2
[1] FALSE
D55V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  11Q LOSS MUTATED                       3                                    0
  11Q LOSS WILD-TYPE                    20                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  11Q LOSS MUTATED                          1                        1
  11Q LOSS WILD-TYPE                       56                        1
D55V10, multiclass
                                      clus
vv                                     11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               3                 20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            1                 56
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  11Q LOSS MUTATED    2  0  1  0
  11Q LOSS WILD-TYPE 15  3 14 11
D55V11, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0                2                 15
  R1                0                  3
  R2                1                 14
  RX                0                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = 12P LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    0  4
  12P LOSS WILD-TYPE 12 69
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 81 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 69 
$`12P LOSS MUTATED`
TCGA-3H-AB3T TCGA-3U-A98F TCGA-SH-A7BH TCGA-SH-A9CT 
       13.61        17.62         7.99        14.76 

$`12P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       27.16        48.99         4.67        38.01        28.27        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       17.95         5.52         8.02         6.08         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       14.73        11.51        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        77.56 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       68.71        19.99         0.66        28.96        13.61         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CU TCGA-TS-A7OU 
        9.76        38.40        23.90        15.09        24.07        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
        8.38        27.75        41.46        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY 
       19.43        15.02        32.28        11.77        10.78        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
       27.72         6.48        25.94         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       28.37        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.37         2.76         8.58         7.50        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              7.99               0.66 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             17.62              91.73 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            14.185             17.950 
[1] "8.0 - 17.6 (14.2)" "0.7 - 91.7 (17.9)"
[1] "hr=" "2.2"
D56V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  12P LOSS MUTATED         1        0        0        1         2        0
  12P LOSS WILD-TYPE       6        2        1       15        43       16
D56V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 1                 15
  STAGE III                2                 43
  STAGE IV                 0                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12P LOSS MUTATED    1  1  2  0
  12P LOSS WILD-TYPE 13 25 30 13
D56V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                1                 13
  T2                1                 25
  T3                2                 30
  T4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  12P LOSS MUTATED    4  0     0
  12P LOSS WILD-TYPE 40 10    29
D56V5, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                   4                 40
  N1                   0                 10
  N2+N3                0                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    4  0
  12P LOSS WILD-TYPE 53  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4    0
  12P LOSS WILD-TYPE   53    3
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                4                 53
  1                0                  3
[1] 2 2
[1] FALSE
D56V7, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    1  3
  12P LOSS WILD-TYPE 15 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1    3
  12P LOSS WILD-TYPE   15   68
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                1                 15
  MALE                  3                 68
[1] 2 2
[1] FALSE
D56V8, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    2  2
  12P LOSS WILD-TYPE 60 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    2
  12P LOSS WILD-TYPE   60   22
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 2                 60
  YES                2                 22
[1] 2 2
[1] FALSE
D56V9, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                 15 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A9CU         TCGA-UT-A88C 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-XT-AASU         TCGA-ZN-A9VO         TCGA-ZN-A9VP 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ZN-A9VQ         TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  12P LOSS MUTATED                       3                                    0
  12P LOSS WILD-TYPE                    20                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  12P LOSS MUTATED                          1                        0
  12P LOSS WILD-TYPE                       56                        2
D56V10, multiclass
                                      clus
vv                                     12P LOSS MUTATED 12P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               3                 20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            1                 56
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  12P LOSS MUTATED    0  0  1  0
  12P LOSS WILD-TYPE 17  3 14 11
D56V11, multiclass
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 45 
        TCGA-3U-A98G         TCGA-LK-A4O4         TCGA-SC-AA5Z 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-UD-AAC4         TCGA-UT-A88D         TCGA-LK-A4NW 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-LK-A4NY         TCGA-LK-A4NZ         TCGA-LK-A4O0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-LK-A4O2         TCGA-LK-A4O5         TCGA-LK-A4O6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-LK-A4O7         TCGA-MQ-A4KX         TCGA-MQ-A4LC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LV         TCGA-MQ-A6BN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-MQ-A6BQ         TCGA-MQ-A6BR         TCGA-MQ-A6BS 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-NQ-A57I         TCGA-NQ-A638         TCGA-SC-A6LM 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SC-A6LN         TCGA-SC-A6LP         TCGA-SC-A6LQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A7BC         TCGA-SH-A7BD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SH-A9CU         TCGA-UD-AABY         TCGA-UD-AABZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-UD-AAC1         TCGA-UD-AAC5         TCGA-UD-AAC6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-UD-AAC7         TCGA-UT-A88C         TCGA-UT-A88E 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-UT-A88G         TCGA-UT-A97Y         TCGA-XT-AASU 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-YS-A95B         TCGA-YS-A95C         TCGA-YS-AA4M 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 

Clustering(57) Variable = 13Q LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    3 30
  13Q LOSS WILD-TYPE  9 43
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                33                 52 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                30                 43 
$`13Q LOSS MUTATED`
TCGA-TS-A8AS TCGA-3H-AB3L TCGA-3H-AB3T TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O2 
       26.14        11.87        13.61        17.95         6.08         1.87 
TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV 
       12.72        80.84        18.81        23.31         5.19         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SH-A7BC TCGA-SH-A7BD 
       10.95        19.99        13.61         2.56        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AI 
        7.99        24.07         8.38         9.30        19.43        10.78 
TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88G TCGA-YS-AA4M 
       15.42         6.48        13.35        28.37         2.50         2.76 
TCGA-ZN-A9VO TCGA-ZN-A9VS TCGA-ZN-A9VU 
        8.58        40.37        32.12 

$`13Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3U TCGA-3H-AB3X 
       23.64        27.06        56.38        29.10        27.16        48.99 
TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NY 
        4.67        17.62        38.01        28.27        24.36         5.52 
TCGA-LK-A4NZ TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LC TCGA-MQ-A4LP TCGA-MQ-A6BN 
        8.02        14.73        11.51        91.73        17.33        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LQ TCGA-SC-A6LR 
       77.56        68.71         0.66        28.96         9.76        38.40 
TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       14.76        55.07        27.75        41.46        18.51        22.65 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC5 
       15.02        32.28        11.77        27.72        25.94         8.32 
TCGA-UD-AAC6 TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       14.99        14.27         4.73         4.67         1.28         4.37 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        43.04         2.76 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              1.87               0.66 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             80.84              91.73 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             13.35              22.24 
[1] "1.9 - 80.8 (13.3)" "0.7 - 91.7 (22.2)"
[1] "hr=" "1.9"
D57V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         2        2        0        7        15        7
  13Q LOSS WILD-TYPE       5        0        1        9        30        9
D57V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  2                  5
  STAGE IA                 2                  0
  STAGE IB                 0                  1
  STAGE II                 7                  9
  STAGE III               15                 30
  STAGE IV                 7                  9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  13Q LOSS MUTATED    5 10 13  4
  13Q LOSS WILD-TYPE  9 16 19  9
D57V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                5                  9
  T2               10                 16
  T3               13                 19
  T4                4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  13Q LOSS MUTATED   20  3    10
  13Q LOSS WILD-TYPE 24  7    19
D57V5, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                  20                 24
  N1                   3                  7
  N2+N3               10                 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"
D57V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   21  3
  13Q LOSS WILD-TYPE 36  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     21    3
  13Q LOSS WILD-TYPE   36    0
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               21                 36
  1                3                  0
[1] 2 2
[1] FALSE
D57V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    5 28
  13Q LOSS WILD-TYPE 11 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      5   28
  13Q LOSS WILD-TYPE   11   43
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                5                 11
  MALE                 28                 43
[1] 2 2
[1] FALSE
D57V8, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   24  9
  13Q LOSS WILD-TYPE 38 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     24    9
  13Q LOSS WILD-TYPE   38   15
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                24                 38
  YES                9                 15
[1] 2 2
[1] FALSE
D57V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  13Q LOSS MUTATED                       8                                    2
  13Q LOSS WILD-TYPE                    15                                    3
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  13Q LOSS MUTATED                         22                        1
  13Q LOSS WILD-TYPE                       35                        1
D57V10, multiclass
                                      clus
vv                                     13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               8                 15
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                2                  3
  EPITHELIOID MESOTHELIOMA                           22                 35
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  13Q LOSS MUTATED    6  2  6  5
  13Q LOSS WILD-TYPE 11  1  9  6
D57V11, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0                6                 11
  R1                2                  1
  R2                6                  9
  RX                5                  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"

