[1] "ofn"        "-oTREAD-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/READ-TP/22507018/READ-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/22532765/transformed.cor.cli.txt"

nPatients in clinical file=171, in cluster file=165, common to both=165
[1] "Reduce the number of clustering variables from 82 to 80."
[1]  80 165
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               12               153 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               12               153 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               33               132 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               33               132 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               40               125 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               40               125 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               41               124 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               41               124 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               27               138 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               27               138 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               33               132 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               33               132 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               156 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               156 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               160 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               160 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               35               130 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               35               130 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               24               141 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               24               141 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               40               125 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               40               125 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               35               130 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               35               130 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              102                63 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              102                63 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               87                78 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               87                78 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               40               125 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               40               125 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               90                75 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               90                75 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               43               122 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               43               122 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               35               130 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               35               130 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                153 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                153 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                158 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                158 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                32                133 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                32                133 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                27                138 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                27                138 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                33                132 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                33                132 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                21                144 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                21                144 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               114                 51 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               114                 51 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                157 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                157 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                161 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                161 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                41                124 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                41                124 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                41                124 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                41                124 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                10                155 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                10                155 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                31                134 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                31                134 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                157 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                157 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                159 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                159 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                33                132 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                33                132 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                33                132 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                33                132 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               105                 60 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               105                 60 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               146                 19 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               146                 19 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                155 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                155 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                156 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                156 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               31               134 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               31               134 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               32               133 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               32               133 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               46               119 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               46               119 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               28               137 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               28               137 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               154 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               154 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                7               158 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                7               158 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               15               150 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               15               150 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               155 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               155 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               60               105 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               60               105 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               67                98 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               67                98 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               27               138 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               27               138 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               40               125 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               40               125 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               14               151 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               14               151 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               23               142 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               23               142 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               162 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               162 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               75                90 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               75                90 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               10               155 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               10               155 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               23               142 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               23               142 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               23               142 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               23               142 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                34                131 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                34                131 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                38                127 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                38                127 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                24                141 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                24                141 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                30                135 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                30                135 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                23                142 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                23                142 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                24                141 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                24                141 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                159 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                159 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                67                 98 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                67                 98 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                72                 93 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                72                 93 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                156 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                156 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                151 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                151 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               105                 60 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               105                 60 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                28                137 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                28                137 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               128                 37 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               128                 37 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               138                 27 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               138                 27 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                24                141 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                24                141 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                22                143 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                22                143 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                24                141 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                24                141 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                68                 97 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                68                 97 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                58                107 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                58                107 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               28               137 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               28               137 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               26               139 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               26               139 
[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] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "TUMOR_STAGE"                         
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "ETHNICITY"                           

Input Data has 18 rows and 165 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=26,	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=102,	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=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	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=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR_STAGE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "1"                "83"                  
freq.contrast "83"               "1"                   
both >= 3     "FALSE"            "FALSE"               
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 165 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"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"       
[10] "NUMBER_OF_LYMPH_NODES"
YEARS_TO_BIRTH, nv=48, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
  9  28 112  14 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  9  28 112  14 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
  9  28 112  14 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  9  28 112  14 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
84 45 33 
[1] "table(vv)"
vv
N0 N1 N2 
84 45 33 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
84 45 33 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
84 45 33 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=18, binary=FALSE, numeric=TRUE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     9   3
  1P GAIN WILD-TYPE 122  24
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               12               146 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                24 
$`1P GAIN MUTATED`
TCGA-AG-3611 TCGA-G5-6641 TCGA-AF-2692 TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3591 
       13.94        26.43        13.55        32.02        46.03        34.03 
TCGA-AG-A026 TCGA-DC-6156 TCGA-DY-A1DF TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6464 
        1.94        31.00        24.13        10.78         8.45         9.96 

$`1P GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       55.76        46.92        39.48        17.23        43.04        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        37.74        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 
        7.07        36.03        20.05        24.00         1.02        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
        1.02        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       36.03        14.04         1.02         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
        1.02        49.97        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       12.00        13.97        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        51.48        32.61         3.48         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 
       16.34        16.31        16.41         8.61        11.51        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       17.46        11.97        49.51        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.94              0.39 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            46.03            129.27 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           19.035            20.995 
[1] "1.9 - 46.0 (19.0)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "2.4"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1P GAIN MUTATED         1        1         4         0         0         0
  1P GAIN WILD-TYPE      29        7        36         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1P GAIN MUTATED            2          0          2        0         1
  1P GAIN WILD-TYPE          5         25         12       18         6
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  1                29
  STAGE II                 1                 7
  STAGE IIA                4                36
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               2                 5
  STAGE IIIB               0                25
  STAGE IIIC               2                12
  STAGE IV                 0                18
  STAGE IVA                1                 6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED     1   1   6   4
  1P GAIN WILD-TYPE   8  27 106  10
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               1                 8
  T2               1                27
  T3               6               106
  T4               4                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
  1P GAIN MUTATED    6  2  4
  1P GAIN WILD-TYPE 78 43 29
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0               6                78
  N1               2                43
  N2               4                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"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    10   1
  1P GAIN WILD-TYPE 115  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     10    1
  1P GAIN WILD-TYPE  115   23
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              10               115
  1               1                23
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    6  6
  1P GAIN WILD-TYPE 70 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      6    6
  1P GAIN WILD-TYPE   70   83
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               6                70
  MALE                 6                83
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     8   2
  1P GAIN WILD-TYPE 104  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8    2
  1P GAIN WILD-TYPE  104   18
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                8               104
  YES               2                18
[1] 2 2
[1] FALSE
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     8   3
  1P GAIN WILD-TYPE 138  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8    3
  1P GAIN WILD-TYPE  138   10
                                clus
vv                               1P GAIN MUTATED 1P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        8               138
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    10   1   0   0
  1P GAIN WILD-TYPE 113   1  12   4
D1V10, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              10               113
  R1               1                 1
  R2               0                12
  RX               0                 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"
D1V11, continuous

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    25   7
  1Q GAIN WILD-TYPE 106  20
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32               126 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                7                20 
$`1Q GAIN MUTATED`
TCGA-AG-3611 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6641 TCGA-AF-2692 
       13.94        36.03        31.00        51.98        26.43        13.55 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 
       24.36        24.59        32.02        46.03        34.03        34.03 
TCGA-AG-3600 TCGA-AG-3881 TCGA-AG-3999 TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 
        6.05        19.04        28.04         1.94        38.04        38.56 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6623 TCGA-DC-6155 TCGA-DC-6156 TCGA-DY-A1DE 
       43.20        27.55        47.44        13.97        31.00       129.27 
TCGA-DY-A1DF TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7004 TCGA-F5-6464 
       24.13         8.61        10.78        13.64         8.45         9.96 
TCGA-F5-6813 TCGA-F5-6863 
       19.66        11.87 

$`1Q GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2689 
       15.95        21.24        18.28        55.76        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       17.23        43.04        37.97        34.49        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       16.83        20.02        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       25.02        32.02        19.99        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
       37.02         9.07         1.02         1.02        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       61.97        41.00         2.50        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       33.17        13.78        44.78        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
       21.01        25.05        26.04        31.00        12.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       17.46        11.97        49.51        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       32.19        36.49        37.18        38.14        12.46        47.08 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1.94              0.39 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           129.27            126.44 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            25.51             20.73 
[1] "1.9 - 129.3 (25.5)" "0.4 - 126.4 (20.7)"
[1] "hr=" "1.4"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1Q GAIN MUTATED         3        2         8         0         0         0
  1Q GAIN WILD-TYPE      27        6        32         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1Q GAIN MUTATED            3          3          6        4         1
  1Q GAIN WILD-TYPE          4         22          8       14         6
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  3                27
  STAGE II                 2                 6
  STAGE IIA                8                32
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               3                 4
  STAGE IIIB               3                22
  STAGE IIIC               6                 8
  STAGE IV                 4                14
  STAGE IVA                1                 6
[1] 11  2
[1] TRUE
[1] "dimension of 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    3  3 19  8
  1Q GAIN WILD-TYPE  6 25 93  6
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               3                 6
  T2               3                25
  T3              19                93
  T4               8                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  1Q GAIN MUTATED   14  8 10
  1Q GAIN WILD-TYPE 70 37 23
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              14                70
  N1               8                37
  N2              10                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    24   5
  1Q GAIN WILD-TYPE 101  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     24    5
  1Q GAIN WILD-TYPE  101   19
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              24               101
  1               5                19
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   18 15
  1Q GAIN WILD-TYPE 58 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     18   15
  1Q GAIN WILD-TYPE   58   74
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              18                58
  MALE                15                74
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   21  7
  1Q GAIN WILD-TYPE 91 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     21    7
  1Q GAIN WILD-TYPE   91   13
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               21                91
  YES               7                13
[1] 2 2
[1] FALSE
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    27   4
  1Q GAIN WILD-TYPE 119   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     27    4
  1Q GAIN WILD-TYPE  119    9
                                clus
vv                               1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       27               119
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED    22   1   2   0
  1Q GAIN WILD-TYPE 101   1  10   4
D2V10, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              22               101
  R1               1                 1
  R2               2                10
  RX               0                 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"
D2V11, continuous

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    31   8
  2P GAIN WILD-TYPE 100  19
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               39               119 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                8                19 
$`2P GAIN MUTATED`
TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2689 
       31.00        21.24        18.28        55.76        46.92        39.48 
TCGA-AF-2690 TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3587 
       17.23        16.83        86.63        65.98        36.03        46.03 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4007 
       34.03        34.03        19.99        19.99         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A032 TCGA-AH-6897 TCGA-CI-6621 TCGA-CL-5917 TCGA-CL-5918 
       46.03        38.04        26.43        13.78        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 
       21.01        31.00        12.00        31.00        51.98        25.05 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6464 
      129.27        51.48        20.55        16.31        13.64         9.96 
TCGA-F5-6465 TCGA-F5-6864 TCGA-G5-6572 
       49.51        12.46        47.08 

$`2P GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6641 TCGA-AF-2691 
       25.97        15.95        36.03        51.98        26.43        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 
       13.55        37.97        34.49        37.74        29.98        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       20.02        24.59        11.84        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 
       36.03        20.05        24.00         1.02        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 
       50.04        12.03         6.05         0.99        15.95        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
        0.99        19.04         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01        48.03        25.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 
       28.04        36.03        14.04         3.98        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
        6.02        23.01        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       49.97         1.94        38.96        61.97        41.00        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        2.50        43.20        27.55        19.46         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 
       44.78        47.44        48.20        25.05        26.04        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        44.02        25.97        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       41.36        57.24        24.13        32.61         3.48         4.18 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.34        16.41         8.61        11.51        10.78        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97         8.45        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       36.49        19.66        37.18        38.14        11.87 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.02              0.39 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           129.27            126.44 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            31.00             20.02 
[1] "1.0 - 129.3 (31.0)" "0.4 - 126.4 (20.0)"
[1] "hr=" "1.3"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2P GAIN MUTATED         6        3         9         0         0         0
  2P GAIN WILD-TYPE      24        5        31         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2P GAIN MUTATED            0          7          6        4         3
  2P GAIN WILD-TYPE          7         18          8       14         4
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  6                24
  STAGE II                 3                 5
  STAGE IIA                9                31
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               7                18
  STAGE IIIC               6                 8
  STAGE IV                 4                14
  STAGE IVA                3                 4
[1] 11  2
[1] TRUE
[1] "dimension of 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    0  7 28  4
  2P GAIN WILD-TYPE  9 21 84 10
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               0                 9
  T2               7                21
  T3              28                84
  T4               4                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
  2P GAIN MUTATED   19  8 12
  2P GAIN WILD-TYPE 65 37 21
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              19                65
  N1               8                37
  N2              12                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"
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   27  7
  2P GAIN WILD-TYPE 98 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     27    7
  2P GAIN WILD-TYPE   98   17
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              27                98
  1               7                17
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   25 15
  2P GAIN WILD-TYPE 51 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     25   15
  2P GAIN WILD-TYPE   51   74
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              25                51
  MALE                15                74
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   28  6
  2P GAIN WILD-TYPE 84 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     28    6
  2P GAIN WILD-TYPE   84   14
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               28                84
  YES               6                14
[1] 2 2
[1] FALSE
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    40   0
  2P GAIN WILD-TYPE 106  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     40    0
  2P GAIN WILD-TYPE  106   13
                                clus
vv                               2P GAIN MUTATED 2P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       40               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  2P GAIN MUTATED   30  1  2  3
  2P GAIN WILD-TYPE 93  1 10  1
D3V10, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              30                93
  R1               1                 1
  R2               2                10
  RX               3                 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"
D3V11, continuous

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    31   9
  2Q GAIN WILD-TYPE 100  18
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               40               118 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                9                18 
$`2Q GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 TCGA-AF-2687 TCGA-AF-2689 
       10.39        31.00        21.24        18.28        46.92        39.48 
TCGA-AF-2690 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 
       17.23        16.83        24.36        86.63        65.98        36.03 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3896 
       46.03        34.03        34.03        19.99        19.99         1.02 
TCGA-AG-3898 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A032 TCGA-AH-6897 TCGA-CI-6621 
       48.03         1.02        46.03        38.04        26.43        13.78 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       78.12         7.17        31.00        12.00        31.00        51.98 
TCGA-DC-6682 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6464 
       25.05       129.27         4.18        16.31        13.64         9.96 
TCGA-F5-6465 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       49.51        11.87        12.46        47.08 

$`2Q GAIN WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2691 
       15.95        36.03        51.98        55.76        26.43        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6655 
       13.55        37.97        34.49        37.74        29.98        20.02 
TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       24.59        11.84        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.04         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       14.04         3.98        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        41.00        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       27.55        19.46         6.05        33.17        44.78        47.44 
TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 
       48.20        21.01        25.05        26.04        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         3.48        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.34        16.41         8.61        11.51        10.78        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97         8.45        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       36.49        19.66        37.18        38.14 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.02              0.39 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           129.27            126.44 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            25.74             20.73 
[1] "1.0 - 129.3 (25.7)" "0.4 - 126.4 (20.7)"
[1] "hr=" "1"  
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2Q GAIN MUTATED         6        3        10         0         0         0
  2Q GAIN WILD-TYPE      24        5        30         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2Q GAIN MUTATED            0          7          6        5         2
  2Q GAIN WILD-TYPE          7         18          8       13         5
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  6                24
  STAGE II                 3                 5
  STAGE IIA               10                30
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               7                18
  STAGE IIIC               6                 8
  STAGE IV                 5                13
  STAGE IVA                2                 5
[1] 11  2
[1] TRUE
[1] "dimension of 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    0  7 28  5
  2Q GAIN WILD-TYPE  9 21 84  9
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               0                 9
  T2               7                21
  T3              28                84
  T4               5                 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
  2Q GAIN MUTATED   20  8 12
  2Q GAIN WILD-TYPE 64 37 21
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              20                64
  N1               8                37
  N2              12                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"
D4V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   28  7
  2Q GAIN WILD-TYPE 97 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     28    7
  2Q GAIN WILD-TYPE   97   17
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              28                97
  1               7                17
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   25 16
  2Q GAIN WILD-TYPE 51 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     25   16
  2Q GAIN WILD-TYPE   51   73
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              25                51
  MALE                16                73
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   29  7
  2Q GAIN WILD-TYPE 83 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     29    7
  2Q GAIN WILD-TYPE   83   13
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               29                83
  YES               7                13
[1] 2 2
[1] FALSE
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    41   0
  2Q GAIN WILD-TYPE 105  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     41    0
  2Q GAIN WILD-TYPE  105   13
                                clus
vv                               2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       41               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  2Q GAIN MUTATED   32  0  2  3
  2Q GAIN WILD-TYPE 91  2 10  1
D4V10, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              32                91
  R1               0                 2
  R2               2                10
  RX               3                 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"
D4V11, continuous