Clustering(58) Variable = 14Q LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    3 31
  14Q LOSS WILD-TYPE  9 42
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                34                 51 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                31                 42 
$`14Q LOSS MUTATED`
TCGA-3H-AB3S TCGA-3H-AB3M TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98I TCGA-3U-A98J 
       12.66        29.10        48.99         4.67        28.27        24.36 
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.87        12.72        14.73        11.51        18.81        23.31 
TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT 
       19.99        13.61         9.76        23.90         7.99        14.76 
TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P8 
       24.07         8.38        27.75        41.46         9.30        15.02 
TCGA-TS-A8AF TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88G TCGA-UT-A97Y 
       11.77        15.42         6.48        13.35         2.50         4.73 
TCGA-YS-A95B TCGA-YS-A95C TCGA-ZN-A9VP TCGA-ZN-A9VS 
        1.28         4.37         7.50        40.37 

$`14Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-TS-A8AS 
       42.81        62.99        20.71        31.20        21.83        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T TCGA-3H-AB3U 
       23.64        27.06        56.38        11.87        13.61        27.16 
TCGA-3U-A98F TCGA-3U-A98H TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 
       17.62        38.01        17.95         5.52         8.02         6.08 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       80.84        91.73         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP 
       24.89        77.56        68.71         0.66        28.96         2.56 
TCGA-SC-A6LR TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 
       38.40        15.09        55.07        18.51        22.65        19.43 
TCGA-TS-A7PB TCGA-TS-A8AI TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 
       32.28        10.78        27.72        25.94         8.32        14.99 
TCGA-UT-A88C TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VQ 
       28.37        14.27         4.67         2.76         8.58        16.41 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              1.28               0.66 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             48.99              91.73 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             13.48              20.71 
[1] "1.3 - 49.0 (13.5)" "0.7 - 91.7 (20.7)"
[1] "hr=" "1.8"
D58V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED         1        0        0        7        23        4
  14Q LOSS WILD-TYPE       6        2        1        9        22       12
D58V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 7                  9
  STAGE III               23                 22
  STAGE IV                 4                 12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  14Q LOSS MUTATED    2 11 18  3
  14Q LOSS WILD-TYPE 12 15 14 10
D58V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                2                 12
  T2               11                 15
  T3               18                 14
  T4                3                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  14Q LOSS MUTATED   14  6    14
  14Q LOSS WILD-TYPE 30  4    15
D58V5, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                  14                 30
  N1                   6                  4
  N2+N3               14                 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"
D58V6, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   25  0
  14Q LOSS WILD-TYPE 32  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     25    0
  14Q LOSS WILD-TYPE   32    3
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               25                 32
  1                0                  3
[1] 2 2
[1] FALSE
D58V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   10 25
  14Q LOSS WILD-TYPE  6 46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10   25
  14Q LOSS WILD-TYPE    6   46
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               10                  6
  MALE                 25                 46
[1] 2 2
[1] FALSE
D58V8, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   25  9
  14Q LOSS WILD-TYPE 37 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     25    9
  14Q LOSS WILD-TYPE   37   15
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                25                 37
  YES                9                 15
[1] 2 2
[1] FALSE
D58V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  14Q LOSS MUTATED                       6                                    0
  14Q LOSS WILD-TYPE                    17                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  14Q LOSS MUTATED                         29                        0
  14Q LOSS WILD-TYPE                       28                        2
D58V10, multiclass
                                      clus
vv                                     14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               6                 17
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                           29                 28
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  14Q LOSS MUTATED    6  2  5  5
  14Q LOSS WILD-TYPE 11  1 10  6
D58V11, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0                6                 11
  R1                2                  1
  R2                5                 10
  RX                5                  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"

Clustering(59) Variable = 15Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    0 11
  15Q LOSS WILD-TYPE 12 62
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                11                 74 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                11                 62 
$`15Q LOSS MUTATED`
TCGA-3H-AB3T TCGA-3U-A98F TCGA-LK-A4O0 TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I 
       13.61        17.62         6.08         3.52        19.99         0.66 
TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P6 TCGA-UD-AABZ 
       23.90         7.99        24.07         9.30         6.48 

$`15Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       27.16        48.99         4.67        38.01        28.27        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
       17.95         5.52         8.02         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM 
       17.33        10.95        24.89        77.56        68.71        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD TCGA-SH-A9CT 
       13.61         2.56         9.76        38.40        15.09        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY 
       19.43        15.02        32.28        11.77        10.78        15.42 
TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       27.72        25.94         8.32        14.99        13.35        28.37 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       14.27         2.50         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        2.76         8.58         7.50        16.41        40.37        32.12 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       43.04         2.76 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.66               1.28 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             24.07              91.73 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              9.30              18.23 
[1] "0.7 - 24.1 (9.3)"  "1.3 - 91.7 (18.2)"
[1] "hr=" "2.6"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         1        1        1        2         5        1
  15Q LOSS WILD-TYPE       6        1        0       14        40       15
D59V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 1                  1
  STAGE IB                 1                  0
  STAGE II                 2                 14
  STAGE III                5                 40
  STAGE IV                 1                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  15Q LOSS MUTATED    3  2  5  1
  15Q LOSS WILD-TYPE 11 24 27 12
D59V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                3                 11
  T2                2                 24
  T3                5                 27
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  15Q LOSS MUTATED    7  0     3
  15Q LOSS WILD-TYPE 37 10    26
D59V5, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                   7                 37
  N1                   0                 10
  N2+N3                3                 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"
D59V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    8  0
  15Q LOSS WILD-TYPE 49  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      8    0
  15Q LOSS WILD-TYPE   49    3
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0                8                 49
  1                0                  3
[1] 2 2
[1] FALSE
D59V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1 10
  15Q LOSS WILD-TYPE 15 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   10
  15Q LOSS WILD-TYPE   15   61
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                1                 15
  MALE                 10                 61
[1] 2 2
[1] FALSE
D59V8, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    7  4
  15Q LOSS WILD-TYPE 55 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7    4
  15Q LOSS WILD-TYPE   55   20
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 7                 55
  YES                4                 20
[1] 2 2
[1] FALSE
D59V9, continuous
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 15 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A9CT         TCGA-UT-A88C 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-XT-AASU         TCGA-ZN-A9VO         TCGA-ZN-A9VP 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ZN-A9VQ         TCGA-ZN-A9VS         TCGA-ZN-A9VU 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  15Q LOSS MUTATED                       5                                    0
  15Q LOSS WILD-TYPE                    18                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  15Q LOSS MUTATED                          5                        1
  15Q LOSS WILD-TYPE                       52                        1
D59V10, multiclass
                                      clus
vv                                     15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               5                 18
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            5                 52
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED    3  0  3  2
  15Q LOSS WILD-TYPE 14  3 12  9
D59V11, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0                3                 14
  R1                0                  3
  R2                3                 12
  RX                2                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = 16P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    2  6
  16P LOSS WILD-TYPE 10 67
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 8                 77 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                 67 
$`16P LOSS MUTATED`
TCGA-3H-AB3X TCGA-3U-A98I TCGA-LK-A4O0 TCGA-MQ-A4LM TCGA-MQ-A6BS TCGA-UT-A88G 
       48.99        28.27         6.08         5.19        19.99         2.50 
TCGA-UT-A97Y TCGA-ZN-A9VQ 
        4.73        16.41 

$`16P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98J 
       13.61        27.16         4.67        17.62        38.01        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
       17.95         5.52         8.02         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP 
       11.51        80.84        91.73        18.81        23.31        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
        3.52        10.95        24.89        77.56        68.71         0.66 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC 
       28.96        13.61         2.56         9.76        38.40        23.90 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       15.09         7.99        14.76        24.07        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
       27.75        41.46        18.51        22.65         9.30        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY 
       15.02        32.28        11.77        10.78        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        6.48        25.94         8.32        14.99        13.35        28.37 
TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO 
       14.27         4.67         1.28         4.37         2.76         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        40.37        32.12        43.04         2.76 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              2.50               0.66 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             48.99              91.73 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            11.245             17.620 
[1] "2.5 - 49.0 (11.2)" "0.7 - 91.7 (17.6)"
[1] "hr=" "1.2"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         2        1        0        1         3        1
  16P LOSS WILD-TYPE       5        1        1       15        42       15
D60V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  2                  5
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 1                 15
  STAGE III                3                 42
  STAGE IV                 1                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  16P LOSS MUTATED    3  1  3  1
  16P LOSS WILD-TYPE 11 25 29 12
D60V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                3                 11
  T2                1                 25
  T3                3                 29
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  16P LOSS MUTATED    7  0     1
  16P LOSS WILD-TYPE 37 10    28
D60V5, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                   7                 37
  N1                   0                 10
  N2+N3                1                 28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    6  0
  16P LOSS WILD-TYPE 51  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      6    0
  16P LOSS WILD-TYPE   51    3
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                6                 51
  1                0                  3
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  7
  16P LOSS WILD-TYPE 15 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    7
  16P LOSS WILD-TYPE   15   64
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                1                 15
  MALE                  7                 64
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    7  1
  16P LOSS WILD-TYPE 55 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7    1
  16P LOSS WILD-TYPE   55   23
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 7                 55
  YES                1                 23
[1] 2 2
[1] FALSE
D60V9, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 16 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A7BH         TCGA-SH-A9CT 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SH-A9CU         TCGA-UT-A88C         TCGA-XT-AASU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ZN-A9VO         TCGA-ZN-A9VP         TCGA-ZN-A9VS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ZN-A9VU 
"16P LOSS WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  16P LOSS MUTATED                       4                                    0
  16P LOSS WILD-TYPE                    19                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  16P LOSS MUTATED                          3                        1
  16P LOSS WILD-TYPE                       54                        1
D60V10, multiclass
                                      clus
vv                                     16P LOSS MUTATED 16P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               4                 19
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            3                 54
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  16P LOSS MUTATED    2  0  0  2
  16P LOSS WILD-TYPE 15  3 15  9
D60V11, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0                2                 15
  R1                0                  3
  R2                0                 15
  RX                2                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = 16Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    2  8
  16Q LOSS WILD-TYPE 10 65
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                 75 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 8                 65 
$`16Q LOSS MUTATED`
TCGA-3H-AB3T TCGA-3H-AB3X TCGA-3U-A98I TCGA-LK-A4O0 TCGA-LK-A4O6 TCGA-MQ-A6BS 
       13.61        48.99        28.27         6.08        14.73        19.99 
TCGA-UD-AABZ TCGA-UT-A88G TCGA-UT-A97Y TCGA-ZN-A9VQ 
        6.48         2.50         4.73        16.41 

$`16Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3U TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NW 
       27.16         4.67        17.62        38.01        24.36        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        5.52         8.02         1.87        12.72        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       91.73        18.81        23.31         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM 
       10.95        24.89        77.56        68.71         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD 
       13.61         2.56         9.76        38.40        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
        7.99        14.76        24.07        55.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
       41.46        18.51        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AAC1 
       32.28        11.77        10.78        15.42        27.72        25.94 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-XT-AASU 
        8.32        14.99        13.35        28.37        14.27         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VS 
        1.28         4.37         2.76         8.58         7.50        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              2.50               0.66 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             48.99              91.73 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             14.17              17.95 
[1] "2.5 - 49.0 (14.2)" "0.7 - 91.7 (17.9)"
[1] "hr=" "1.3"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         3        1        0        3         3        1
  16Q LOSS WILD-TYPE       4        1        1       13        42       15
D61V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  3                  4
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 3                 13
  STAGE III                3                 42
  STAGE IV                 1                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  16Q LOSS MUTATED    4  3  3  1
  16Q LOSS WILD-TYPE 10 23 29 12
D61V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                4                 10
  T2                3                 23
  T3                3                 29
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  16Q LOSS MUTATED    8  1     1
  16Q LOSS WILD-TYPE 36  9    28
D61V5, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                   8                 36
  N1                   1                  9
  N2+N3                1                 28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    9  0
  16Q LOSS WILD-TYPE 48  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      9    0
  16Q LOSS WILD-TYPE   48    3
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                9                 48
  1                0                  3
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    2  9
  16Q LOSS WILD-TYPE 14 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    9
  16Q LOSS WILD-TYPE   14   62
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                2                 14
  MALE                  9                 62
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    7  3
  16Q LOSS WILD-TYPE 55 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7    3
  16Q LOSS WILD-TYPE   55   21
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 7                 55
  YES                3                 21
[1] 2 2
[1] FALSE
D61V9, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 16 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A7BH         TCGA-SH-A9CT 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SH-A9CU         TCGA-UT-A88C         TCGA-XT-AASU 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ZN-A9VO         TCGA-ZN-A9VP         TCGA-ZN-A9VS 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ZN-A9VU 
"16Q LOSS WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  16Q LOSS MUTATED                       5                                    0
  16Q LOSS WILD-TYPE                    18                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  16Q LOSS MUTATED                          5                        1
  16Q LOSS WILD-TYPE                       52                        1
D61V10, multiclass
                                      clus
vv                                     16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               5                 18
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            5                 52
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  16Q LOSS MUTATED    3  0  0  4
  16Q LOSS WILD-TYPE 14  3 15  7
D61V11, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0                3                 14
  R1                0                  3
  R2                0                 15
  RX                4                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = 17P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED    3 20
  17P LOSS WILD-TYPE  9 53
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                23                 62 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                20                 53 
$`17P LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T TCGA-LK-A4NW TCGA-MQ-A6BS TCGA-NQ-A57I 
       11.87        29.10        13.61        17.95        19.99         0.66 
TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU 
       13.61         9.76         7.99        14.76        24.07        55.07 
TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A8AY TCGA-UD-AAC7 TCGA-UT-A88C 
        8.38        41.46        22.65        15.42        13.35        28.37 
TCGA-UT-A88G TCGA-YS-A95B TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VS 
        2.50         1.28         8.58         7.50        40.37 