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    24   2
  3P GAIN WILD-TYPE 107  25
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               26               132 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                25 
$`3P GAIN MUTATED`
TCGA-AG-3611 TCGA-AG-3612 TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3591 
       13.94        19.99        37.74        20.02        24.59        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3725 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4005 
       34.03        34.03        20.98         1.02        36.03        14.04 
TCGA-AG-A016 TCGA-AG-A020 TCGA-CI-6623 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6156 
        9.07         1.02        47.44        21.01        31.00        31.00 
TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-7002 
       25.97        41.36       129.27         4.18        18.28        11.97 
TCGA-F5-6702 TCGA-F5-6811 
       28.57        32.19 

$`3P GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       10.39         8.02        17.03        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       36.03        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K 
       37.97        34.49        29.98        16.83        24.36        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       65.98        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
       36.03        20.05        24.00         1.02        46.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       13.02        35.01        14.01        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       19.99        28.04         1.02         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A025 
       13.94         6.02        23.01        37.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       33.17        13.78        44.78        48.20        78.12         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       25.05        26.04        12.00        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD 
       44.02        25.05        25.05        12.62       126.44        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         3.48        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
        8.45         9.96        49.51        42.35         0.39        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1.02              0.39 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           129.27            126.44 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            25.28             20.73 
[1] "1.0 - 129.3 (25.3)" "0.4 - 126.4 (20.7)"
[1] "hr=" "2.3"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3P GAIN MUTATED         2        0         9         0         0         2
  3P GAIN WILD-TYPE      28        8        31         2         1         2
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3P GAIN MUTATED            1          4          1        4         3
  3P GAIN WILD-TYPE          6         21         13       14         4
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  2                28
  STAGE II                 0                 8
  STAGE IIA                9                31
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                2                 2
  STAGE IIIA               1                 6
  STAGE IIIB               4                21
  STAGE IIIC               1                13
  STAGE IV                 4                14
  STAGE IVA                3                 4
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3P GAIN MUTATED    1  3 21  2
  3P GAIN WILD-TYPE  8 25 91 12
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               1                 8
  T2               3                25
  T3              21                91
  T4               2                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
  3P GAIN MUTATED   12  7  8
  3P GAIN WILD-TYPE 72 38 25
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              12                72
  N1               7                38
  N2               8                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"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    18   6
  3P GAIN WILD-TYPE 107  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     18    6
  3P GAIN WILD-TYPE  107   18
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              18               107
  1               6                18
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   14 13
  3P GAIN WILD-TYPE 62 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     14   13
  3P GAIN WILD-TYPE   62   76
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              14                62
  MALE                13                76
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   17  4
  3P GAIN WILD-TYPE 95 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     17    4
  3P GAIN WILD-TYPE   95   16
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               17                95
  YES               4                16
[1] 2 2
[1] FALSE
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    26   1
  3P GAIN WILD-TYPE 120  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     26    1
  3P GAIN WILD-TYPE  120   12
                                clus
vv                               3P GAIN MUTATED 3P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       26               120
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    20   0   1   0
  3P GAIN WILD-TYPE 103   2  11   4
D5V10, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              20               103
  R1               0                 2
  R2               1                11
  RX               0                 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"
D5V11, continuous

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    29   3
  3Q GAIN WILD-TYPE 102  24
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               32               126 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                24 
$`3Q GAIN MUTATED`
TCGA-AG-3611 TCGA-AG-3612 TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3591 
       13.94        19.99        37.74        20.02        24.59        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3885 TCGA-AG-3896 
       34.03        34.03        20.98         7.99        17.95         1.02 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A016 TCGA-AG-A020 TCGA-CI-6623 TCGA-CL-5917 
       36.03        14.04         9.07         1.02        47.44        78.12 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC 
       21.01        31.00        31.00        25.97        25.05        41.36 
TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6810 
        4.18        18.28        16.31        11.97        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6863 
       32.19        11.87 

$`3Q GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       10.39         8.02        17.03        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       36.03        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K 
       37.97        34.49        29.98        16.83        24.36        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       65.98        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
       36.03        20.05        24.00         1.02        46.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.04        19.99         1.02        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       23.01        37.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
       44.78        48.20         7.17        25.05        26.04        12.00 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 
       13.97        51.98        10.98        44.02        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 
        3.48        20.55        19.96        20.91        17.00        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46         8.45         9.96        49.51        42.35 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       36.49        19.66        37.18        38.14        12.46        47.08 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.39              0.99 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            78.12            129.27 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           20.995            21.110 
[1] "0.4 - 78.1 (21.0)"  "1.0 - 129.3 (21.1)"
[1] "hr=" "1.6"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3Q GAIN MUTATED         3        0        10         0         0         2
  3Q GAIN WILD-TYPE      27        8        30         2         1         2
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3Q GAIN MUTATED            1          6          2        4         3
  3Q GAIN WILD-TYPE          6         19         12       14         4
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  3                27
  STAGE II                 0                 8
  STAGE IIA               10                30
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                2                 2
  STAGE IIIA               1                 6
  STAGE IIIB               6                19
  STAGE IIIC               2                12
  STAGE IV                 4                14
  STAGE IVA                3                 4
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED    1  4 24  3
  3Q GAIN WILD-TYPE  8 24 88 11
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               1                 8
  T2               4                24
  T3              24                88
  T4               3                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
  3Q GAIN MUTATED   14  9  9
  3Q GAIN WILD-TYPE 70 36 24
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              14                70
  N1               9                36
  N2               9                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"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    22   6
  3Q GAIN WILD-TYPE 103  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     22    6
  3Q GAIN WILD-TYPE  103   18
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              22               103
  1               6                18
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   18 15
  3Q GAIN WILD-TYPE 58 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     18   15
  3Q GAIN WILD-TYPE   58   74
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              18                58
  MALE                15                74
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   22  5
  3Q GAIN WILD-TYPE 90 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     22    5
  3Q GAIN WILD-TYPE   90   15
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               22                90
  YES               5                15
[1] 2 2
[1] FALSE
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    32   1
  3Q GAIN WILD-TYPE 114  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     32    1
  3Q GAIN WILD-TYPE  114   12
                                clus
vv                               3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       32               114
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  3Q GAIN MUTATED   26  0  1  1
  3Q GAIN WILD-TYPE 97  2 11  3
D6V10, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              26                97
  R1               0                 2
  R2               1                11
  RX               1                 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"
D6V11, continuous

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     8   1
  4P GAIN WILD-TYPE 123  26
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               149 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                26 
$`4P GAIN MUTATED`
TCGA-AG-3890 TCGA-AG-3902 TCGA-AG-4022 TCGA-AG-A011 TCGA-CI-6621 TCGA-DC-4749 
       17.03        32.02        46.03        37.02        13.78        25.05 
TCGA-DC-6682 TCGA-DY-A1DG TCGA-EI-6510 
       25.05        51.48        18.28 

$`4P GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        13.94        19.99        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       55.76        26.43        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       13.55        37.97        34.49        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       24.00         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        25.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        1.02         3.98        20.98        13.94         6.02        23.01 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       27.55        26.43        19.46         6.05        33.17        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
       47.44        48.20        78.12         7.17        21.01        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        32.61         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        17.00        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            13.78              0.39 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            51.48            129.27 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            25.05             20.98 
[1] "13.8 - 51.5 (25.1)" "0.4 - 129.3 (21.0)"
[1] "hr=" "1.8"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4P GAIN MUTATED         2        1         3         0         0         0
  4P GAIN WILD-TYPE      28        7        37         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4P GAIN MUTATED            0          1          0        0         1
  4P GAIN WILD-TYPE          7         24         14       18         6
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  2                28
  STAGE II                 1                 7
  STAGE IIA                3                37
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               1                24
  STAGE IIIC               0                14
  STAGE IV                 0                18
  STAGE IVA                1                 6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED     0   3   6   0
  4P GAIN WILD-TYPE   9  25 106  14
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               0                 9
  T2               3                25
  T3               6               106
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  4P GAIN MUTATED    7  2  0
  4P GAIN WILD-TYPE 77 43 33
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               7                77
  N1               2                43
  N2               0                33
[1] 3 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
  4P GAIN MUTATED     6   1
  4P GAIN WILD-TYPE 119  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6    1
  4P GAIN WILD-TYPE  119   23
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               6               119
  1               1                23
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  7
  4P GAIN WILD-TYPE 74 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    7
  4P GAIN WILD-TYPE   74   82
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               2                74
  MALE                 7                82
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     6   1
  4P GAIN WILD-TYPE 106  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6    1
  4P GAIN WILD-TYPE  106   19
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                6               106
  YES               1                19
[1] 2 2
[1] FALSE
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     9   0
  4P GAIN WILD-TYPE 137  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      9    0
  4P GAIN WILD-TYPE  137   13
                                clus
vv                               4P GAIN MUTATED 4P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        9               137
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED     7   0   0   0
  4P GAIN WILD-TYPE 116   2  12   4
D7V10, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               7               116
  R1               0                 2
  R2               0                12
  RX               0                 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"
D7V11, continuous

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     4   1
  4Q GAIN WILD-TYPE 127  26
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               153 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                26 
$`4Q GAIN MUTATED`
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3902 TCGA-DC-6682 TCGA-DY-A1DG 
       17.03        35.01        32.02        25.05        51.48 

$`4Q GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        13.94        19.99        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       55.76        26.43        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       13.55        37.97        34.49        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       24.00         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        13.02        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       25.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.62       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         3.48         4.18        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            17.03              0.39 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            51.48            129.27 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            32.02             20.98 
[1] "17.0 - 51.5 (32.0)" "0.4 - 129.3 (21.0)"
[1] "hr=" "1.1"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4Q GAIN MUTATED         1        0         2         0         0         0
  4Q GAIN WILD-TYPE      29        8        38         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4Q GAIN MUTATED            0          1          0        0         1
  4Q GAIN WILD-TYPE          7         24         14       18         6
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  1                29
  STAGE II                 0                 8
  STAGE IIA                2                38
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               1                24
  STAGE IIIC               0                14
  STAGE IV                 0                18
  STAGE IVA                1                 6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED     0   1   4   0
  4Q GAIN WILD-TYPE   9  27 108  14
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               0                 9
  T2               1                27
  T3               4               108
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  4Q GAIN MUTATED    3  2  0
  4Q GAIN WILD-TYPE 81 43 33
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               3                81
  N1               2                43
  N2               0                33
[1] 3 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
  4Q GAIN MUTATED     4   1
  4Q GAIN WILD-TYPE 121  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    1
  4Q GAIN WILD-TYPE  121   23
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               4               121
  1               1                23
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0  5
  4Q GAIN WILD-TYPE 76 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    5
  4Q GAIN WILD-TYPE   76   84
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               0                76
  MALE                 5                84
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4   0
  4Q GAIN WILD-TYPE 108  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    0
  4Q GAIN WILD-TYPE  108   20
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                4               108
  YES               0                20
[1] 2 2
[1] FALSE
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     5   0
  4Q GAIN WILD-TYPE 141  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5    0
  4Q GAIN WILD-TYPE  141   13
                                clus
vv                               4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        5               141
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     4   0   0   0
  4Q GAIN WILD-TYPE 119   2  12   4
D8V10, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               4               119
  R1               0                 2
  R2               0                12
  RX               0                 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"
D8V11, continuous

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    27   7
  5P GAIN WILD-TYPE 104  20
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               34               124 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                20 
$`5P GAIN MUTATED`
TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-AF-3911 
       17.03        25.97        36.03        31.00        21.24        37.74 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 
       20.02        24.59        86.63        65.98        36.03        46.03 
TCGA-AG-3591 TCGA-AG-3609 TCGA-AG-3885 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A026 
       34.03        19.99        17.95        36.03         1.02         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-5869 
       38.96        41.00        38.04        43.20        27.55        31.00 
TCGA-DC-6156 TCGA-DC-6683 TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6464 
       31.00        25.05         4.18        16.31        11.51         9.96 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 
       28.57        32.19        37.18        11.87 

$`5P GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A014 
       10.39         8.02        13.94        19.99        17.03        15.95 
TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 
       51.98        18.28        55.76        26.43        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       17.23        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        24.36        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3593 
        7.07        20.05        24.00         1.02        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 
       32.02        19.99        28.04        14.04         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 
        1.02         1.02        49.97        61.97        38.56         2.50 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       26.04        12.00        13.97        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      129.27        24.13        51.48        32.61         3.48        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.34        16.41         8.61        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       11.97         8.45        49.51        42.35         0.39        36.49 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       19.66        38.14        12.46        47.08 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             1.02              0.39 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            86.63            129.27 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           29.785            19.990 
[1] "1.0 - 86.6 (29.8)"  "0.4 - 129.3 (20.0)"
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5P GAIN MUTATED         4        1         8         0         1         0
  5P GAIN WILD-TYPE      26        7        32         2         0         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5P GAIN MUTATED            1          7          5        5         2
  5P GAIN WILD-TYPE          6         18          9       13         5
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  4                26
  STAGE II                 1                 7
  STAGE IIA                8                32
  STAGE IIB                0                 2
  STAGE IIC                1                 0
  STAGE III                0                 4
  STAGE IIIA               1                 6
  STAGE IIIB               7                18
  STAGE IIIC               5                 9
  STAGE IV                 5                13
  STAGE IVA                2                 5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5P GAIN MUTATED    1  6 22  6
  5P GAIN WILD-TYPE  8 22 90  8
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               1                 8
  T2               6                22
  T3              22                90
  T4               6                 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
  5P GAIN MUTATED   15 11  8
  5P GAIN WILD-TYPE 69 34 25
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              15                69
  N1              11                34
  N2               8                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"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    25   6
  5P GAIN WILD-TYPE 100  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     25    6
  5P GAIN WILD-TYPE  100   18
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              25               100
  1               6                18
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   12 23
  5P GAIN WILD-TYPE 64 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     12   23
  5P GAIN WILD-TYPE   64   66
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              12                64
  MALE                23                66
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   24  7
  5P GAIN WILD-TYPE 88 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     24    7
  5P GAIN WILD-TYPE   88   13
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               24                88
  YES               7                13
[1] 2 2
[1] FALSE
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    35   0
  5P GAIN WILD-TYPE 111  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     35    0
  5P GAIN WILD-TYPE  111   13
                                clus
vv                               5P GAIN MUTATED 5P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       35               111
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED   25  1  4  1
  5P GAIN WILD-TYPE 98  1  8  3
D9V10, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              25                98
  R1               1                 1
  R2               4                 8
  RX               1                 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"
D9V11, continuous

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    20   3
  5Q GAIN WILD-TYPE 111  24
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               23               135 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                24 
$`5Q GAIN MUTATED`
TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A01N TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       17.03        25.97        31.00        20.02        24.59        65.98 
TCGA-AG-3582 TCGA-AG-3591 TCGA-AG-3609 TCGA-AG-3885 TCGA-AG-4007 TCGA-AG-A02X 
       36.03        34.03        19.99        17.95         1.02        41.00 
TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-5869 TCGA-DC-6683 TCGA-EI-6514 
       38.04        43.20        27.55        31.00        25.05        16.31 
TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6811 TCGA-F5-6814 
       11.51        11.97         9.96        32.19        37.18 