$`17P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3U TCGA-3H-AB3X 
       26.14        23.64        27.06        56.38        27.16        48.99 
TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NY 
        4.67        17.62        38.01        28.27        24.36         5.52 
TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
        8.02         6.08         1.87        12.72        14.73        11.51 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       80.84        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM 
        3.52        10.95        24.89        77.56        68.71        28.96 
TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-TS-A7OZ TCGA-TS-A7P1 
        2.56        38.40        23.90        15.09        27.75        18.51 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88E 
       27.72         6.48        25.94         8.32        14.99        14.27 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VU 
        4.73         4.67         4.37         2.76        16.41        32.12 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       43.04         2.76 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.66               1.87 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             55.07              91.73 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             13.61              18.66 
[1] "0.7 - 55.1 (13.6)" "1.9 - 91.7 (18.7)"
[1] "hr=" "1.4"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         1        0        1        3        12        6
  17P LOSS WILD-TYPE       6        2        0       13        33       10
D62V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 3                 13
  STAGE III               12                 33
  STAGE IV                 6                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17P LOSS MUTATED    2  4 11  5
  17P LOSS WILD-TYPE 12 22 21  8
D62V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                2                 12
  T2                4                 22
  T3               11                 21
  T4                5                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  17P LOSS MUTATED    9  1    12
  17P LOSS WILD-TYPE 35  9    17
D62V5, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                   9                 35
  N1                   1                  9
  N2+N3               12                 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"
D62V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   13  1
  17P LOSS WILD-TYPE 44  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     13    1
  17P LOSS WILD-TYPE   44    2
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               13                 44
  1                1                  2
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    5 18
  17P LOSS WILD-TYPE 11 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5   18
  17P LOSS WILD-TYPE   11   53
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                5                 11
  MALE                 18                 53
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   17  6
  17P LOSS WILD-TYPE 45 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     17    6
  17P LOSS WILD-TYPE   45   18
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                17                 45
  YES                6                 18
[1] 2 2
[1] FALSE
D62V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  17P LOSS MUTATED                       5                                    1
  17P LOSS WILD-TYPE                    18                                    4
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  17P LOSS MUTATED                         17                        0
  17P LOSS WILD-TYPE                       40                        2
D62V10, multiclass
                                      clus
vv                                     17P LOSS MUTATED 17P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               5                 18
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                1                  4
  EPITHELIOID MESOTHELIOMA                           17                 40
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  17P LOSS MUTATED    4  0  4  3
  17P LOSS WILD-TYPE 13  3 11  8
D62V11, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0                4                 13
  R1                0                  3
  R2                4                 11
  RX                3                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = 17Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    1  6
  17Q LOSS WILD-TYPE 11 67
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                 78 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                 67 
$`17Q LOSS MUTATED`
TCGA-NQ-A57I TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-UT-A88G TCGA-YS-A95B 
        0.66         7.99        24.07        41.46         2.50         1.28 
TCGA-ZN-A9VS 
       40.37 

$`17Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H 
       13.61        27.16        48.99         4.67        17.62        38.01 
TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 
       28.27        24.36        17.95         5.52         8.02         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        1.87        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN 
       24.89        77.56        68.71        19.99        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT 
        2.56         9.76        38.40        23.90        15.09        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
       55.07         8.38        27.75        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY 
       19.43        15.02        32.28        11.77        10.78        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
       27.72         6.48        25.94         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M 
       28.37        14.27         4.73         4.67         4.37         2.76 
TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        8.58         7.50        16.41        32.12        43.04         2.76 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.66               1.87 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             41.46              91.73 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             7.990             17.475 
[1] "0.7 - 41.5 (8.0)"  "1.9 - 91.7 (17.5)"
[1] "hr=" "1.3"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED         0        0        1        0         4        2
  17Q LOSS WILD-TYPE       7        2        0       16        41       14
D63V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 0                 16
  STAGE III                4                 41
  STAGE IV                 2                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17Q LOSS MUTATED    1  0  4  2
  17Q LOSS WILD-TYPE 13 26 28 11
D63V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                1                 13
  T2                0                 26
  T3                4                 28
  T4                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  17Q LOSS MUTATED    4  0     2
  17Q LOSS WILD-TYPE 40 10    27
D63V5, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                   4                 40
  N1                   0                 10
  N2+N3                2                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    4  0
  17Q LOSS WILD-TYPE 53  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    0
  17Q LOSS WILD-TYPE   53    3
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0                4                 53
  1                0                  3
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    2  5
  17Q LOSS WILD-TYPE 14 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    5
  17Q LOSS WILD-TYPE   14   66
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                2                 14
  MALE                  5                 66
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    7  0
  17Q LOSS WILD-TYPE 55 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7    0
  17Q LOSS WILD-TYPE   55   24
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 7                 55
  YES                0                 24
[1] 2 2
[1] FALSE
D63V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  17Q LOSS MUTATED                       3                                    0
  17Q LOSS WILD-TYPE                    20                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  17Q LOSS MUTATED                          4                        0
  17Q LOSS WILD-TYPE                       53                        2
D63V10, multiclass
                                      clus
vv                                     17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               3                 20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            4                 53
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  17Q LOSS MUTATED    0  0  3  2
  17Q LOSS WILD-TYPE 17  3 12  9
D63V11, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                0                 17
  R1                0                  3
  R2                3                 12
  RX                2                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = 18P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    1  8
  18P LOSS WILD-TYPE 11 65
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 9                 76 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 8                 65 
$`18P LOSS MUTATED`
TCGA-3U-A98I TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-TS-A7P8 
       28.27        18.81         5.19        10.95        19.99        15.02 
TCGA-UT-A88G TCGA-YS-A95C TCGA-ZN-A9VS 
        2.50         4.37        40.37 

$`18P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H 
       13.61        27.16        48.99         4.67        17.62        38.01 
TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       24.36        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ 
       12.72        14.73        11.51        80.84        91.73        23.31 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
       17.33         3.52        24.89        77.56        68.71         0.66 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC 
       28.96        13.61         2.56         9.76        38.40        23.90 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       15.09         7.99        14.76        24.07        55.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
       27.75        41.46        18.51        22.65         9.30        19.43 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       32.28        11.77        10.78        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E 
       25.94         8.32        14.99        13.35        28.37        14.27 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP 
        4.73         4.67         1.28         2.76         8.58         7.50 
TCGA-ZN-A9VQ TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       16.41        32.12        43.04         2.76 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              2.50               0.66 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             40.37              91.73 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            15.020             17.475 
[1] "2.5 - 40.4 (15.0)" "0.7 - 91.7 (17.5)"
[1] "hr=" "1.4"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  18P LOSS MUTATED         0        0        0        3         5        1
  18P LOSS WILD-TYPE       7        2        1       13        40       15
D64V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 3                 13
  STAGE III                5                 40
  STAGE IV                 1                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18P LOSS MUTATED    1  3  3  1
  18P LOSS WILD-TYPE 13 23 29 12
D64V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                1                 13
  T2                3                 23
  T3                3                 29
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  18P LOSS MUTATED    6  1     2
  18P LOSS WILD-TYPE 38  9    27
D64V5, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                   6                 38
  N1                   1                  9
  N2+N3                2                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    6  0
  18P LOSS WILD-TYPE 51  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      6    0
  18P LOSS WILD-TYPE   51    3
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0                6                 51
  1                0                  3
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    1  8
  18P LOSS WILD-TYPE 15 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    8
  18P LOSS WILD-TYPE   15   63
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                1                 15
  MALE                  8                 63
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    9  0
  18P LOSS WILD-TYPE 53 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      9    0
  18P LOSS WILD-TYPE   53   24
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 9                 53
  YES                0                 24
[1] 2 2
[1] FALSE
D64V9, continuous
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                 16 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A7BH         TCGA-SH-A9CT 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-SH-A9CU         TCGA-UT-A88C         TCGA-XT-AASU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ZN-A9VO         TCGA-ZN-A9VP         TCGA-ZN-A9VQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ZN-A9VU 
"18P LOSS WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  18P LOSS MUTATED                       4                                    0
  18P LOSS WILD-TYPE                    19                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  18P LOSS MUTATED                          5                        0
  18P LOSS WILD-TYPE                       52                        2
D64V10, multiclass
                                      clus
vv                                     18P LOSS MUTATED 18P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               4                 19
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            5                 52
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  18P LOSS MUTATED    2  1  0  1
  18P LOSS WILD-TYPE 15  2 15 10
D64V11, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0                2                 15
  R1                1                  2
  R2                0                 15
  RX                1                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = 18Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    1 13
  18Q LOSS WILD-TYPE 11 60
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                14                 71 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                13                 60 
$`18Q LOSS MUTATED`
TCGA-3H-AB3M TCGA-LK-A4NY TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BS 
       29.10         5.52        18.81         5.19        10.95        19.99 
TCGA-SC-A6LM TCGA-SC-A6LQ TCGA-TS-A7P0 TCGA-TS-A7P8 TCGA-TS-A8AF TCGA-UT-A88G 
       28.96         9.76        41.46        15.02        11.77         2.50 
TCGA-YS-A95C TCGA-ZN-A9VS 
        4.37        40.37 

$`18Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        11.87        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I 
       27.16        48.99         4.67        17.62        38.01        28.27 
TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       24.36        17.95         8.02         6.08         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LP 
       14.73        11.51        80.84        91.73        23.31        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LN 
        3.52        24.89        77.56        68.71         0.66        13.61 
TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
        2.56        38.40        23.90        15.09         7.99        14.76 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 
       24.07        55.07         8.38        27.75        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY 
        9.30        19.43        32.28        10.78        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        6.48        25.94         8.32        14.99        13.35        28.37 
TCGA-UT-A88E TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VO 
       14.27         4.73         4.67         1.28         2.76         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        32.12        43.04         2.76 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              2.50               0.66 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             41.46              91.73 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            13.395             17.620 
[1] "2.5 - 41.5 (13.4)" "0.7 - 91.7 (17.6)"
[1] "hr=" "1.4"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED         0        0        0        3        10        1
  18Q LOSS WILD-TYPE       7        2        1       13        35       15
D65V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 0                  1
  STAGE II                 3                 13
  STAGE III               10                 35
  STAGE IV                 1                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS MUTATED    1  4  7  1
  18Q LOSS WILD-TYPE 13 22 25 12
D65V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                1                 13
  T2                4                 22
  T3                7                 25
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  18Q LOSS MUTATED    8  1     4
  18Q LOSS WILD-TYPE 36  9    25
D65V5, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                   8                 36
  N1                   1                  9
  N2+N3                4                 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"
D65V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    9  0
  18Q LOSS WILD-TYPE 48  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      9    0
  18Q LOSS WILD-TYPE   48    3
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0                9                 48
  1                0                  3
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    5  9
  18Q LOSS WILD-TYPE 11 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5    9
  18Q LOSS WILD-TYPE   11   62
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                5                 11
  MALE                  9                 62
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   12  2
  18Q LOSS WILD-TYPE 50 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     12    2
  18Q LOSS WILD-TYPE   50   22
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                12                 50
  YES                2                 22
[1] 2 2
[1] FALSE
D65V9, continuous
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                 15 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-SC-A6LN         TCGA-SC-A6LP         TCGA-SC-A6LR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-SH-A7BH         TCGA-SH-A9CT         TCGA-SH-A9CU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-UT-A88C         TCGA-XT-AASU         TCGA-ZN-A9VO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ZN-A9VP         TCGA-ZN-A9VQ         TCGA-ZN-A9VU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  18Q LOSS MUTATED                       4                                    0
  18Q LOSS WILD-TYPE                    19                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  18Q LOSS MUTATED                         10                        0
  18Q LOSS WILD-TYPE                       47                        2
D65V10, multiclass
                                      clus
vv                                     18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               4                 19
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                           10                 47
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  18Q LOSS MUTATED    4  1  1  1
  18Q LOSS WILD-TYPE 13  2 14 10
D65V11, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0                4                 13
  R1                1                  2
  R2                1                 14
  RX                1                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = 19P LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    0  4
  19P LOSS WILD-TYPE 12 69
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 81 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 69 
$`19P LOSS MUTATED`
TCGA-3U-A98F TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-TS-A7OZ 
       17.62        19.99         0.66        27.75 