$`5Q GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A014 
       10.39         8.02        13.94        19.99        17.03        15.95 
TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       36.03        51.98        21.24        18.28        55.76        26.43 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.92        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K 
       34.49        37.74        29.98        16.83        24.36        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 
       11.84        36.03        12.00        32.02         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
       24.00         1.02        46.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 
       50.04        12.03         6.05         0.99        15.95        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.99        19.04        19.99         1.02        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 
       19.99        28.04        36.03        14.04         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       38.56         2.50        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       21.01        25.05        26.04        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       51.98        10.98        44.02        25.97        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         3.48         4.18        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       17.00        18.28        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 
        8.61        10.78        13.64        17.46         8.45        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
       42.35        28.57         0.39        36.49        19.66        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             1.02              0.39 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            65.98            129.27 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            25.97             20.91 
[1] "1.0 - 66.0 (26.0)"  "0.4 - 129.3 (20.9)"
[1] "hr=" "1.3"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5Q GAIN MUTATED         2        0         5         0         1         0
  5Q GAIN WILD-TYPE      28        8        35         2         0         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5Q GAIN MUTATED            1          5          4        5         0
  5Q GAIN WILD-TYPE          6         20         10       13         7
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  2                28
  STAGE II                 0                 8
  STAGE IIA                5                35
  STAGE IIB                0                 2
  STAGE IIC                1                 0
  STAGE III                0                 4
  STAGE IIIA               1                 6
  STAGE IIIB               5                20
  STAGE IIIC               4                10
  STAGE IV                 5                13
  STAGE IVA                0                 7
[1] 11  2
[1] TRUE
[1] "dimension of 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    0  4 17  3
  5Q GAIN WILD-TYPE  9 24 95 11
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               0                 9
  T2               4                24
  T3              17                95
  T4               3                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
  5Q GAIN MUTATED    9  7  7
  5Q GAIN WILD-TYPE 75 38 26
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               9                75
  N1               7                38
  N2               7                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"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    18   4
  5Q GAIN WILD-TYPE 107  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     18    4
  5Q GAIN WILD-TYPE  107   20
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              18               107
  1               4                20
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    9 15
  5Q GAIN WILD-TYPE 67 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      9   15
  5Q GAIN WILD-TYPE   67   74
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               9                67
  MALE                15                74
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   16  5
  5Q GAIN WILD-TYPE 96 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     16    5
  5Q GAIN WILD-TYPE   96   15
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               16                96
  YES               5                15
[1] 2 2
[1] FALSE
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    24   0
  5Q GAIN WILD-TYPE 122  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     24    0
  5Q GAIN WILD-TYPE  122   13
                                clus
vv                               5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       24               122
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    17   0   3   1
  5Q GAIN WILD-TYPE 106   2   9   3
D10V10, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              17               106
  R1               0                 2
  R2               3                 9
  RX               1                 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"
D10V11, continuous

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   34  3
  6P GAIN WILD-TYPE 97 24
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               37               121 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                24 
$`6P GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 
       10.39        19.99        36.03        31.00        21.24        18.28 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 
       26.43        46.92        43.04        37.74        29.98        24.36 
TCGA-AF-A56L TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3883 
       65.98        46.03        34.03        20.98        29.98         1.02 
TCGA-AG-3896 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A016 TCGA-AH-6644 
        1.02        14.04         1.02        46.03         9.07        27.55 
TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
        6.05        47.44        31.00        12.00        31.00        51.98 
TCGA-DY-A1DE TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 
      129.27        20.55        15.85        17.69        49.51        28.57 
TCGA-F5-6810 
        0.39 

$`6P GAIN WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
        8.02        13.94        17.03        17.03        25.97        15.95 
TCGA-AG-A023 TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 
       51.98        55.76        39.48        17.23        13.55        37.97 
TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N 
       34.49        16.83        20.02        24.59        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        3.98        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       41.00        38.04        38.56         2.50        43.20        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
       19.46        33.17        13.78        44.78        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 
        7.17        21.01        25.05        26.04        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 
        4.18        19.96        20.91        17.00        18.28        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 
       17.46        11.97         8.45         9.96        42.35        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.39              0.99 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           129.27            126.44 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            27.55             20.02 
[1] "0.4 - 129.3 (27.6)" "1.0 - 126.4 (20.0)"
[1] "hr=" "2.9"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6P GAIN MUTATED         7        1         4         0         0         1
  6P GAIN WILD-TYPE      23        7        36         2         1         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6P GAIN MUTATED            1          9          4        6         4
  6P GAIN WILD-TYPE          6         16         10       12         3
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  7                23
  STAGE II                 1                 7
  STAGE IIA                4                36
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                1                 3
  STAGE IIIA               1                 6
  STAGE IIIB               9                16
  STAGE IIIC               4                10
  STAGE IV                 6                12
  STAGE IVA                4                 3
[1] 11  2
[1] TRUE
[1] "dimension of 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    4  5 25  5
  6P GAIN WILD-TYPE  5 23 87  9
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               4                 5
  T2               5                23
  T3              25                87
  T4               5                 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
  6P GAIN MUTATED   13 13 12
  6P GAIN WILD-TYPE 71 32 21
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              13                71
  N1              13                32
  N2              12                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"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    24   9
  6P GAIN WILD-TYPE 101  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     24    9
  6P GAIN WILD-TYPE  101   15
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              24               101
  1               9                15
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   16 24
  6P GAIN WILD-TYPE 60 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     16   24
  6P GAIN WILD-TYPE   60   65
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              16                60
  MALE                24                65
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   24  6
  6P GAIN WILD-TYPE 88 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     24    6
  6P GAIN WILD-TYPE   88   14
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               24                88
  YES               6                14
[1] 2 2
[1] FALSE
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    38   1
  6P GAIN WILD-TYPE 108  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     38    1
  6P GAIN WILD-TYPE  108   12
                                clus
vv                               6P GAIN MUTATED 6P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       38               108
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  6P GAIN MUTATED   29  0  4  1
  6P GAIN WILD-TYPE 94  2  8  3
D11V10, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              29                94
  R1               0                 2
  R2               4                 8
  RX               1                 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"
D11V11, continuous

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    29   4
  6Q GAIN WILD-TYPE 102  23
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               33               125 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                23 
$`6Q GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-AF-2687 
       10.39        19.99        36.03        31.00        21.24        46.92 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3592 TCGA-AG-3725 
       37.74        29.98        24.36        65.98        34.03        20.98 
TCGA-AG-3728 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       29.98         1.02         1.02         1.02         3.98        46.03 
TCGA-AG-A016 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-5869 TCGA-DC-6154 
        9.07        27.55         6.05        47.44        31.00        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 
       31.00        51.98        51.48        20.55        15.85        17.69 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       49.51        28.57         0.39 

$`6Q GAIN WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
        8.02        13.94        17.03        17.03        25.97        15.95 
TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2690 
       51.98        18.28        55.76        26.43        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6655 
       43.04        13.55        37.97        34.49        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.59        86.63        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 
       32.98         0.99         0.99        19.04        19.99        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 
       36.95        13.02        35.01        14.01        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A002 
       32.02        19.99        28.04        36.03        14.04        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 
       13.94         6.02        23.01        37.02         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       38.56         2.50        43.20        26.43        19.46        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       13.78        44.78        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       25.05        26.04        13.97        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
      129.27        24.13        32.61         3.48         4.18        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       20.91        17.00        18.28        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        8.45         9.96        42.35        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.39              0.99 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            65.98            129.27 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            27.55             20.05 
[1] "0.4 - 66.0 (27.6)"  "1.0 - 129.3 (20.1)"
[1] "hr=" "1.7"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6Q GAIN MUTATED         5        1         3         0         0         1
  6Q GAIN WILD-TYPE      25        7        37         2         1         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6Q GAIN MUTATED            0          9          3        6         5
  6Q GAIN WILD-TYPE          7         16         11       12         2
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  5                25
  STAGE II                 1                 7
  STAGE IIA                3                37
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                1                 3
  STAGE IIIA               0                 7
  STAGE IIIB               9                16
  STAGE IIIC               3                11
  STAGE IV                 6                12
  STAGE IVA                5                 2
[1] 11  2
[1] TRUE
[1] "dimension of 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    2  4 23  5
  6Q GAIN WILD-TYPE  7 24 89  9
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               2                 7
  T2               4                24
  T3              23                89
  T4               5                 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
  6Q GAIN MUTATED   10 13 10
  6Q GAIN WILD-TYPE 74 32 23
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              10                74
  N1              13                32
  N2              10                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"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    19  10
  6Q GAIN WILD-TYPE 106  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     19   10
  6Q GAIN WILD-TYPE  106   14
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              19               106
  1              10                14
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   14 21
  6Q GAIN WILD-TYPE 62 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     14   21
  6Q GAIN WILD-TYPE   62   68
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              14                62
  MALE                21                68
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   21  5
  6Q GAIN WILD-TYPE 91 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     21    5
  6Q GAIN WILD-TYPE   91   15
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               21                91
  YES               5                15
[1] 2 2
[1] FALSE
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    34   0
  6Q GAIN WILD-TYPE 112  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     34    0
  6Q GAIN WILD-TYPE  112   13
                                clus
vv                               6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       34               112
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    23   0   5   1
  6Q GAIN WILD-TYPE 100   2   7   3
D12V10, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              23               100
  R1               0                 2
  R2               5                 7
  RX               1                 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"
D12V11, continuous

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   79 19
  7P GAIN WILD-TYPE 52  8
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               98                60 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               19                 8 
$`7P GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       15.95        36.03        31.00        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-4110 
       26.43        46.92        39.48        17.23        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3581 
       16.83        24.36        20.02        86.63        65.98         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3599 
       36.03        24.00        46.03        34.03        34.03        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 
        6.05         0.99        15.95        19.99        20.98        29.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 
        0.99         0.99        19.99        17.95        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A016 
       48.03        19.99        36.03         1.02        46.03         9.07 
TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
        1.02         1.94        38.96        38.04        38.56        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       27.55        26.43         6.05        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
        7.17        21.01        25.05        31.00        12.00        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       51.98        10.98        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 
       57.24       129.27        24.13         3.48         4.18        20.91 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 
       18.28        15.85        17.69        16.34        16.31        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 
       10.78        13.64        11.97         8.45         9.96        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       28.57         0.39        32.19        36.49        19.66        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

$`7P GAIN WILD-TYPE`
TCGA-AG-3580 TCGA-AG-A023 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
        8.02        51.98        43.04        13.55        37.97        34.49 
TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3583 
       24.59        11.84        36.03        12.00        32.02        20.05 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3726 TCGA-AG-3727 
        1.02        34.03         2.01        50.04         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
       37.02        32.98        19.04         1.02        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 
       14.01        25.02        32.02        28.04        14.04         3.98 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A020 
       20.98        13.94         6.02        23.01        37.02         1.02 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 
       49.97        61.97        41.00         2.50        19.46        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 
       13.78        44.78        26.04        13.97        44.02        25.97 
TCGA-DC-6682 TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 
       25.05        51.48        32.61        20.55        19.96        17.00 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 
       16.41         8.61        17.46        49.51        37.18        38.14 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.39              0.99 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           129.27             61.97 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           20.945            23.800 
[1] "0.4 - 129.3 (20.9)" "1.0 - 62.0 (23.8)" 
[1] "hr=" "1.3"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  7P GAIN MUTATED        17        4        20         1         1         1
  7P GAIN WILD-TYPE      13        4        20         1         0         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  7P GAIN MUTATED            3         21         11       12         4
  7P GAIN WILD-TYPE          4          4          3        6         3
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 17                13
  STAGE II                 4                 4
  STAGE IIA               20                20
  STAGE IIB                1                 1
  STAGE IIC                1                 0
  STAGE III                1                 3
  STAGE IIIA               3                 4
  STAGE IIIB              21                 4
  STAGE IIIC              11                 3
  STAGE IV                12                 6
  STAGE IVA                4                 3
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED    4 18 67 11
  7P GAIN WILD-TYPE  5 10 45  3
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               4                 5
  T2              18                10
  T3              67                45
  T4              11                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  7P GAIN MUTATED   45 31 23
  7P GAIN WILD-TYPE 39 14 10
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              45                39
  N1              31                14
  N2              23                10
[1] 3 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
  7P GAIN MUTATED   74 16
  7P GAIN WILD-TYPE 51  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     74   16
  7P GAIN WILD-TYPE   51    8
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              74                51
  1              16                 8
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   45 57
  7P GAIN WILD-TYPE 31 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     45   57
  7P GAIN WILD-TYPE   31   32
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              45                31
  MALE                57                32
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   69 12
  7P GAIN WILD-TYPE 43  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     69   12
  7P GAIN WILD-TYPE   43    8
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               69                43
  YES              12                 8
[1] 2 2
[1] FALSE
D13V9, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   97  3
  7P GAIN WILD-TYPE 49 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     97    3
  7P GAIN WILD-TYPE   49   10
                                clus
vv                               7P GAIN MUTATED 7P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       97                49
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED   74  2  8  4
  7P GAIN WILD-TYPE 49  0  4  0
D13V10, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              74                49
  R1               2                 0
  R2               8                 4
  RX               4                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   68 16
  7Q GAIN WILD-TYPE 63 11
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               84                74 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               16                11 
$`7Q GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A014 
       10.39        13.94        19.99        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       36.03        31.00        21.24        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       39.48        29.98        16.83        24.36        20.02        86.63 
TCGA-AF-A56L TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3592 
       65.98         7.07        36.03        24.00        46.03        34.03 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 
       12.03         0.99        15.95        19.99        20.98        29.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 
        0.99         0.99        19.99        17.95        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 
       48.03        19.99        28.04        36.03         1.02        46.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
        9.07         1.02        38.96        38.04        38.56        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
       27.55        26.43         6.05        47.44        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       21.01        25.05        31.00        12.00        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.98        25.05        12.62        41.36        57.24        24.13 
TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        3.48        20.91        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       16.31        11.51        11.97         9.96        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
        0.39        32.19        19.66        11.87        12.46        47.08 

$`7Q GAIN WILD-TYPE`
TCGA-AG-3580 TCGA-AG-4008 TCGA-AG-A023 TCGA-G5-6233 TCGA-AF-2690 TCGA-AF-2691 
        8.02        17.03        51.98        18.28        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-6672 TCGA-AF-A56N 
       13.55        37.97        34.49        37.74        24.59        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3591 
       36.03        12.00        32.02        20.05         1.02        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3726 TCGA-AG-3727 
       34.03         2.01        50.04         6.05         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
       37.02        32.98        19.04         1.02        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A002 
       14.01        25.02        32.02        14.04         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A020 TCGA-AG-A025 
       13.94         6.02        23.01        37.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 
        1.94        61.97        41.00         2.50        19.46        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 
       13.78        44.78        48.20        26.04        13.97        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
       25.97        25.05       126.44       129.27        51.48        32.61 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6881 TCGA-EI-6882 
        4.18        20.55        19.96        17.00        16.41         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6812 
       10.78        13.64        17.46         8.45        49.51        36.49 
TCGA-F5-6814 TCGA-F5-6861 
       37.18        38.14 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.39              0.99 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            86.63            129.27 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           21.125            20.765 
[1] "0.4 - 86.6 (21.1)"  "1.0 - 129.3 (20.8)"
[1] "hr=" "1.3"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  7Q GAIN MUTATED        16        3        13         1         1         1
  7Q GAIN WILD-TYPE      14        5        27         1         0         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  7Q GAIN MUTATED            2         21          9       11         4
  7Q GAIN WILD-TYPE          5          4          5        7         3
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 16                14
  STAGE II                 3                 5
  STAGE IIA               13                27
  STAGE IIB                1                 1
  STAGE IIC                1                 0
  STAGE III                1                 3
  STAGE IIIA               2                 5
  STAGE IIIB              21                 4
  STAGE IIIC               9                 5
  STAGE IV                11                 7
  STAGE IVA                4                 3
[1] 11  2
[1] TRUE
[1] "dimension of 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    4 17 55  9
  7Q GAIN WILD-TYPE  5 11 57  5
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               4                 5
  T2              17                11
  T3              55                57
  T4               9                 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
  7Q GAIN MUTATED   36 29 19
  7Q GAIN WILD-TYPE 48 16 14
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              36                48
  N1              29                16
  N2              19                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"
D14V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   61 15
  7Q GAIN WILD-TYPE 64  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     61   15
  7Q GAIN WILD-TYPE   64    9
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              61                64
  1              15                 9
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   38 49
  7Q GAIN WILD-TYPE 38 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     38   49
  7Q GAIN WILD-TYPE   38   40
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              38                38
  MALE                49                40
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   62  9
  7Q GAIN WILD-TYPE 50 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     62    9
  7Q GAIN WILD-TYPE   50   11
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               62                50
  YES               9                11
[1] 2 2
[1] FALSE
D14V9, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   83  2
  7Q GAIN WILD-TYPE 63 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     83    2
  7Q GAIN WILD-TYPE   63   11
                                clus
vv                               7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       83                63
  RECTAL MUCINOUS ADENOCARCINOMA               2                11
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED   64  1  8  4
  7Q GAIN WILD-TYPE 59  1  4  0
D14V10, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              64                59
  R1               1                 1
  R2               8                 4
  RX               4                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    30   8
  8P GAIN WILD-TYPE 101  19
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               38               120 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                8                19 
$`8P GAIN MUTATED`
TCGA-AG-A01N TCGA-AF-3400 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3587 
       31.00        34.49        65.98        36.03        32.02        46.03 
TCGA-AG-3598 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 
       50.04        37.02        19.04        36.95         1.02        48.03 
TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A032 
       32.02         1.02         3.98        46.03         9.07        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 
       38.56        43.20        27.55         6.05        13.78        47.44 
TCGA-CL-5918 TCGA-DC-6156 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        7.17        31.00        25.05        41.36        57.24        24.13 
TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6465 TCGA-F5-6810 
        3.48        17.00        16.31        11.51        49.51         0.39 
TCGA-F5-6863 TCGA-G5-6572 
       11.87        47.08 