$`19P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98H TCGA-3U-A98I 
       13.61        27.16        48.99         4.67        38.01        28.27 
TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       24.36        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       77.56        68.71        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
       38.40        23.90        15.09         7.99        14.76        24.07 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
       55.07         8.38        41.46        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY 
       19.43        15.02        32.28        11.77        10.78        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
       27.72         6.48        25.94         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       28.37        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.37         2.76         8.58         7.50        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.66               1.28 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             27.75              91.73 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            18.805             16.410 
[1] "0.7 - 27.8 (18.8)" "1.3 - 91.7 (16.4)"
[1] "hr=" "1.5"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         0        0        1        1         2        0
  19P LOSS WILD-TYPE       7        2        0       15        43       16
D66V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 1                 15
  STAGE III                2                 43
  STAGE IV                 0                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19P LOSS MUTATED    1  1  2  0
  19P LOSS WILD-TYPE 13 25 30 13
D66V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                1                 13
  T2                1                 25
  T3                2                 30
  T4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  19P LOSS MUTATED    2  1     0
  19P LOSS WILD-TYPE 42  9    29
D66V5, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                   2                 42
  N1                   1                  9
  N2+N3                0                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    1  0
  19P LOSS WILD-TYPE 56  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1    0
  19P LOSS WILD-TYPE   56    3
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                1                 56
  1                0                  3
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    0  4
  19P LOSS WILD-TYPE 16 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    4
  19P LOSS WILD-TYPE   16   67
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                0                 16
  MALE                  4                 67
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    3  1
  19P LOSS WILD-TYPE 59 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    1
  19P LOSS WILD-TYPE   59   23
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 3                 59
  YES                1                 23
[1] 2 2
[1] FALSE
D66V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  19P LOSS MUTATED                       2                                    0
  19P LOSS WILD-TYPE                    21                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  19P LOSS MUTATED                          2                        0
  19P LOSS WILD-TYPE                       55                        2
D66V10, multiclass
                                      clus
vv                                     19P LOSS MUTATED 19P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               2                 21
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            2                 55
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  19P LOSS MUTATED    1  0  1  0
  19P LOSS WILD-TYPE 16  3 14 11
D66V11, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 44 
        TCGA-3U-A98G         TCGA-LK-A4O4         TCGA-SC-AA5Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UD-AAC4         TCGA-UT-A88D         TCGA-LK-A4NW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-LK-A4NY         TCGA-LK-A4NZ         TCGA-LK-A4O0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-LK-A4O2         TCGA-LK-A4O5         TCGA-LK-A4O6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-LK-A4O7         TCGA-MQ-A4KX         TCGA-MQ-A4LC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MQ-A4LI         TCGA-MQ-A4LV         TCGA-MQ-A6BN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MQ-A6BQ         TCGA-MQ-A6BR         TCGA-NQ-A638 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-SC-A6LQ         TCGA-SC-A6LR         TCGA-SH-A7BC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-SH-A7BD         TCGA-SH-A7BH         TCGA-SH-A9CU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UD-AABY         TCGA-UD-AABZ         TCGA-UD-AAC1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UD-AAC5         TCGA-UD-AAC6         TCGA-UD-AAC7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UT-A88C         TCGA-UT-A88E         TCGA-UT-A88G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UT-A97Y         TCGA-XT-AASU         TCGA-YS-A95B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-YS-A95C         TCGA-YS-AA4M 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 

Clustering(67) Variable = 19Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    2  5
  19Q LOSS WILD-TYPE 10 68
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 7                 78 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                 68 
$`19Q LOSS MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3X TCGA-3U-A98F TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I 
       29.10        48.99        17.62        77.56        19.99         0.66 
TCGA-TS-A7OZ 
       27.75 

$`19Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        11.87        13.61 
TCGA-3H-AB3U TCGA-3U-A98D TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW 
       27.16         4.67        38.01        28.27        24.36        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       11.51        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-SC-A6LM 
       17.33         3.52        10.95        24.89        68.71        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD 
       13.61         2.56         9.76        38.40        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7P0 
        7.99        14.76        24.07        55.07         8.38        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       11.77        10.78        15.42        27.72         6.48        25.94 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G 
        8.32        14.99        13.35        28.37        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO 
        4.73         4.67         1.28         4.37         2.76         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        40.37        32.12        43.04         2.76 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.66               1.28 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             77.56              91.73 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            27.750             15.255 
[1] "0.7 - 77.6 (27.8)" "1.3 - 91.7 (15.3)"
[1] "hr=" "1.8"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         0        0        1        2         4        0
  19Q LOSS WILD-TYPE       7        2        0       14        41       16
D67V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  0                  7
  STAGE IA                 0                  2
  STAGE IB                 1                  0
  STAGE II                 2                 14
  STAGE III                4                 41
  STAGE IV                 0                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19Q LOSS MUTATED    1  2  4  0
  19Q LOSS WILD-TYPE 13 24 28 13
D67V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                1                 13
  T2                2                 24
  T3                4                 28
  T4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  19Q LOSS MUTATED    4  1     1
  19Q LOSS WILD-TYPE 40  9    28
D67V5, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                   4                 40
  N1                   1                  9
  N2+N3                1                 28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    3  0
  19Q LOSS WILD-TYPE 54  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    0
  19Q LOSS WILD-TYPE   54    3
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                3                 54
  1                0                  3
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    1  6
  19Q LOSS WILD-TYPE 15 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    6
  19Q LOSS WILD-TYPE   15   65
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                1                 15
  MALE                  6                 65
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    4  3
  19Q LOSS WILD-TYPE 58 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4    3
  19Q LOSS WILD-TYPE   58   21
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 4                 58
  YES                3                 21
[1] 2 2
[1] FALSE
D67V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  19Q LOSS MUTATED                       2                                    0
  19Q LOSS WILD-TYPE                    21                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  19Q LOSS MUTATED                          5                        0
  19Q LOSS WILD-TYPE                       52                        2
D67V10, multiclass
                                      clus
vv                                     19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               2                 21
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            5                 52
  SARCOMATOID MESOTHELIOMA                            0                  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                 R0 R1 R2 RX
  19Q LOSS MUTATED    1  1  1  0
  19Q LOSS WILD-TYPE 16  2 14 11
D67V11, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                1                 16
  R1                1                  2
  R2                1                 14
  RX                0                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = 20P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    3 11
  20P LOSS WILD-TYPE  9 62
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                14                 71 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                11                 62 
$`20P LOSS MUTATED`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O5 
       56.38        11.87        29.10        17.95         6.08        12.72 
TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-TS-A7P0 TCGA-TS-A7P7 TCGA-UT-A88E 
       77.56        19.99        13.61        41.46        19.43        14.27 
TCGA-ZN-A9VQ TCGA-ZN-A9VU 
       16.41        32.12 

$`20P LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X 
       26.14        23.64        27.06        13.61        27.16        48.99 
TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NY 
        4.67        17.62        38.01        28.27        24.36         5.52 
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        8.02         1.87        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ 
       24.89        68.71         0.66        28.96         2.56         9.76 
TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
       38.40        23.90        15.09         7.99        14.76        24.07 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
       55.07         8.38        27.75        18.51        22.65         9.30 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY 
       15.02        32.28        11.77        10.78        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        6.48        25.94         8.32        14.99        13.35        28.37 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
        2.50         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VS TCGA-ZN-A9VV TCGA-ZN-A9VW 
        8.58         7.50        40.37        43.04         2.76 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              6.08               0.66 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             77.56              91.73 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             18.69              15.42 
[1] "6.1 - 77.6 (18.7)" "0.7 - 91.7 (15.4)"
[1] "hr=" "1.4"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         2        1        0        4         6        1
  20P LOSS WILD-TYPE       5        1        1       12        39       15
D68V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  2                  5
  STAGE IA                 1                  1
  STAGE IB                 0                  1
  STAGE II                 4                 12
  STAGE III                6                 39
  STAGE IV                 1                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20P LOSS MUTATED    3  5  4  1
  20P LOSS WILD-TYPE 11 21 28 12
D68V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                3                 11
  T2                5                 21
  T3                4                 28
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  20P LOSS MUTATED    9  0     5
  20P LOSS WILD-TYPE 35 10    24
D68V5, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                   9                 35
  N1                   0                 10
  N2+N3                5                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    8  0
  20P LOSS WILD-TYPE 49  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8    0
  20P LOSS WILD-TYPE   49    3
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                8                 49
  1                0                  3
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    2 12
  20P LOSS WILD-TYPE 14 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   12
  20P LOSS WILD-TYPE   14   59
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                2                 14
  MALE                 12                 59
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                  0  1
  20P LOSS MUTATED   11  3
  20P LOSS WILD-TYPE 51 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     11    3
  20P LOSS WILD-TYPE   51   21
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                11                 51
  YES                3                 21
[1] 2 2
[1] FALSE
D68V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  20P LOSS MUTATED                       2                                    2
  20P LOSS WILD-TYPE                    21                                    3
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  20P LOSS MUTATED                          9                        1
  20P LOSS WILD-TYPE                       48                        1
D68V10, multiclass
                                      clus
vv                                     20P LOSS MUTATED 20P LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               2                 21
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                2                  3
  EPITHELIOID MESOTHELIOMA                            9                 48
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  20P LOSS MUTATED    3  2  0  2
  20P LOSS WILD-TYPE 14  1 15  9
D68V11, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0                3                 14
  R1                2                  1
  R2                0                 15
  RX                2                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = 21Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    1  9
  21Q LOSS WILD-TYPE 11 64
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                10                 75 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 9                 64 
$`21Q LOSS MUTATED`
TCGA-SC-AA5Z TCGA-3U-A98D TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-MQ-A6BS TCGA-NQ-A57I 
       21.83         4.67         6.08         1.87        19.99         0.66 
TCGA-SH-A9CT TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A8AF 
       14.76        41.46        18.51        11.77 