$`8P GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       25.97        15.95        36.03        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       55.76        26.43        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        37.97        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3581 
       20.02        24.59        86.63        11.84        12.00         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 
       36.03        20.05        24.00         1.02        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
       19.99        20.98         7.99         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3892 
        0.99         0.99        19.99         1.02        17.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       35.01        14.01        25.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       14.04        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
       41.00         2.50        26.43        19.46        33.17        44.78 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       48.20        78.12        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       12.00        13.97        51.98        10.98        44.02        25.97 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
       25.05        12.62       126.44       129.27        51.48        32.61 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        4.18        20.55        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34        16.41         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       17.46        11.97         8.45         9.96        42.35        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       32.19        36.49        19.66        37.18        38.14        12.46 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.39              0.99 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            65.98            129.27 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           31.510            20.035 
[1] "0.4 - 66.0 (31.5)"  "1.0 - 129.3 (20.0)"
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8P GAIN MUTATED         3        4        12         1         1         0
  8P GAIN WILD-TYPE      27        4        28         1         0         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8P GAIN MUTATED            0          4          4        6         1
  8P GAIN WILD-TYPE          7         21         10       12         6
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  3                27
  STAGE II                 4                 4
  STAGE IIA               12                28
  STAGE IIB                1                 1
  STAGE IIC                1                 0
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               4                21
  STAGE IIIC               4                10
  STAGE IV                 6                12
  STAGE IVA                1                 6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8P GAIN MUTATED    1  3 30  4
  8P GAIN WILD-TYPE  8 25 82 10
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               1                 8
  T2               3                25
  T3              30                82
  T4               4                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
  8P GAIN MUTATED   22  7  8
  8P GAIN WILD-TYPE 62 38 25
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              22                62
  N1               7                38
  N2               8                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"
D15V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   27  8
  8P GAIN WILD-TYPE 98 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     27    8
  8P GAIN WILD-TYPE   98   16
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              27                98
  1               8                16
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   17 23
  8P GAIN WILD-TYPE 59 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     17   23
  8P GAIN WILD-TYPE   59   66
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              17                59
  MALE                23                66
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   24  5
  8P GAIN WILD-TYPE 88 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     24    5
  8P GAIN WILD-TYPE   88   15
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               24                88
  YES               5                15
[1] 2 2
[1] FALSE
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    36   3
  8P GAIN WILD-TYPE 110  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     36    3
  8P GAIN WILD-TYPE  110   10
                                clus
vv                               8P GAIN MUTATED 8P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       36               110
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    23   0   5   2
  8P GAIN WILD-TYPE 100   2   7   2
D15V10, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              23               100
  R1               0                 2
  R2               5                 7
  RX               2                 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"
D15V11, continuous

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   65 21
  8Q GAIN WILD-TYPE 66  6
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               86                72 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               21                 6 
$`8Q GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N 
       10.39        19.99        17.03        25.97        15.95        31.00 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       51.98        21.24        18.28        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 
       39.48        17.23        43.04        13.55        34.49        37.74 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 
       20.02        24.59        65.98        36.03        32.02        36.03 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3598 
       24.00         1.02        46.03        34.03        34.03        50.04 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 
        6.05         0.99         7.99        37.02        32.98        19.04 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 
       36.95         1.02        48.03        32.02        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
        1.02         3.98        46.03        37.02         9.07         1.02 
TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
        1.94        38.04        38.56         2.50        43.20        27.55 
TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        13.78        47.44        48.20        78.12         7.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       31.00        13.97        31.00        10.98        25.05        25.05 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         3.48 
TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.00        16.34        16.31        11.51        10.78        13.64 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 
        9.96        49.51        28.57         0.39        32.19        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

$`8Q GAIN WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-A015 TCGA-AF-2693 TCGA-AF-4110 
        8.02        13.94        17.03        36.03        37.97        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3581 
       16.83        24.36        86.63        11.84        12.00         7.07 
TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 
       20.05        34.03         2.01        12.03        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       20.98         0.99        29.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 
        1.02        17.95        13.02        35.01        14.01        25.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       19.99        36.03        20.98        13.94         6.02        23.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6897 
        1.02        49.97        38.96        61.97        41.00        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       19.46        33.17        44.78        21.01        25.05        26.04 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE 
       12.00        51.98        44.02        25.97        12.62       129.27 
TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48         4.18        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 
       15.85        17.69        16.41         8.61        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        8.45        42.35        36.49        19.66        37.18        38.14 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.39              0.99 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           126.44            129.27 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            25.51             19.99 
[1] "0.4 - 126.4 (25.5)" "1.0 - 129.3 (20.0)"
[1] "hr=" "2.5"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8Q GAIN MUTATED         9        5        22         1         1         1
  8Q GAIN WILD-TYPE      21        3        18         1         0         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8Q GAIN MUTATED            5         12         11       15         2
  8Q GAIN WILD-TYPE          2         13          3        3         5
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  9                21
  STAGE II                 5                 3
  STAGE IIA               22                18
  STAGE IIB                1                 1
  STAGE IIC                1                 0
  STAGE III                1                 3
  STAGE IIIA               5                 2
  STAGE IIIB              12                13
  STAGE IIIC              11                 3
  STAGE IV                15                 3
  STAGE IVA                2                 5
[1] 11  2
[1] TRUE
[1] "dimension of 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    3 11 65  9
  8Q GAIN WILD-TYPE  6 17 47  5
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               3                 6
  T2              11                17
  T3              65                47
  T4               9                 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
  8Q GAIN MUTATED   40 24 23
  8Q GAIN WILD-TYPE 44 21 10
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              40                44
  N1              24                21
  N2              23                10
[1] 3 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
  8Q GAIN MUTATED   61 17
  8Q GAIN WILD-TYPE 64  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     61   17
  8Q GAIN WILD-TYPE   64    7
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              61                64
  1              17                 7
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   42 48
  8Q GAIN WILD-TYPE 34 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     42   48
  8Q GAIN WILD-TYPE   34   41
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              42                34
  MALE                48                41
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   58 11
  8Q GAIN WILD-TYPE 54  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     58   11
  8Q GAIN WILD-TYPE   54    9
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               58                54
  YES              11                 9
[1] 2 2
[1] FALSE
D16V9, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   83  4
  8Q GAIN WILD-TYPE 63  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     83    4
  8Q GAIN WILD-TYPE   63    9
                                clus
vv                               8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       83                63
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED   58  2 10  3
  8Q GAIN WILD-TYPE 65  0  2  1
D16V10, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              58                65
  R1               2                 0
  R2              10                 2
  RX               3                 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"
D16V11, continuous

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    31  10
  9P GAIN WILD-TYPE 100  17
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               41               117 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               10                17 
$`9P GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-A023 TCGA-G5-6233 
       10.39        13.94        19.99        17.03        51.98        18.28 
TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-6655 TCGA-AG-3587 
       26.43        39.48        17.23        34.49        20.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3725 
       34.03        34.03         2.01        50.04         0.99        20.98 
TCGA-AG-3726 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-4001 
        7.99         0.99        19.04         1.02        32.02        36.03 
TCGA-AG-A020 TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-4745 TCGA-DC-6157 
        1.02        38.04        43.20        27.55        21.01        51.98 
TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6464 
      129.27         4.18        11.51        10.78         8.45         9.96 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 
       28.57         0.39        19.66        38.14        12.46 

$`9P GAIN WILD-TYPE`
TCGA-AG-3580 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
        8.02        17.03        25.97        15.95        36.03        31.00 
TCGA-BM-6198 TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       21.24        55.76        46.92        43.04        13.55        37.97 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K 
       37.74        29.98        16.83        24.36        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       65.98        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3599 
       36.03        20.05        24.00         1.02        34.03        12.03 
TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        6.05        15.95        19.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
       32.98         0.99        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 
       13.02        35.01        14.01        48.03        25.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       28.04        14.04         1.02         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       49.97         1.94        38.96        61.97        41.00        38.56 
TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
        2.50        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
       44.78        47.44        48.20        78.12         7.17        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
       26.04        31.00        12.00        13.97        31.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         3.48 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 
       17.69        16.34        16.31        16.41         8.61        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       17.46        11.97        49.51        42.35        32.19        36.49 
TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6572 
       37.18        11.87        47.08 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.39              0.99 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           129.27            126.44 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            19.99             24.00 
[1] "0.4 - 129.3 (20.0)" "1.0 - 126.4 (24.0)"
[1] "hr=" "1.9"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9P GAIN MUTATED         6        1        13         0         1         2
  9P GAIN WILD-TYPE      24        7        27         2         0         2
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9P GAIN MUTATED            3          4          4        4         1
  9P GAIN WILD-TYPE          4         21         10       14         6
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  6                24
  STAGE II                 1                 7
  STAGE IIA               13                27
  STAGE IIB                0                 2
  STAGE IIC                1                 0
  STAGE III                2                 2
  STAGE IIIA               3                 4
  STAGE IIIB               4                21
  STAGE IIIC               4                10
  STAGE IV                 4                14
  STAGE IVA                1                 6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9P GAIN MUTATED    1  7 30  4
  9P GAIN WILD-TYPE  8 21 82 10
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               1                 8
  T2               7                21
  T3              30                82
  T4               4                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
  9P GAIN MUTATED   21 10 10
  9P GAIN WILD-TYPE 63 35 23
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              21                63
  N1              10                35
  N2              10                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"
D17V6, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   35  5
  9P GAIN WILD-TYPE 90 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     35    5
  9P GAIN WILD-TYPE   90   19
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              35                90
  1               5                19
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   20 23
  9P GAIN WILD-TYPE 56 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     20   23
  9P GAIN WILD-TYPE   56   66
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              20                56
  MALE                23                66
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   31  4
  9P GAIN WILD-TYPE 81 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     31    4
  9P GAIN WILD-TYPE   81   16
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               31                81
  YES               4                16
[1] 2 2
[1] FALSE
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    37   5
  9P GAIN WILD-TYPE 109   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     37    5
  9P GAIN WILD-TYPE  109    8
                                clus
vv                               9P GAIN MUTATED 9P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       37               109
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  9P GAIN MUTATED   38  0  2  0
  9P GAIN WILD-TYPE 85  2 10  4
D17V10, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              38                85
  R1               0                 2
  R2               2                10
  RX               0                 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"
D17V11, continuous

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    27   7
  9Q GAIN WILD-TYPE 104  20
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               34               124 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7                20 
$`9Q GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6641 
       10.39        13.94        17.03        51.98        18.28        26.43 
TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-6655 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 
       39.48        34.49        20.02        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3878 TCGA-AG-3881 
       50.04         0.99        20.98         7.99         0.99        19.04 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-A020 TCGA-AG-A032 TCGA-AH-6644 TCGA-DC-4745 
        1.02        32.02         1.02        38.04        27.55        21.01 
TCGA-DC-6157 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6883 TCGA-EI-6884 TCGA-F5-6464 
       51.98       129.27         4.18        11.51        10.78         9.96 
TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 
        0.39        19.66        38.14        12.46 

$`9Q GAIN WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 
        8.02        19.99        17.03        25.97        15.95        36.03 
TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
       31.00        21.24        55.76        46.92        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        37.97        37.74        29.98        16.83        24.36 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 
       46.03        34.03        12.03         6.05        15.95        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 
        0.99        29.98        37.02        32.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        25.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         9.07         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        41.00        38.56         2.50        43.20 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
       47.44        48.20        78.12         7.17        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       31.00        12.00        13.97        31.00        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       25.97        25.05        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         3.48        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
       16.34        16.31        16.41         8.61        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       11.97         8.45        49.51        42.35        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6572 
       36.49        37.18        11.87        47.08 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.39              0.99 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           129.27            126.44 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           19.350            24.065 
[1] "0.4 - 129.3 (19.4)" "1.0 - 126.4 (24.1)"
[1] "hr=" "1.5"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9Q GAIN MUTATED         5        0        12         0         1         2
  9Q GAIN WILD-TYPE      25        8        28         2         0         2
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9Q GAIN MUTATED            3          3          2        4         0
  9Q GAIN WILD-TYPE          4         22         12       14         7
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  5                25
  STAGE II                 0                 8
  STAGE IIA               12                28
  STAGE IIB                0                 2
  STAGE IIC                1                 0
  STAGE III                2                 2
  STAGE IIIA               3                 4
  STAGE IIIB               3                22
  STAGE IIIC               2                12
  STAGE IV                 4                14
  STAGE IVA                0                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9Q GAIN MUTATED    1  6 24  3
  9Q GAIN WILD-TYPE  8 22 88 11
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               1                 8
  T2               6                22
  T3              24                88
  T4               3                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
  9Q GAIN MUTATED   18  8  7
  9Q GAIN WILD-TYPE 66 37 26
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              18                66
  N1               8                37
  N2               7                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"
D18V6, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   28  4
  9Q GAIN WILD-TYPE 97 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     28    4
  9Q GAIN WILD-TYPE   97   20
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              28                97
  1               4                20
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   15 20
  9Q GAIN WILD-TYPE 61 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     15   20
  9Q GAIN WILD-TYPE   61   69
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              15                61
  MALE                20                69
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   25  3
  9Q GAIN WILD-TYPE 87 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     25    3
  9Q GAIN WILD-TYPE   87   17
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               25                87
  YES               3                17
[1] 2 2
[1] FALSE
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    30   4
  9Q GAIN WILD-TYPE 116   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     30    4
  9Q GAIN WILD-TYPE  116    9
                                clus
vv                               9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       30               116
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  9Q GAIN MUTATED   30  0  2  0
  9Q GAIN WILD-TYPE 93  2 10  4
D18V10, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              30                93
  R1               0                 2
  R2               2                10
  RX               0                 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"
D18V11, continuous

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     8   2
  10P GAIN WILD-TYPE 123  25
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                10                148 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 25 
$`10P GAIN MUTATED`
TCGA-AG-A014 TCGA-BM-6198 TCGA-AF-2689 TCGA-AF-A56K TCGA-AG-3902 TCGA-AG-A016 
       15.95        21.24        39.48        86.63        32.02         9.07 
TCGA-DC-4745 TCGA-DY-A1DF TCGA-F5-6571 TCGA-F5-6812 
       21.01        24.13        42.35        36.49 

$`10P GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       25.97        36.03        31.00        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       26.43        46.92        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        37.74        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.59        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       34.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        25.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       28.04        36.03        14.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       20.98        13.94         6.02        23.01        37.02         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       19.46         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       48.20        78.12         7.17        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       25.97        25.05        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        51.48        32.61         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
       49.51        28.57         0.39        32.19        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              9.07               0.39 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             86.63             129.27 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            28.075             20.730 
[1] "9.1 - 86.6 (28.1)"  "0.4 - 129.3 (20.7)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10P GAIN MUTATED         1        1         5         0         0         0
  10P GAIN WILD-TYPE      29        7        35         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10P GAIN MUTATED            0          2          1        2         0
  10P GAIN WILD-TYPE          7         23         13       16         7
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   1                 29
  STAGE II                  1                  7
  STAGE IIA                 5                 35
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                0                  7
  STAGE IIIB                2                 23
  STAGE IIIC                1                 13
  STAGE IV                  2                 16
  STAGE IVA                 0                  7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P GAIN MUTATED     0   1  11   0
  10P GAIN WILD-TYPE   9  27 101  14
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                0                  9
  T2                1                 27
  T3               11                101
  T4                0                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  10P GAIN MUTATED    7  2  3
  10P GAIN WILD-TYPE 77 43 30
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                7                 77
  N1                2                 43
  N2                3                 30
[1] 3 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
  10P GAIN MUTATED     9   2
  10P GAIN WILD-TYPE 116  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      9    2
  10P GAIN WILD-TYPE  116   22
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                9                116
  1                2                 22
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    6  6
  10P GAIN WILD-TYPE 70 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6    6
  10P GAIN WILD-TYPE   70   83
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                6                 70
  MALE                  6                 83
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     8   0
  10P GAIN WILD-TYPE 104  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      8    0
  10P GAIN WILD-TYPE  104   20
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 8                104
  YES                0                 20
[1] 2 2
[1] FALSE
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    12   0
  10P GAIN WILD-TYPE 134  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     12    0
  10P GAIN WILD-TYPE  134   13
                                clus
vv                               10P GAIN MUTATED 10P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        12                134
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    10   0   1   0
  10P GAIN WILD-TYPE 113   2  11   4
D19V10, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               10                113
  R1                0                  2
  R2                1                 11
  RX                0                  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"
D19V11, continuous

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     4   1
  10Q GAIN WILD-TYPE 127  26
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 5                153 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 26 
$`10Q GAIN MUTATED`
TCGA-BM-6198 TCGA-AF-2689 TCGA-AF-A56K TCGA-AG-3999 TCGA-DC-4745 
       21.24        39.48        86.63        28.04        21.01 

$`10Q GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 
       25.97        15.95        36.03        31.00        51.98        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       55.76        26.43        46.92        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        24.59        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       46.03        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       12.03         6.05         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       32.02        19.99        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
       44.78        47.44        48.20        78.12         7.17        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       26.04        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         3.48         4.18        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             21.01               0.39 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             86.63             129.27 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             28.04              20.91 
[1] "21.0 - 86.6 (28.0)" "0.4 - 129.3 (20.9)"
[1] "hr=" "1.4"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10Q GAIN MUTATED         0        1         2         0         0         0
  10Q GAIN WILD-TYPE      30        7        38         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10Q GAIN MUTATED            0          2          1        1         0
  10Q GAIN WILD-TYPE          7         23         13       17         7
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                 30
  STAGE II                  1                  7
  STAGE IIA                 2                 38
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                0                  7
  STAGE IIIB                2                 23
  STAGE IIIC                1                 13
  STAGE IV                  1                 17
  STAGE IVA                 0                  7
[1] 11  2
[1] TRUE
[1] "dimension of 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     0   0   7   0
  10Q GAIN WILD-TYPE   9  28 105  14
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                  9
  T2                0                 28
  T3                7                105
  T4                0                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  10Q GAIN MUTATED    3  2  2
  10Q GAIN WILD-TYPE 81 43 31
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                3                 81
  N1                2                 43
  N2                2                 31
[1] 3 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
  10Q GAIN MUTATED     5   1
  10Q GAIN WILD-TYPE 120  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5    1
  10Q GAIN WILD-TYPE  120   23
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                5                120
  1                1                 23
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    5  2
  10Q GAIN WILD-TYPE 71 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5    2
  10Q GAIN WILD-TYPE   71   87
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                5                 71
  MALE                  2                 87
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     5   0
  10Q GAIN WILD-TYPE 107  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5    0
  10Q GAIN WILD-TYPE  107   20
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 5                107
  YES                0                 20
[1] 2 2
[1] FALSE
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     7   0
  10Q GAIN WILD-TYPE 139  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      7    0
  10Q GAIN WILD-TYPE  139   13
                                clus
vv                               10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         7                139
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED     7   0   0   0
  10Q GAIN WILD-TYPE 116   2  12   4
D20V10, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0                7                116
  R1                0                  2
  R2                0                 12
  RX                0                  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"
D20V11, continuous

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    29   3
  11P GAIN WILD-TYPE 102  24
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                32                126 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 24 
$`11P GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A00H TCGA-AG-A01N TCGA-BM-6198 
       10.39        13.94        19.99        25.97        31.00        21.24 
TCGA-G5-6233 TCGA-AF-2690 TCGA-AF-6655 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3587 
       18.28        17.23        20.02        65.98        12.00        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3609 TCGA-AG-4001 TCGA-AG-4007 TCGA-AH-6897 
       34.03        34.03        19.99        36.03         1.02        26.43 
TCGA-CI-6621 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       13.78        47.44        48.20        25.05        31.00        12.00 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6885 
       51.98        44.02       126.44         4.18        16.31        13.64 
TCGA-F5-6810 TCGA-F5-6811 
        0.39        32.19 

$`11P GAIN WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 
        8.02        17.03        17.03        15.95        36.03        51.98 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       55.76        26.43        46.92        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3581 
       24.59        86.63        11.84        36.03        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 
       36.03        20.05        24.00         1.02        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 
       50.04        12.03         6.05         0.99        15.95        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 
       32.02        19.99        28.04        14.04         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 
       19.46         6.05        33.17        44.78        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 
       21.01        26.04        13.97        31.00        10.98        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        25.05        12.62        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         3.48        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 
        8.45         9.96        49.51        42.35        28.57        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.39               0.99 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            126.44             129.27 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            23.145             20.980 
[1] "0.4 - 126.4 (23.1)" "1.0 - 129.3 (21.0)"
[1] "hr=" "2.4"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11P GAIN MUTATED         7        1         9         0         0         0
  11P GAIN WILD-TYPE      23        7        31         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11P GAIN MUTATED            1          4          3        4         1
  11P GAIN WILD-TYPE          6         21         11       14         6
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   7                 23
  STAGE II                  1                  7
  STAGE IIA                 9                 31
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                1                  6
  STAGE IIIB                4                 21
  STAGE IIIC                3                 11
  STAGE IV                  4                 14
  STAGE IVA                 1                  6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11P GAIN MUTATED    1  8 20  2
  11P GAIN WILD-TYPE  8 20 92 12
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                1                  8
  T2                8                 20
  T3               20                 92
  T4                2                 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
  11P GAIN MUTATED   18  7  6
  11P GAIN WILD-TYPE 66 38 27
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               18                 66
  N1                7                 38
  N2                6                 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"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    24   5
  11P GAIN WILD-TYPE 101  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     24    5
  11P GAIN WILD-TYPE  101   19
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               24                101
  1                5                 19
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED   14 18
  11P GAIN WILD-TYPE 62 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     14   18
  11P GAIN WILD-TYPE   62   71
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               14                 62
  MALE                 18                 71
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                  0  1
  11P GAIN MUTATED   23  3
  11P GAIN WILD-TYPE 89 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     23    3
  11P GAIN WILD-TYPE   89   17
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                23                 89
  YES                3                 17
[1] 2 2
[1] FALSE
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    32   0
  11P GAIN WILD-TYPE 114  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     32    0
  11P GAIN WILD-TYPE  114   13
                                clus
vv                               11P GAIN MUTATED 11P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        32                114
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  11P GAIN MUTATED   24  0  2  1
  11P GAIN WILD-TYPE 99  2 10  3
D21V10, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               24                 99
  R1                0                  2
  R2                2                 10
  RX                1                  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"
D21V11, continuous

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    25   2
  11Q GAIN WILD-TYPE 106  25
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                27                131 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 25 
$`11Q GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-A00H TCGA-AG-A01N TCGA-AF-2690 TCGA-AF-A56L 
       10.39        19.99        25.97        31.00        17.23        65.98 
TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3883 TCGA-AG-4001 TCGA-AG-4007 
       12.00        46.03        34.03         1.02        36.03         1.02 
TCGA-AH-6897 TCGA-CI-6621 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 
       26.43        13.78        47.44        48.20        25.05        31.00 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A0XA TCGA-EI-6514 TCGA-EI-6885 
       12.00        31.00        51.98       126.44        16.31        13.64 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        0.39        32.19        36.49 

$`11Q GAIN WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 
        8.02        13.94        17.03        17.03        15.95        36.03 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       51.98        21.24        18.28        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       39.48        43.04        13.55        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       29.98        16.83        24.36        20.02        24.59        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.84        36.03        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       12.03         6.05         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
        0.99        19.04        19.99        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       19.99        28.04        14.04         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 
       38.04        38.56         2.50        43.20        27.55        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.05        33.17        44.78        78.12         7.17        21.01 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       26.04        13.97        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       25.05        12.62        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 
        8.45         9.96        49.51        42.35        28.57        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.39               0.99 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            126.44             129.27 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             26.43              20.91 
[1] "0.4 - 126.4 (26.4)" "1.0 - 129.3 (20.9)"
[1] "hr=" "3.2"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11Q GAIN MUTATED         7        1         7         0         0         0
  11Q GAIN WILD-TYPE      23        7        33         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11Q GAIN MUTATED            0          3          2        4         2
  11Q GAIN WILD-TYPE          7         22         12       14         5
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   7                 23
  STAGE II                  1                  7
  STAGE IIA                 7                 33
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                0                  7
  STAGE IIIB                3                 22
  STAGE IIIC                2                 12
  STAGE IV                  4                 14
  STAGE IVA                 2                  5
[1] 11  2
[1] TRUE
[1] "dimension of 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    1  7 15  3
  11Q GAIN WILD-TYPE  8 21 97 11
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                1                  8
  T2                7                 21
  T3               15                 97
  T4                3                 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
  11Q GAIN MUTATED   16  5  5
  11Q GAIN WILD-TYPE 68 40 28
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               16                 68
  N1                5                 40
  N2                5                 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"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    19   6
  11Q GAIN WILD-TYPE 106  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     19    6
  11Q GAIN WILD-TYPE  106   18
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               19                106
  1                6                 18
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED   12 15
  11Q GAIN WILD-TYPE 64 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     12   15
  11Q GAIN WILD-TYPE   64   74
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               12                 64
  MALE                 15                 74
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED   18  2
  11Q GAIN WILD-TYPE 94 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     18    2
  11Q GAIN WILD-TYPE   94   18
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                18                 94
  YES                2                 18
[1] 2 2
[1] FALSE
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    27   0
  11Q GAIN WILD-TYPE 119  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     27    0
  11Q GAIN WILD-TYPE  119   13
                                clus
vv                               11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        27                119
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    19   0   2   1
  11Q GAIN WILD-TYPE 104   2  10   3
D22V10, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               19                104
  R1                0                  2
  R2                2                 10
  RX                1                  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"
D22V11, continuous

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    26   6
  12P GAIN WILD-TYPE 105  21
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                32                126 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 6                 21 
$`12P GAIN MUTATED`
TCGA-AG-3611 TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6233 TCGA-AF-3400 TCGA-AF-3911 
       13.94        15.95        36.03        18.28        34.49        37.74 
TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 
       16.83        24.59        36.03        46.03         2.01         6.05 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 
       19.99         7.99        19.04         1.02        36.95         1.02 
TCGA-AG-4001 TCGA-AG-A02G TCGA-AG-A02N TCGA-CL-5917 TCGA-DC-6682 TCGA-DC-6683 
       36.03        38.96        61.97        78.12        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 
       12.62       126.44        32.61        19.96        18.28        17.69 
TCGA-EI-6885 TCGA-EI-7002 
       13.64        11.97 

$`12P GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       31.00        51.98        21.24        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 
       39.48        17.23        43.04        13.55        37.97        29.98 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 
       24.36        20.02        86.63        65.98        11.84        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       34.03        34.03        34.03        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       15.95        20.98         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99        19.99        17.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
        6.02        23.01        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       49.97         1.94        41.00        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4745 
       13.78        44.78        47.44        48.20         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DD 
       51.98        10.98        44.02        25.97        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        51.48         3.48         4.18        20.55 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       20.91        17.00        15.85        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
        8.61        11.51        10.78        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        42.35        28.57         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.02               0.39 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            126.44             129.27 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            19.975             21.125 
[1] "1.0 - 126.4 (20.0)" "0.4 - 129.3 (21.1)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12P GAIN MUTATED         7        3         9         0         0         0
  12P GAIN WILD-TYPE      23        5        31         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12P GAIN MUTATED            1          3          4        4         0
  12P GAIN WILD-TYPE          6         22         10       14         7
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   7                 23
  STAGE II                  3                  5
  STAGE IIA                 9                 31
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                1                  6
  STAGE IIIB                3                 22
  STAGE IIIC                4                 10
  STAGE IV                  4                 14
  STAGE IVA                 0                  7
[1] 11  2
[1] TRUE
[1] "dimension of 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    1  9 21  2
  12P GAIN WILD-TYPE  8 19 91 12
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                1                  8
  T2                9                 19
  T3               21                 91
  T4                2                 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
  12P GAIN MUTATED   20  6  7
  12P GAIN WILD-TYPE 64 39 26
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               20                 64
  N1                6                 39
  N2                7                 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"
D23V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   26  3
  12P GAIN WILD-TYPE 99 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     26    3
  12P GAIN WILD-TYPE   99   21
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               26                 99
  1                3                 21
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   14 19
  12P GAIN WILD-TYPE 62 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     14   19
  12P GAIN WILD-TYPE   62   70
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               14                 62
  MALE                 19                 70
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   19  7
  12P GAIN WILD-TYPE 93 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     19    7
  12P GAIN WILD-TYPE   93   13
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                19                 93
  YES                7                 13
[1] 2 2
[1] FALSE
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    28   4
  12P GAIN WILD-TYPE 118   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     28    4
  12P GAIN WILD-TYPE  118    9
                                clus
vv                               12P GAIN MUTATED 12P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        28                118
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  12P GAIN MUTATED   24  0  2  2
  12P GAIN WILD-TYPE 99  2 10  2
D23V10, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               24                 99
  R1                0                  2
  R2                2                 10
  RX                2                  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"
D23V11, continuous

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    15   5
  12Q GAIN WILD-TYPE 116  22
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                20                138 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                 22 
$`12Q GAIN MUTATED`
TCGA-AG-A015 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3609 
       36.03        16.83        36.03        46.03         2.01        19.99 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-A02G TCGA-AG-A02N TCGA-DC-6682 
       19.04         1.02         1.02        38.96        61.97        25.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 
       25.05       126.44        32.61        19.96        18.28        17.69 
TCGA-EI-6885 TCGA-EI-7002 
       13.64        11.97 