$`21Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       23.64        27.06        56.38        11.87        29.10        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       27.16        48.99        17.62        38.01        28.27        24.36 
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
       17.95         5.52         8.02        12.72        14.73        11.51 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       80.84        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM 
        3.52        10.95        24.89        77.56        68.71        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD 
       13.61         2.56         9.76        38.40        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P3 
        7.99        24.07        55.07         8.38        27.75        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AY 
        9.30        19.43        15.02        32.28        10.78        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
       27.72         6.48        25.94         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       28.37        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.37         2.76         8.58         7.50        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.66               1.28 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             41.46              91.73 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            13.265             17.620 
[1] "0.7 - 41.5 (13.3)" "1.3 - 91.7 (17.6)"
[1] "hr=" "1.8"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED         1        1        1        3         4        1
  21Q LOSS WILD-TYPE       6        1        0       13        41       15
D69V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  1                  6
  STAGE IA                 1                  1
  STAGE IB                 1                  0
  STAGE II                 3                 13
  STAGE III                4                 41
  STAGE IV                 1                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS MUTATED    3  5  2  1
  21Q LOSS WILD-TYPE 11 21 30 12
D69V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                3                 11
  T2                5                 21
  T3                2                 30
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  21Q LOSS MUTATED    6  0     3
  21Q LOSS WILD-TYPE 38 10    26
D69V5, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                   6                 38
  N1                   0                 10
  N2+N3                3                 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"
D69V6, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    6  0
  21Q LOSS WILD-TYPE 51  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      6    0
  21Q LOSS WILD-TYPE   51    3
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0                6                 51
  1                0                  3
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    1 10
  21Q LOSS WILD-TYPE 15 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   10
  21Q LOSS WILD-TYPE   15   61
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                1                 15
  MALE                 10                 61
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    9  1
  21Q LOSS WILD-TYPE 53 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      9    1
  21Q LOSS WILD-TYPE   53   23
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 9                 53
  YES                1                 23
[1] 2 2
[1] FALSE
D69V9, continuous
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 1                 16 
        TCGA-3U-A98E         TCGA-UT-A88D         TCGA-3U-A98J 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-SC-A6LM         TCGA-SC-A6LN         TCGA-SC-A6LP 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-SC-A6LR         TCGA-SH-A7BH         TCGA-SH-A9CU 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-UT-A88C         TCGA-XT-AASU         TCGA-ZN-A9VO 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ZN-A9VP         TCGA-ZN-A9VQ         TCGA-ZN-A9VS 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ZN-A9VU 
"21Q LOSS WILD-TYPE" 
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  21Q LOSS MUTATED                       2                                    0
  21Q LOSS WILD-TYPE                    21                                    5
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  21Q LOSS MUTATED                          8                        1
  21Q LOSS WILD-TYPE                       49                        1
D69V10, multiclass
                                      clus
vv                                     21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                               2                 21
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                0                  5
  EPITHELIOID MESOTHELIOMA                            8                 49
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED    3  0  3  0
  21Q LOSS WILD-TYPE 14  3 12 11
D69V11, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0                3                 14
  R1                0                  3
  R2                3                 12
  RX                0                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = 22Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    8 58
  22Q LOSS WILD-TYPE  4 15
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                66                 19 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                58                 15 
$`22Q LOSS MUTATED`
TCGA-3H-AB3S TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       12.66        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I 
       13.61        48.99         4.67        17.62        38.01        28.27 
TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       24.36         5.52         8.02         6.08         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       14.73        11.51        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I 
       17.33         3.52        24.89        77.56        19.99         0.66 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT 
       28.96        13.61         9.76        23.90        15.09        14.76 
TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       24.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       27.72         6.48         8.32        14.99        13.35        28.37 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-YS-A95B TCGA-YS-A95C TCGA-ZN-A9VO 
       14.27         2.50         4.73         1.28         4.37         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        40.37        32.12        43.04         2.76 

$`22Q LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-TS-A8AS 
       42.81        62.99        20.71        31.20        21.83        26.14 
TCGA-3H-AB3U TCGA-LK-A4NW TCGA-MQ-A4KX TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-SC-A6LP 
       27.16        17.95        80.84        10.95        68.71         2.56 
TCGA-SC-A6LR TCGA-SH-A7BH TCGA-TS-A7OU TCGA-TS-A8AY TCGA-UD-AAC1 TCGA-XT-AASU 
       38.40         7.99        55.07        15.42        25.94         4.67 
TCGA-YS-AA4M 
        2.76 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.66               2.56 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             91.73              80.84 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            15.005             25.940 
[1] "0.7 - 91.7 (15.0)" "2.6 - 80.8 (25.9)"
[1] "hr=" "1.6"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED         6        1        1       14        35       10
  22Q LOSS WILD-TYPE       1        1        0        2        10        6
D70V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  6                  1
  STAGE IA                 1                  1
  STAGE IB                 1                  0
  STAGE II                14                  2
  STAGE III               35                 10
  STAGE IV                10                  6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  22Q LOSS MUTATED    9 21 27  8
  22Q LOSS WILD-TYPE  5  5  5  5
D70V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                9                  5
  T2               21                  5
  T3               27                  5
  T4                8                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  22Q LOSS MUTATED   34  7    23
  22Q LOSS WILD-TYPE 10  3     6
D70V5, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                  34                 10
  N1                   7                  3
  N2+N3               23                  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"
D70V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   44  2
  22Q LOSS WILD-TYPE 13  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     44    2
  22Q LOSS WILD-TYPE   13    1
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               44                 13
  1                2                  1
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   11 56
  22Q LOSS WILD-TYPE  5 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     11   56
  22Q LOSS WILD-TYPE    5   15
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               11                  5
  MALE                 56                 15
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   46 20
  22Q LOSS WILD-TYPE 16  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     46   20
  22Q LOSS WILD-TYPE   16    4
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                46                 16
  YES               20                  4
[1] 2 2
[1] FALSE
D70V9, continuous
                    vv
clus                 BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  22Q LOSS MUTATED                      18                                    3
  22Q LOSS WILD-TYPE                     5                                    2
                    vv
clus                 EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  22Q LOSS MUTATED                         45                        1
  22Q LOSS WILD-TYPE                       12                        1
D70V10, multiclass
                                      clus
vv                                     22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              18                  5
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                3                  2
  EPITHELIOID MESOTHELIOMA                           45                 12
  SARCOMATOID MESOTHELIOMA                            1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED   13  3 10  8
  22Q LOSS WILD-TYPE  4  0  5  3
D70V11, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               13                  4
  R1                3                  0
  R2               10                  5
  RX                8                  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"