$`12Q GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       25.97        15.95        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       55.76        26.43        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 
       13.55        37.97        34.49        37.74        29.98        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 
       20.02        24.59        86.63        65.98        11.84        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03        34.03        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 
       37.02        32.98         0.99         0.99        19.99        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 
       36.95        13.02        35.01        14.01        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        49.97         1.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       26.04        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       10.98        44.02        25.97        12.62        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        51.48         3.48         4.18        20.55 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       20.91        17.00        15.85        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
        8.61        11.51        10.78        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        42.35        28.57         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.02               0.39 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            126.44             129.27 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            19.975             21.125 
[1] "1.0 - 126.4 (20.0)" "0.4 - 129.3 (21.1)"
[1] "hr=" "1.5"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12Q GAIN MUTATED         5        2         5         0         0         0
  12Q GAIN WILD-TYPE      25        6        35         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12Q GAIN MUTATED            1          3          1        3         0
  12Q GAIN WILD-TYPE          6         22         13       15         7
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   5                 25
  STAGE II                  2                  6
  STAGE IIA                 5                 35
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                1                  6
  STAGE IIIB                3                 22
  STAGE IIIC                1                 13
  STAGE IV                  3                 15
  STAGE IVA                 0                  7
[1] 11  2
[1] TRUE
[1] "dimension of 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     1   7  12   1
  12Q GAIN WILD-TYPE   8  21 100  13
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                1                  8
  T2                7                 21
  T3               12                100
  T4                1                 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
  12Q GAIN MUTATED   13  6  2
  12Q GAIN WILD-TYPE 71 39 31
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               13                 71
  N1                6                 39
  N2                2                 31
[1] 3 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
  12Q GAIN MUTATED    17   3
  12Q GAIN WILD-TYPE 108  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     17    3
  12Q GAIN WILD-TYPE  108   21
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               17                108
  1                3                 21
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   11 10
  12Q GAIN WILD-TYPE 65 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     11   10
  12Q GAIN WILD-TYPE   65   79
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               11                 65
  MALE                 10                 79
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   14  1
  12Q GAIN WILD-TYPE 98 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     14    1
  12Q GAIN WILD-TYPE   98   19
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                14                 98
  YES                1                 19
[1] 2 2
[1] FALSE
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    19   1
  12Q GAIN WILD-TYPE 127  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     19    1
  12Q GAIN WILD-TYPE  127   12
                                clus
vv                               12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        19                127
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    16   0   2   0
  12Q GAIN WILD-TYPE 107   2  10   4
D24V10, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               16                107
  R1                0                  2
  R2                2                 10
  RX                0                  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"
D24V11, continuous

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED   87 21
  13Q GAIN WILD-TYPE 44  6
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               108                 50 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                21                  6 
$`13Q GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       15.95        36.03        51.98        18.28        55.76        26.43 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.92        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       37.74        29.98        24.36        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       65.98        11.84         7.07        36.03        20.05         1.02 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3725 
       46.03        34.03        34.03         0.99        19.99        20.98 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 
        0.99        29.98         0.99        19.99        17.95        36.95 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A016 
       36.03        14.04         1.02        46.03         6.02         9.07 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       49.97         1.94        38.96        38.04        38.56        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       27.55        26.43         6.05        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       31.00        12.00        31.00        51.98        10.98        44.02 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       25.05        25.05        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 
       51.48        32.61         3.48        20.55        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       10.78        11.97         9.96        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6572 
        0.39        32.19        36.49        19.66        11.87        47.08 

$`13Q GAIN WILD-TYPE`
TCGA-AG-3580 TCGA-AG-A01N TCGA-BM-6198 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 
        8.02        31.00        21.24        34.49        16.83        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3598 
       12.00        32.02        24.00        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 
       12.03         6.05        15.95         7.99        37.02        32.98 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-3901 
        0.99        19.04         1.02        13.02        48.03        25.02 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
        3.98        20.98        13.94        23.01        37.02         1.02 
TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 
        1.02        61.97        41.00         2.50        19.46        33.17 
TCGA-DC-6155 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-EF-5831 TCGA-EI-6507 
       13.97        25.97        12.62       126.44         4.18        19.96 
TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 
       20.91         8.61        13.64        17.46         8.45        37.18 
TCGA-F5-6861 TCGA-F5-6864 
       38.14        12.46 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.39               0.99 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            129.27             126.44 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             24.82              19.25 
[1] "0.4 - 129.3 (24.8)" "1.0 - 126.4 (19.2)"
[1] "hr=" "1.2"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  13Q GAIN MUTATED        19        4        22         2         1         3
  13Q GAIN WILD-TYPE      11        4        18         0         0         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  13Q GAIN MUTATED            5         20         13       13         5
  13Q GAIN WILD-TYPE          2          5          1        5         2
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  19                 11
  STAGE II                  4                  4
  STAGE IIA                22                 18
  STAGE IIB                 2                  0
  STAGE IIC                 1                  0
  STAGE III                 3                  1
  STAGE IIIA                5                  2
  STAGE IIIB               20                  5
  STAGE IIIC               13                  1
  STAGE IV                 13                  5
  STAGE IVA                 5                  2
[1] 11  2
[1] TRUE
[1] "dimension of 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    7 17 75 13
  13Q GAIN WILD-TYPE  2 11 37  1
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                7                  2
  T2               17                 11
  T3               75                 37
  T4               13                  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                 N0 N1 N2
  13Q GAIN MUTATED   49 35 27
  13Q GAIN WILD-TYPE 35 10  6
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               49                 35
  N1               35                 10
  N2               27                  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"
D25V6, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   83 17
  13Q GAIN WILD-TYPE 42  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     83   17
  13Q GAIN WILD-TYPE   42    7
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               83                 42
  1               17                  7
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   50 64
  13Q GAIN WILD-TYPE 26 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     50   64
  13Q GAIN WILD-TYPE   26   25
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               50                 26
  MALE                 64                 25
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   73 16
  13Q GAIN WILD-TYPE 39  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     73   16
  13Q GAIN WILD-TYPE   39    4
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                73                 39
  YES               16                  4
[1] 2 2
[1] FALSE
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   107   3
  13Q GAIN WILD-TYPE  39  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    107    3
  13Q GAIN WILD-TYPE   39   10
                                clus
vv                               13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       107                 39
  RECTAL MUCINOUS ADENOCARCINOMA                3                 10
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  13Q GAIN MUTATED   81  2  8  3
  13Q GAIN WILD-TYPE 42  0  4  1
D25V10, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               81                 42
  R1                2                  0
  R2                8                  4
  RX                3                  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"
D25V11, continuous

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     6   0
  14Q GAIN WILD-TYPE 125  27
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 6                152 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 0                 27 
$`14Q GAIN MUTATED`
TCGA-AG-3611 TCGA-AG-A014 TCGA-AF-6136 TCGA-AG-3999 TCGA-EI-6512 TCGA-EI-6885 
       13.94        15.95        24.36        28.04        17.69        13.64 

$`14Q GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       36.03        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       37.97        34.49        37.74        29.98        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       46.03        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       12.03         6.05         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       32.02        19.99        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       51.98        10.98        44.02        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.62       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        18.28        15.85        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             13.64               0.39 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             28.04             129.27 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            16.820             21.125 
[1] "13.6 - 28.0 (16.8)" "0.4 - 129.3 (21.1)"
[1] "hr="     "9500000"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  14Q GAIN MUTATED         1        1         1         0         0         0
  14Q GAIN WILD-TYPE      29        7        39         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  14Q GAIN MUTATED            0          3          1        1         0
  14Q GAIN WILD-TYPE          7         22         13       17         7
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   1                 29
  STAGE II                  1                  7
  STAGE IIA                 1                 39
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                0                  7
  STAGE IIIB                3                 22
  STAGE IIIC                1                 13
  STAGE IV                  1                 17
  STAGE IVA                 0                  7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED     0   1   7   0
  14Q GAIN WILD-TYPE   9  27 105  14
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                0                  9
  T2                1                 27
  T3                7                105
  T4                0                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  14Q GAIN MUTATED    3  4  1
  14Q GAIN WILD-TYPE 81 41 32
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                3                 81
  N1                4                 41
  N2                1                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     6   1
  14Q GAIN WILD-TYPE 119  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      6    1
  14Q GAIN WILD-TYPE  119   23
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                6                119
  1                1                 23
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    5  3
  14Q GAIN WILD-TYPE 71 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5    3
  14Q GAIN WILD-TYPE   71   86
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                5                 71
  MALE                  3                 86
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     4   1
  14Q GAIN WILD-TYPE 108  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4    1
  14Q GAIN WILD-TYPE  108   19
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 4                108
  YES                1                 19
[1] 2 2
[1] FALSE
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     8   0
  14Q GAIN WILD-TYPE 138  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      8    0
  14Q GAIN WILD-TYPE  138   13
                                clus
vv                               14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         8                138
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED     7   0   0   0
  14Q GAIN WILD-TYPE 116   2  12   4
D26V10, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0                7                116
  R1                0                  2
  R2                0                 12
  RX                0                  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"
D26V11, continuous

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     2   1
  15Q GAIN WILD-TYPE 129  26
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                155 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 26 
$`15Q GAIN MUTATED`
TCGA-AF-3400 TCGA-EI-7004 TCGA-F5-6464 
       34.49         8.45         9.96 

$`15Q GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       18.28        55.76        26.43        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        37.97        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       24.00         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
        6.02        23.01        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       25.97        25.05        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 
       11.51        10.78        13.64        17.46        11.97        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              8.45               0.39 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             34.49             129.27 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              9.96              21.01 
[1] "8.4 - 34.5 (10.0)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "4.4"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  15Q GAIN MUTATED         0        1         1         0         0         0
  15Q GAIN WILD-TYPE      30        7        39         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  15Q GAIN MUTATED            0          0          1        0         0
  15Q GAIN WILD-TYPE          7         25         13       18         7
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   0                 30
  STAGE II                  1                  7
  STAGE IIA                 1                 39
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                0                  7
  STAGE IIIB                0                 25
  STAGE IIIC                1                 13
  STAGE IV                  0                 18
  STAGE IVA                 0                  7
[1] 11  2
[1] TRUE
[1] "dimension of 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     0   0   2   2
  15Q GAIN WILD-TYPE   9  28 110  12
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                0                  9
  T2                0                 28
  T3                2                110
  T4                2                 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
  15Q GAIN MUTATED    2  0  2
  15Q GAIN WILD-TYPE 82 45 31
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                2                 82
  N1                0                 45
  N2                2                 31
[1] 3 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
  15Q GAIN MUTATED     4   0
  15Q GAIN WILD-TYPE 121  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4    0
  15Q GAIN WILD-TYPE  121   24
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                4                121
  1                0                 24
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    3  1
  15Q GAIN WILD-TYPE 73 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    1
  15Q GAIN WILD-TYPE   73   88
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 73
  MALE                  1                 88
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     2   1
  15Q GAIN WILD-TYPE 110  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2    1
  15Q GAIN WILD-TYPE  110   19
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 2                110
  YES                1                 19
[1] 2 2
[1] FALSE
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     2   2
  15Q GAIN WILD-TYPE 144  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2    2
  15Q GAIN WILD-TYPE  144   11
                                clus
vv                               15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         2                144
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED     4   0   0   0
  15Q GAIN WILD-TYPE 119   2  12   4
D27V10, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                4                119
  R1                0                  2
  R2                0                 12
  RX                0                  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"
D27V11, continuous

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   34  5
  16P GAIN WILD-TYPE 97 22
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                39                119 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 22 
$`16P GAIN MUTATED`
TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 
       13.94        17.03        15.95        36.03        31.00        21.24 
TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       39.48        37.74        24.36        20.02        86.63        65.98 
TCGA-AG-3592 TCGA-AG-3600 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3885 TCGA-AG-3909 
       34.03         6.05        20.98         7.99        17.95        19.99 
TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 
       36.03        46.03         9.07        38.96        38.04        27.55 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       44.78        47.44        78.12        25.05        31.00        12.00 
TCGA-DC-6683 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 
       25.05        24.13         3.48        17.69        16.31        49.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6863 
       28.57         0.39        11.87 

$`16P GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A023 
       10.39         8.02        19.99        17.03        25.97        51.98 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
       18.28        55.76        26.43        46.92        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 
       13.55        37.97        34.49        29.98        16.83        24.59 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.04        19.99         1.02        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3999 
       14.01         1.02        48.03        25.02        32.02        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02         3.98        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         1.02         1.02        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       61.97        41.00        38.56         2.50        43.20        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6624 TCGA-CL-5918 
       19.46         6.05        33.17        13.78        48.20         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       21.01        26.04        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
       57.24       129.27        51.48        32.61         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       11.97         8.45         9.96        42.35        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        12.46        47.08 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.39               0.99 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             86.63             129.27 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             25.05              20.05 
[1] "0.4 - 86.6 (25.1)"  "1.0 - 129.3 (20.1)"
[1] "hr=" "1.7"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16P GAIN MUTATED         6        1         6         2         0         1
  16P GAIN WILD-TYPE      24        7        34         0         1         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16P GAIN MUTATED            1         11          5        4         2
  16P GAIN WILD-TYPE          6         14          9       14         5
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   6                 24
  STAGE II                  1                  7
  STAGE IIA                 6                 34
  STAGE IIB                 2                  0
  STAGE IIC                 0                  1
  STAGE III                 1                  3
  STAGE IIIA                1                  6
  STAGE IIIB               11                 14
  STAGE IIIC                5                  9
  STAGE IV                  4                 14
  STAGE IVA                 2                  5
[1] 11  2
[1] TRUE
[1] "dimension of 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    2  7 26  5
  16P GAIN WILD-TYPE  7 21 86  9
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                2                  7
  T2                7                 21
  T3               26                 86
  T4                5                  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
  16P GAIN MUTATED   16 14  9
  16P GAIN WILD-TYPE 68 31 24
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               16                 68
  N1               14                 31
  N2                9                 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"
D28V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   29  6
  16P GAIN WILD-TYPE 96 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     29    6
  16P GAIN WILD-TYPE   96   18
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               29                 96
  1                6                 18
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   19 22
  16P GAIN WILD-TYPE 57 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     19   22
  16P GAIN WILD-TYPE   57   67
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               19                 57
  MALE                 22                 67
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   28  7
  16P GAIN WILD-TYPE 84 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     28    7
  16P GAIN WILD-TYPE   84   13
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                28                 84
  YES                7                 13
[1] 2 2
[1] FALSE
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    41   0
  16P GAIN WILD-TYPE 105  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     41    0
  16P GAIN WILD-TYPE  105   13
                                clus
vv                               16P GAIN MUTATED 16P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        41                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  16P GAIN MUTATED   29  0  4  2
  16P GAIN WILD-TYPE 94  2  8  2
D28V10, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               29                 94
  R1                0                  2
  R2                4                  8
  RX                2                  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"
D28V11, continuous

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   32  8
  16Q GAIN WILD-TYPE 99 19
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                40                118 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                 19 
$`16Q GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       10.39        13.94        17.03        15.95        36.03        31.00 
TCGA-BM-6198 TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       21.24        39.48        37.74        24.36        20.02        86.63 
TCGA-AF-A56L TCGA-AG-3592 TCGA-AG-3725 TCGA-AG-3885 TCGA-AG-3909 TCGA-AG-4001 
       65.98        34.03        20.98        17.95        19.99        36.03 
TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 TCGA-CI-6623 
       46.03         9.07        38.96        38.04        27.55        47.44 
TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A1DF 
       78.12        25.05        31.00        12.00        25.05        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6702 
       51.48         3.48        17.69        16.31        49.51        28.57 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
        0.39        36.49        19.66        11.87 