Clustering(71) Variable = XP LOSS MUTATION ANALYSIS
D71V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED    5 22
  XP LOSS WILD-TYPE  7 51
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               27                58 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               22                51 
$`XP LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98I 
       11.87        29.10        48.99         4.67        17.62        28.27 
TCGA-LK-A4NY TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LP TCGA-MQ-A6BS TCGA-SC-A6LN 
        5.52        11.51        18.81        17.33        19.99        13.61 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P7 
       15.09        14.76        24.07        27.75        18.51        19.43 
TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88E TCGA-ZN-A9VO 
       10.78        15.42         6.48        13.35        14.27         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        7.50        16.41        40.37 

$`XP LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3T TCGA-3H-AB3U 
       26.14        23.64        27.06        56.38        13.61        27.16 
TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       38.01        24.36        17.95         8.02         6.08         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       12.72        14.73        80.84        91.73        23.31         5.19 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
        3.52        10.95        24.89        77.56        68.71         0.66 
TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BH 
       28.96         2.56         9.76        38.40        23.90         7.99 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P8 
       55.07         8.38        41.46        22.65         9.30        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 
       32.28        11.77        27.72        25.94         8.32        14.99 
TCGA-UT-A88C TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       28.37         2.50         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        2.76        32.12        43.04         2.76 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             4.67              0.66 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            48.99             91.73 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            15.42             21.27 
[1] "4.7 - 49.0 (15.4)" "0.7 - 91.7 (21.3)"
[1] "hr=" "1.3"
D71V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  XP LOSS MUTATED         3        0        0        5        14        5
  XP LOSS WILD-TYPE       4        2        1       11        31       11
D71V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 3                 4
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                5                11
  STAGE III              14                31
  STAGE IV                5                11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XP LOSS MUTATED    3  8 11  4
  XP LOSS WILD-TYPE 11 18 21  9
D71V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               3                11
  T2               8                18
  T3              11                21
  T4               4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  XP LOSS MUTATED   14  4     9
  XP LOSS WILD-TYPE 30  6    20
D71V5, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  N0                 14                30
  N1                  4                 6
  N2+N3               9                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"
D71V6, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   16  2
  XP LOSS WILD-TYPE 41  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     16    2
  XP LOSS WILD-TYPE   41    1
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              16                41
  1               2                 1
[1] 2 2
[1] FALSE
D71V7, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    4 23
  XP LOSS WILD-TYPE 12 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      4   23
  XP LOSS WILD-TYPE   12   48
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE               4                12
  MALE                23                48
[1] 2 2
[1] FALSE
D71V8, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   19  8
  XP LOSS WILD-TYPE 43 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     19    8
  XP LOSS WILD-TYPE   43   16
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               19                43
  YES               8                16
[1] 2 2
[1] FALSE
D71V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  XP LOSS MUTATED                       7                                    0
  XP LOSS WILD-TYPE                    16                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  XP LOSS MUTATED                         20                        0
  XP LOSS WILD-TYPE                       37                        2
D71V10, multiclass
                                      clus
vv                                     XP LOSS MUTATED XP LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              7                16
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                          20                37
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  XP LOSS MUTATED    4  1  2  3
  XP LOSS WILD-TYPE 13  2 13  8
D71V11, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0               4                13
  R1               1                 2
  R2               2                13
  RX               3                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = XQ LOSS MUTATION ANALYSIS
D72V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    5 23
  XQ LOSS WILD-TYPE  7 50
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               28                57 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               23                50 
$`XQ LOSS MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98I 
       11.87        29.10        48.99         4.67        17.62        28.27 
TCGA-LK-A4NY TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LP TCGA-MQ-A6BS TCGA-SC-A6LN 
        5.52        11.51        18.81        17.33        19.99        13.61 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P7 
       15.09        14.76        24.07        27.75        18.51        19.43 
TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88E 
       10.78        15.42         6.48        14.99        13.35        14.27 
TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        8.58         7.50        16.41        40.37 

$`XQ LOSS WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3T TCGA-3H-AB3U 
       26.14        23.64        27.06        56.38        13.61        27.16 
TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       38.01        24.36        17.95         8.02         6.08         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       12.72        14.73        80.84        91.73        23.31         5.19 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
        3.52        10.95        24.89        77.56        68.71         0.66 
TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BH 
       28.96         2.56         9.76        38.40        23.90         7.99 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P8 
       55.07         8.38        41.46        22.65         9.30        15.02 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UT-A88C 
       32.28        11.77        27.72        25.94         8.32        28.37 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
        2.50         4.73         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       32.12        43.04         2.76 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             4.67              0.66 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            48.99             91.73 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           15.255            21.830 
[1] "4.7 - 49.0 (15.3)" "0.7 - 91.7 (21.8)"
[1] "hr=" "1.3"
D72V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         3        0        0        6        14        5
  XQ LOSS WILD-TYPE       4        2        1       10        31       11
D72V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 3                 4
  STAGE IA                0                 2
  STAGE IB                0                 1
  STAGE II                6                10
  STAGE III              14                31
  STAGE IV                5                11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XQ LOSS MUTATED    3  9 11  4
  XQ LOSS WILD-TYPE 11 17 21  9
D72V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               3                11
  T2               9                17
  T3              11                21
  T4               4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  XQ LOSS MUTATED   15  4     9
  XQ LOSS WILD-TYPE 29  6    20
D72V5, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0                 15                29
  N1                  4                 6
  N2+N3               9                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"
D72V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   17  2
  XQ LOSS WILD-TYPE 40  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     17    2
  XQ LOSS WILD-TYPE   40    1
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              17                40
  1               2                 1
[1] 2 2
[1] FALSE
D72V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    4 24
  XQ LOSS WILD-TYPE 12 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4   24
  XQ LOSS WILD-TYPE   12   47
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               4                12
  MALE                24                47
[1] 2 2
[1] FALSE
D72V8, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   19  9
  XQ LOSS WILD-TYPE 43 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     19    9
  XQ LOSS WILD-TYPE   43   15
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               19                43
  YES               9                15
[1] 2 2
[1] FALSE
D72V9, continuous
                   vv
clus                BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  XQ LOSS MUTATED                       8                                    0
  XQ LOSS WILD-TYPE                    15                                    5
                   vv
clus                EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  XQ LOSS MUTATED                         20                        0
  XQ LOSS WILD-TYPE                       37                        2
D72V10, multiclass
                                      clus
vv                                     XQ LOSS MUTATED XQ LOSS WILD-TYPE
  BIPHASIC MESOTHELIOMA                              8                15
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS               0                 5
  EPITHELIOID MESOTHELIOMA                          20                37
  SARCOMATOID MESOTHELIOMA                           0                 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                R0 R1 R2 RX
  XQ LOSS MUTATED    4  1  3  3
  XQ LOSS WILD-TYPE 13  2 12  8
D72V11, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0               4                13
  R1               1                 2
  R2               3                12
  RX               3                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