$`16Q GAIN WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A023 TCGA-G5-6233 
        8.02        19.99        17.03        25.97        51.98        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       55.76        26.43        46.92        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56N 
       37.97        34.49        29.98        16.83        24.59        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 
       24.00         1.02        46.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.99        19.04        19.99         1.02        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 
       28.04        14.04         1.02         3.98        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
        6.02        23.01        37.02         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        61.97        41.00        38.56         2.50        43.20 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 
       48.20         7.17        21.01        26.04        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       51.98        10.98        44.02        25.97        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 
      126.44        41.36        57.24       129.27        32.61         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 
       17.46        11.97         8.45         9.96        42.35        32.19 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        12.46        47.08 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.39               0.99 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             86.63             129.27 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             25.05              20.02 
[1] "0.4 - 86.6 (25.1)"  "1.0 - 129.3 (20.0)"
[1] "hr=" "1"  
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16Q GAIN MUTATED         5        1         7         1         0         1
  16Q GAIN WILD-TYPE      25        7        33         1         1         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16Q GAIN MUTATED            1         10          5        5         3
  16Q GAIN WILD-TYPE          6         15          9       13         4
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   5                 25
  STAGE II                  1                  7
  STAGE IIA                 7                 33
  STAGE IIB                 1                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  3
  STAGE IIIA                1                  6
  STAGE IIIB               10                 15
  STAGE IIIC                5                  9
  STAGE IV                  5                 13
  STAGE IVA                 3                  4
[1] 11  2
[1] TRUE
[1] "dimension of 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  6 28  4
  16Q GAIN WILD-TYPE  7 22 84 10
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                2                  7
  T2                6                 22
  T3               28                 84
  T4                4                 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
  16Q GAIN MUTATED   15 15  9
  16Q GAIN WILD-TYPE 69 30 24
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               15                 69
  N1               15                 30
  N2                9                 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"
D29V6, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   27  8
  16Q GAIN WILD-TYPE 98 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     27    8
  16Q GAIN WILD-TYPE   98   16
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               27                 98
  1                8                 16
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   18 23
  16Q GAIN WILD-TYPE 58 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     18   23
  16Q GAIN WILD-TYPE   58   66
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               18                 58
  MALE                 23                 66
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   30  5
  16Q GAIN WILD-TYPE 82 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     30    5
  16Q GAIN WILD-TYPE   82   15
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                30                 82
  YES                5                 15
[1] 2 2
[1] FALSE
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    41   0
  16Q GAIN WILD-TYPE 105  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     41    0
  16Q GAIN WILD-TYPE  105   13
                                clus
vv                               16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        41                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  16Q GAIN MUTATED   30  0  3  2
  16Q GAIN WILD-TYPE 93  2  9  2
D29V10, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               30                 93
  R1                0                  2
  R2                3                  9
  RX                2                  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"
D29V11, continuous

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    10   0
  17P GAIN WILD-TYPE 121  27
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                10                148 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 0                 27 
$`17P GAIN MUTATED`
TCGA-G5-6641 TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3882 
       26.43         7.07        46.03        15.95        19.99        19.99 
TCGA-AG-4007 TCGA-CI-6623 TCGA-DC-6154 TCGA-DC-6682 
        1.02        47.44        12.00        25.05 

$`17P GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       18.28        55.76        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       13.55        37.97        34.49        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00        32.02        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        1.02        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       12.03         6.05         0.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
       29.98        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
        1.02        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
        6.02        23.01        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        6.05        33.17        13.78        44.78        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        7.17        21.01        25.05        26.04        31.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.62       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.02               0.39 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             47.44             129.27 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            19.990             21.125 
[1] "1.0 - 47.4 (20.0)"  "0.4 - 129.3 (21.1)"
[1] "hr="     "2.7e+07"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17P GAIN MUTATED         4        0         2         0         0         0
  17P GAIN WILD-TYPE      26        8        38         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17P GAIN MUTATED            1          0          1        1         1
  17P GAIN WILD-TYPE          6         25         13       17         6
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   4                 26
  STAGE II                  0                  8
  STAGE IIA                 2                 38
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                1                  6
  STAGE IIIB                0                 25
  STAGE IIIC                1                 13
  STAGE IV                  1                 17
  STAGE IVA                 1                  6
[1] 11  2
[1] TRUE
[1] "dimension of 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   3   3   2
  17P GAIN WILD-TYPE   7  25 109  12
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                2                  7
  T2                3                 25
  T3                3                109
  T4                2                 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
  17P GAIN MUTATED    6  1  3
  17P GAIN WILD-TYPE 78 44 30
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                6                 78
  N1                1                 44
  N2                3                 30
[1] 3 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
  17P GAIN MUTATED     7   2
  17P GAIN WILD-TYPE 118  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      7    2
  17P GAIN WILD-TYPE  118   22
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                7                118
  1                2                 22
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    4  6
  17P GAIN WILD-TYPE 72 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    6
  17P GAIN WILD-TYPE   72   83
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                4                 72
  MALE                  6                 83
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     7   1
  17P GAIN WILD-TYPE 105  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      7    1
  17P GAIN WILD-TYPE  105   19
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 7                105
  YES                1                 19
[1] 2 2
[1] FALSE
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     9   1
  17P GAIN WILD-TYPE 137  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      9    1
  17P GAIN WILD-TYPE  137   12
                                clus
vv                               17P GAIN MUTATED 17P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         9                137
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED     8   0   1   0
  17P GAIN WILD-TYPE 115   2  11   4
D30V10, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                8                115
  R1                0                  2
  R2                1                 11
  RX                0                  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"
D30V11, continuous

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    27   3
  17Q GAIN WILD-TYPE 104  24
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                128 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 24 
$`17Q GAIN MUTATED`
TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A01N TCGA-G5-6641 TCGA-AF-2690 TCGA-AF-A56K 
       17.03        15.95        31.00        26.43        17.23        86.63 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3608 
       11.84        12.00         7.07        46.03        34.03        15.95 
TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A016 TCGA-AH-6643 
       19.99        19.99        36.03         1.02         9.07        43.20 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6621 TCGA-DC-6154 TCGA-DC-6682 TCGA-DY-A1DG 
       26.43         6.05        13.78        12.00        25.05        51.48 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6811 TCGA-F5-6864 
       17.00        18.28        16.31        11.97        32.19        12.46 

$`17Q GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-A00H 
       10.39         8.02        13.94        19.99        17.03        25.97 
TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-AF-2687 
       36.03        51.98        21.24        18.28        55.76        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       39.48        43.04        13.55        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       29.98        16.83        24.36        20.02        24.59        65.98 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       36.03        32.02        36.03        20.05        24.00         1.02 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.04         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 
       25.02        32.02        19.99        28.04        14.04         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6903 
       41.00        38.04        38.56         2.50        27.55        19.46 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       33.17        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       21.01        25.05        26.04        31.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       51.98        10.98        44.02        25.97        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6511 
        3.48         4.18        20.55        19.96        20.91        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       28.57         0.39        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-G5-6572 
       11.87        47.08 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              1.02               0.39 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             86.63             129.27 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            17.130             24.065 
[1] "1.0 - 86.6 (17.1)"  "0.4 - 129.3 (24.1)"
[1] "hr=" "1.5"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17Q GAIN MUTATED         5        1         9         0         0         0
  17Q GAIN WILD-TYPE      25        7        31         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17Q GAIN MUTATED            1          3          4        5         2
  17Q GAIN WILD-TYPE          6         22         10       13         5
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   5                 25
  STAGE II                  1                  7
  STAGE IIA                 9                 31
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                1                  6
  STAGE IIIB                3                 22
  STAGE IIIC                4                 10
  STAGE IV                  5                 13
  STAGE IVA                 2                  5
[1] 11  2
[1] TRUE
[1] "dimension of 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    1  7 20  3
  17Q GAIN WILD-TYPE  8 21 92 11
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                1                  8
  T2                7                 21
  T3               20                 92
  T4                3                 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
  17Q GAIN MUTATED   17  5  9
  17Q GAIN WILD-TYPE 67 40 24
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               17                 67
  N1                5                 40
  N2                9                 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"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    21   7
  17Q GAIN WILD-TYPE 104  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     21    7
  17Q GAIN WILD-TYPE  104   17
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               21                104
  1                7                 17
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   13 18
  17Q GAIN WILD-TYPE 63 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     13   18
  17Q GAIN WILD-TYPE   63   71
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               13                 63
  MALE                 18                 71
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   22  3
  17Q GAIN WILD-TYPE 90 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     22    3
  17Q GAIN WILD-TYPE   90   17
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                22                 90
  YES                3                 17
[1] 2 2
[1] FALSE
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    30   1
  17Q GAIN WILD-TYPE 116  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     30    1
  17Q GAIN WILD-TYPE  116   12
                                clus
vv                               17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        30                116
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    23   0   4   0
  17Q GAIN WILD-TYPE 100   2   8   4
D31V10, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               23                100
  R1                0                  2
  R2                4                  8
  RX                0                  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"
D31V11, continuous

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     5   2
  18P GAIN WILD-TYPE 126  25
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                151 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 25 
$`18P GAIN MUTATED`
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3600 TCGA-AG-A02G TCGA-CI-6621 TCGA-DT-5265 
       24.59        32.02         6.05        38.96        13.78        12.62 
TCGA-F5-6464 
        9.96 

$`18P GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       18.28        55.76        26.43        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       16.83        24.36        20.02        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       50.04        12.03         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       27.55        26.43        19.46         6.05        33.17        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       26.04        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       10.98        44.02        25.97        25.05        25.05       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        3.48         4.18        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              6.05               0.39 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             38.96             129.27 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             13.78              21.01 
[1] "6.0 - 39.0 (13.8)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "3"  
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18P GAIN MUTATED         0        2         1         0         0         0
  18P GAIN WILD-TYPE      30        6        39         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18P GAIN MUTATED            0          1          2        2         0
  18P GAIN WILD-TYPE          7         24         12       16         7
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   0                 30
  STAGE II                  2                  6
  STAGE IIA                 1                 39
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                0                  7
  STAGE IIIB                1                 24
  STAGE IIIC                2                 12
  STAGE IV                  2                 16
  STAGE IVA                 0                  7
[1] 11  2
[1] TRUE
[1] "dimension of 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     0   1   5   2
  18P GAIN WILD-TYPE   9  27 107  12
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                0                  9
  T2                1                 27
  T3                5                107
  T4                2                 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
  18P GAIN MUTATED    3  2  3
  18P GAIN WILD-TYPE 81 43 30
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                3                 81
  N1                2                 43
  N2                3                 30
[1] 3 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
  18P GAIN MUTATED     5   1
  18P GAIN WILD-TYPE 120  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5    1
  18P GAIN WILD-TYPE  120   23
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                5                120
  1                1                 23
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    3  5
  18P GAIN WILD-TYPE 73 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    5
  18P GAIN WILD-TYPE   73   84
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                3                 73
  MALE                  5                 84
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     3   3
  18P GAIN WILD-TYPE 109  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    3
  18P GAIN WILD-TYPE  109   17
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 3                109
  YES                3                 17
[1] 2 2
[1] FALSE
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     6   2
  18P GAIN WILD-TYPE 140  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6    2
  18P GAIN WILD-TYPE  140   11
                                clus
vv                               18P GAIN MUTATED 18P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         6                140
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED     4   0   1   1
  18P GAIN WILD-TYPE 119   2  11   3
D32V10, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                4                119
  R1                0                  2
  R2                1                 11
  RX                1                  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"
D32V11, continuous

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     4   2
  18Q GAIN WILD-TYPE 127  25
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                152 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 25 
$`18Q GAIN MUTATED`
TCGA-AF-6672 TCGA-AG-3600 TCGA-AG-A02G TCGA-CI-6621 TCGA-DT-5265 TCGA-F5-6464 
       24.59         6.05        38.96        13.78        12.62         9.96 

$`18Q GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       18.28        55.76        26.43        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       16.83        24.36        20.02        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       24.00         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        61.97        41.00        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       51.98        10.98        44.02        25.97        25.05        25.05 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         3.48         4.18        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45        49.51        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              6.05               0.39 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             38.96             129.27 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            13.200             21.125 
[1] "6.0 - 39.0 (13.2)"  "0.4 - 129.3 (21.1)"
[1] "hr=" "3.8"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18Q GAIN MUTATED         0        1         0         0         0         0
  18Q GAIN WILD-TYPE      30        7        40         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18Q GAIN MUTATED            0          1          2        2         0
  18Q GAIN WILD-TYPE          7         24         12       16         7
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   0                 30
  STAGE II                  1                  7
  STAGE IIA                 0                 40
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                0                  7
  STAGE IIIB                1                 24
  STAGE IIIC                2                 12
  STAGE IV                  2                 16
  STAGE IVA                 0                  7
[1] 11  2
[1] TRUE
[1] "dimension of 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     0   1   3   2
  18Q GAIN WILD-TYPE   9  27 109  12
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                0                  9
  T2                1                 27
  T3                3                109
  T4                2                 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
  18Q GAIN MUTATED    1  2  3
  18Q GAIN WILD-TYPE 83 43 30
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                1                 83
  N1                2                 43
  N2                3                 30
[1] 3 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
  18Q GAIN MUTATED     3   1
  18Q GAIN WILD-TYPE 122  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    1
  18Q GAIN WILD-TYPE  122   23
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                3                122
  1                1                 23
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    1  5
  18Q GAIN WILD-TYPE 75 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    5
  18Q GAIN WILD-TYPE   75   84
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 75
  MALE                  5                 84
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2   3
  18Q GAIN WILD-TYPE 110  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    3
  18Q GAIN WILD-TYPE  110   17
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 2                110
  YES                3                 17
[1] 2 2
[1] FALSE
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     5   1
  18Q GAIN WILD-TYPE 141  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    1
  18Q GAIN WILD-TYPE  141   12
                                clus
vv                               18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         5                141
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED     2   0   1   1
  18Q GAIN WILD-TYPE 121   2  11   3
D33V10, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                2                121
  R1                0                  2
  R2                1                 11
  RX                1                  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"
D33V11, continuous

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    27   5
  19P GAIN WILD-TYPE 104  22
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                32                126 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 22 
$`19P GAIN MUTATED`
TCGA-AG-A014 TCGA-AG-A01N TCGA-BM-6198 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-A56K 
       15.95        31.00        21.24        39.48        17.23        86.63 
TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3600 
       65.98        36.03        46.03        34.03        34.03         6.05 
TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 
       19.99         0.99        19.99         1.02        28.04        36.03 
TCGA-AG-4007 TCGA-AG-A026 TCGA-AG-A032 TCGA-CI-6619 TCGA-CI-6621 TCGA-DC-4745 
        1.02         1.94        38.04         6.05        13.78        21.01 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6506 TCGA-EI-6512 
       12.00        51.98        25.05       129.27        20.55        17.69 
TCGA-EI-6514 TCGA-F5-6863 
       16.31        11.87 

$`19P GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       25.97        36.03        51.98        18.28        55.76        26.43 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       46.92        43.04        13.55        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N 
       29.98        16.83        24.36        20.02        24.59        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00        32.02         7.07        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
       32.98         0.99        19.04         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       13.02        35.01        14.01        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       19.99        14.04         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
        6.02        23.01        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 
       49.97        38.96        61.97        41.00        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
       43.20        27.55        26.43        19.46        33.17        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
       47.44        48.20        78.12         7.17        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       31.00        13.97        31.00        10.98        44.02        25.97 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       25.05        12.62       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         3.48         4.18        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       17.00        18.28        15.85        16.34        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       36.49        19.66        37.18        38.14        12.46        47.08 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.99               0.39 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            129.27             126.44 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            20.780             21.995 
[1] "1.0 - 129.3 (20.8)" "0.4 - 126.4 (22.0)"
[1] "hr=" "1.3"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19P GAIN MUTATED         6        1         8         0         0         0
  19P GAIN WILD-TYPE      24        7        32         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19P GAIN MUTATED            0          7          5        5         1
  19P GAIN WILD-TYPE          7         18          9       13         6
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   6                 24
  STAGE II                  1                  7
  STAGE IIA                 8                 32
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                0                  7
  STAGE IIIB                7                 18
  STAGE IIIC                5                  9
  STAGE IV                  5                 13
  STAGE IVA                 1                  6
[1] 11  2
[1] TRUE
[1] "dimension of 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    0  7 22  4
  19P GAIN WILD-TYPE  9 21 90 10
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                0                  9
  T2                7                 21
  T3               22                 90
  T4                4                 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
  19P GAIN MUTATED   16  9  8
  19P GAIN WILD-TYPE 68 36 25
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               16                 68
  N1                9                 36
  N2                8                 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"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    25   6
  19P GAIN WILD-TYPE 100  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     25    6
  19P GAIN WILD-TYPE  100   18
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               25                100
  1                6                 18
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   17 16
  19P GAIN WILD-TYPE 59 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     17   16
  19P GAIN WILD-TYPE   59   73
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               17                 59
  MALE                 16                 73
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   20  4
  19P GAIN WILD-TYPE 92 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     20    4
  19P GAIN WILD-TYPE   92   16
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                20                 92
  YES                4                 16
[1] 2 2
[1] FALSE
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    33   0
  19P GAIN WILD-TYPE 113  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     33    0
  19P GAIN WILD-TYPE  113   13
                                clus
vv                               19P GAIN MUTATED 19P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        33                113
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  19P GAIN MUTATED   25  1  3  1
  19P GAIN WILD-TYPE 98  1  9  3
D34V10, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               25                 98
  R1                1                  1
  R2                3                  9
  RX                1                  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"
D34V11, continuous

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    26   3
  19Q GAIN WILD-TYPE 105  24
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                29                129 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                 24 
$`19Q GAIN MUTATED`
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-AF-2689 TCGA-AF-A56K 
       15.95        36.03        31.00        21.24        39.48        86.63 
TCGA-AF-A56L TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3882 
       65.98        46.03        34.03        19.99         0.99        19.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-A016 TCGA-AG-A026 TCGA-AG-A032 
        1.02        28.04         1.02         9.07         1.94        38.04 
TCGA-CI-6619 TCGA-CI-6621 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE 
        6.05        13.78        12.00        51.98        25.05       129.27 
TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6863 
       20.55        17.69        16.31        13.64        11.87 

$`19Q GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        51.98        18.28        55.76        26.43        46.92 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N 
       29.98        16.83        24.36        20.02        24.59        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 
        0.99        29.98        37.02        32.98         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
       48.03        25.02        32.02        19.99        36.03        14.04 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       37.02         1.02         1.02        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       19.46        33.17        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        7.17        21.01        25.05        26.04        31.00        13.97 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       31.00        10.98        44.02        25.97        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        3.48         4.18        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       38.14        12.46        47.08 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.99               0.39 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            129.27             126.44 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             19.99              23.01 
[1] "1.0 - 129.3 (20.0)" "0.4 - 126.4 (23.0)"
[1] "hr=" "2.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19Q GAIN MUTATED         7        1         7         0         0         0
  19Q GAIN WILD-TYPE      23        7        33         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19Q GAIN MUTATED            0          7          3        6         1
  19Q GAIN WILD-TYPE          7         18         11       12         6
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   7                 23
  STAGE II                  1                  7
  STAGE IIA                 7                 33
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                0                  7
  STAGE IIIB                7                 18
  STAGE IIIC                3                 11
  STAGE IV                  6                 12
  STAGE IVA                 1                  6
[1] 11  2
[1] TRUE
[1] "dimension of 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    1  7 20  5
  19Q GAIN WILD-TYPE  8 21 92  9
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                1                  8
  T2                7                 21
  T3               20                 92
  T4                5                  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
  19Q GAIN MUTATED   16 10  7
  19Q GAIN WILD-TYPE 68 35 26
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               16                 68
  N1               10                 35
  N2                7                 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"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    24   7
  19Q GAIN WILD-TYPE 101  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     24    7
  19Q GAIN WILD-TYPE  101   17
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               24                101
  1                7                 17
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   17 16
  19Q GAIN WILD-TYPE 59 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     17   16
  19Q GAIN WILD-TYPE   59   73
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               17                 59
  MALE                 16                 73
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   20  2
  19Q GAIN WILD-TYPE 92 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     20    2
  19Q GAIN WILD-TYPE   92   18
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                20                 92
  YES                2                 18
[1] 2 2
[1] FALSE
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    33   0
  19Q GAIN WILD-TYPE 113  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     33    0
  19Q GAIN WILD-TYPE  113   13
                                clus
vv                               19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        33                113
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    23   1   4   1
  19Q GAIN WILD-TYPE 100   1   8   3
D35V10, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               23                100
  R1                1                  1
  R2                4                  8
  RX                1                  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"
D35V11, continuous

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   87 17
  20P GAIN WILD-TYPE 44 10
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               104                 54 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                17                 10 
$`20P GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       25.97        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 
       55.76        46.92        39.48        17.23        37.97        37.74 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3581 TCGA-AG-3582 
       16.83        20.02        24.59        65.98         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3727 
       34.03        50.04        12.03        15.95        20.98         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
       29.98        37.02         0.99         0.99         1.02        36.95 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        25.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       36.03        14.04         1.02        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       37.02         9.07        41.00        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6621 
       43.20        27.55        26.43        19.46         6.05        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
       44.78        47.44        48.20        21.01        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 
       25.97       126.44       129.27        24.13        32.61         4.18 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 
       20.55        20.91        17.00        18.28        17.69        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 
       16.41        11.51        10.78        13.64        11.97         9.96 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
       49.51         0.39        32.19        36.49        37.18        38.14 
TCGA-F5-6863 TCGA-G5-6572 
       11.87        47.08 

$`20P GAIN WILD-TYPE`
TCGA-AG-A014 TCGA-G5-6641 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 
       15.95        26.43        43.04        13.55        34.49        29.98 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.36        86.63        11.84        36.03        12.00        32.02 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3732 
        2.01         6.05         0.99        19.99         7.99        32.98 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3902 
       19.04        19.99        17.95        13.02        35.01        32.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
        3.98        46.03        20.98         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-CI-6620 TCGA-CL-5917 TCGA-CL-5918 
        1.94        38.96        61.97        33.17        78.12         7.17 
TCGA-DC-4749 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        25.05        12.62        41.36        57.24 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6882 
       51.48         3.48        19.96        15.85        16.34         8.61 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 
       17.46         8.45        42.35        28.57        19.66        12.46 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.39               0.99 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            129.27              86.63 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            22.125             19.990 
[1] "0.4 - 129.3 (22.1)" "1.0 - 86.6 (20.0)" 
[1] "hr=" "1.1"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  20P GAIN MUTATED        21        0        24         1         1         3
  20P GAIN WILD-TYPE       9        8        16         1         0         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  20P GAIN MUTATED            5         15          9       15         3
  20P GAIN WILD-TYPE          2         10          5        3         4
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  21                  9
  STAGE II                  0                  8
  STAGE IIA                24                 16
  STAGE IIB                 1                  1
  STAGE IIC                 1                  0
  STAGE III                 3                  1
  STAGE IIIA                5                  2
  STAGE IIIB               15                 10
  STAGE IIIC                9                  5
  STAGE IV                 15                  3
  STAGE IVA                 3                  4
[1] 11  2
[1] TRUE
[1] "dimension of 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    5 21 69  8
  20P GAIN WILD-TYPE  4  7 43  6
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                5                  4
  T2               21                  7
  T3               69                 43
  T4                8                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  20P GAIN MUTATED   50 28 24
  20P GAIN WILD-TYPE 34 17  9
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               50                 34
  N1               28                 17
  N2               24                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   76 18
  20P GAIN WILD-TYPE 49  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     76   18
  20P GAIN WILD-TYPE   49    6
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               76                 49
  1               18                  6
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   45 60
  20P GAIN WILD-TYPE 31 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     45   60
  20P GAIN WILD-TYPE   31   29
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               45                 31
  MALE                 60                 29
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   76 12
  20P GAIN WILD-TYPE 36  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     76   12
  20P GAIN WILD-TYPE   36    8
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                76                 36
  YES               12                  8
[1] 2 2
[1] FALSE
D36V9, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   97  5
  20P GAIN WILD-TYPE 49  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     97    5
  20P GAIN WILD-TYPE   49    8
                                clus
vv                               20P GAIN MUTATED 20P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        97                 49
  RECTAL MUCINOUS ADENOCARCINOMA                5                  8
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED   77  1  8  1
  20P GAIN WILD-TYPE 46  1  4  3
D36V10, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               77                 46
  R1                1                  1
  R2                8                  4
  RX                1                  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"
D36V11, continuous

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   114  25
  20Q GAIN WILD-TYPE  17   2
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               139                 19 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                25                  2 
$`20Q GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       18.28        55.76        26.43        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       43.04        37.97        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       34.03        34.03        34.03        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       37.02         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       36.95        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       46.03        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
        1.02         1.02         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        31.00        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        25.05       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         3.48         4.18        20.55 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       16.31        16.41        11.51        10.78        13.64        11.97 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

$`20Q GAIN WILD-TYPE`
TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 
       13.55        34.49        12.00        32.02         2.01         6.05 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A025 
       32.98        19.04        13.02         3.98        20.98        49.97 
TCGA-AG-A02N TCGA-CL-5917 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 
       61.97        78.12        12.62        19.96         8.61        17.46 
TCGA-EI-7004 
        8.45 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.39               2.01 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            129.27              78.12 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             24.00              17.46 
[1] "0.4 - 129.3 (24.0)" "2.0 - 78.1 (17.5)" 
[1] "hr=" "1.7"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  20Q GAIN MUTATED        26        5        33         2         1         4
  20Q GAIN WILD-TYPE       4        3         7         0         0         0
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  20Q GAIN MUTATED            6         25         12       17         7
  20Q GAIN WILD-TYPE          1          0          2        1         0
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  26                  4
  STAGE II                  5                  3
  STAGE IIA                33                  7
  STAGE IIB                 2                  0
  STAGE IIC                 1                  0
  STAGE III                 4                  0
  STAGE IIIA                6                  1
  STAGE IIIB               25                  0
  STAGE IIIC               12                  2
  STAGE IV                 17                  1
  STAGE IVA                 7                  0
[1] 11  2
[1] TRUE
[1] "dimension of 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    7 26 98 13
  20Q GAIN WILD-TYPE  2  2 14  1
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                7                  2
  T2               26                  2
  T3               98                 14
  T4               13                  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                 N0 N1 N2
  20Q GAIN MUTATED   70 44 29
  20Q GAIN WILD-TYPE 14  1  4
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               70                 14
  N1               44                  1
  N2               29                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   108  23
  20Q GAIN WILD-TYPE  17   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    108   23
  20Q GAIN WILD-TYPE   17    1
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              108                 17
  1               23                  1
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   67 79
  20Q GAIN WILD-TYPE  9 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     67   79
  20Q GAIN WILD-TYPE    9   10
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               67                  9
  MALE                 79                 10
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   98 17
  20Q GAIN WILD-TYPE 14  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     98   17
  20Q GAIN WILD-TYPE   14    3
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                98                 14
  YES               17                  3
[1] 2 2
[1] FALSE
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   135   7
  20Q GAIN WILD-TYPE  11   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    135    7
  20Q GAIN WILD-TYPE   11    6
                                clus
vv                               20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       135                 11
  RECTAL MUCINOUS ADENOCARCINOMA                7                  6
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   108   2  11   2
  20Q GAIN WILD-TYPE  15   0   1   2
D37V10, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              108                 15
  R1                2                  0
  R2               11                  1
  RX                2                  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"
D37V11, continuous

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED     9   1
  21Q GAIN WILD-TYPE 122  26
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                148 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 26 
$`21Q GAIN MUTATED`
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3732 TCGA-AG-3885 TCGA-AG-4021 TCGA-AG-A011 
       13.94        19.99        32.98        17.95         3.98        37.02 
TCGA-AH-6644 TCGA-CI-6623 TCGA-EF-5830 TCGA-EI-6885 
       27.55        47.44         3.48        13.64 

$`21Q GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       10.39         8.02        17.03        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       36.03        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 
       20.98         7.99         0.99        29.98        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.99        19.04        19.99         1.02        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       19.99        28.04        36.03        14.04         1.02        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A01J 
       20.98        13.94         6.02        23.01         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       38.04        38.56         2.50        43.20        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        6.05        33.17        13.78        44.78        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        31.00        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        51.48        32.61         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              3.48               0.39 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             47.44             129.27 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            18.970             21.125 
[1] "3.5 - 47.4 (19.0)"  "0.4 - 129.3 (21.1)"
[1] "hr=" "1.3"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  21Q GAIN MUTATED         2        0         2         1         0         0
  21Q GAIN WILD-TYPE      28        8        38         1         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  21Q GAIN MUTATED            0          2          0        2         0
  21Q GAIN WILD-TYPE          7         23         14       16         7
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   2                 28
  STAGE II                  0                  8
  STAGE IIA                 2                 38
  STAGE IIB                 1                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                0                  7
  STAGE IIIB                2                 23
  STAGE IIIC                0                 14
  STAGE IV                  2                 16
  STAGE IVA                 0                  7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q GAIN MUTATED     1   1   7   1
  21Q GAIN WILD-TYPE   8  27 105  13
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                1                  8
  T2                1                 27
  T3                7                105
  T4                1                 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
  21Q GAIN MUTATED    5  3  1
  21Q GAIN WILD-TYPE 79 42 32
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                5                 79
  N1                3                 42
  N2                1                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     7   2
  21Q GAIN WILD-TYPE 118  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7    2
  21Q GAIN WILD-TYPE  118   22
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                7                118
  1                2                 22
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    5  5
  21Q GAIN WILD-TYPE 71 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5    5
  21Q GAIN WILD-TYPE   71   84
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                5                 71
  MALE                  5                 84
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     8   1
  21Q GAIN WILD-TYPE 104  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8    1
  21Q GAIN WILD-TYPE  104   19
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 8                104
  YES                1                 19
[1] 2 2
[1] FALSE
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    10   0
  21Q GAIN WILD-TYPE 136  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10    0
  21Q GAIN WILD-TYPE  136   13
                                clus
vv                               21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        10                136
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED     7   0   1   0
  21Q GAIN WILD-TYPE 116   2  11   4
D38V10, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0                7                116
  R1                0                  2
  R2                1                 11
  RX                0                  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"
D38V11, continuous

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     6   3
  22Q GAIN WILD-TYPE 125  24
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                149 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 24 
$`22Q GAIN MUTATED`
TCGA-AG-3612 TCGA-AF-2690 TCGA-AG-3582 TCGA-AG-3609 TCGA-AG-3893 TCGA-AG-A00Y 
       19.99        17.23        36.03        19.99        35.01        23.01 
TCGA-AH-6897 TCGA-CI-6623 TCGA-DY-A1DF 
       26.43        47.44        24.13 

$`22Q GAIN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        13.94        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       55.76        26.43        46.92        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00        32.02         7.07        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       46.03        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       14.01         1.02        48.03        25.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       28.04        36.03        14.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       20.98        13.94         6.02        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 
       38.04        38.56         2.50        43.20        27.55        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        6.05        33.17        13.78        44.78        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        31.00        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        51.48        32.61         3.48         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             17.23               0.39 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             47.44             129.27 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             24.13              20.98 
[1] "17.2 - 47.4 (24.1)" "0.4 - 129.3 (21.0)"
[1] "hr=" "2.2"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  22Q GAIN MUTATED         2        0         1         0         0         0
  22Q GAIN WILD-TYPE      28        8        39         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  22Q GAIN MUTATED            0          2          3        1         0
  22Q GAIN WILD-TYPE          7         23         11       17         7
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   2                 28
  STAGE II                  0                  8
  STAGE IIA                 1                 39
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                0                  7
  STAGE IIIB                2                 23
  STAGE IIIC                3                 11
  STAGE IV                  1                 17
  STAGE IVA                 0                  7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED     1   1   7   0
  22Q GAIN WILD-TYPE   8  27 105  14
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                1                  8
  T2                1                 27
  T3                7                105
  T4                0                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  22Q GAIN MUTATED    3  3  3
  22Q GAIN WILD-TYPE 81 42 30
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                3                 81
  N1                3                 42
  N2                3                 30
[1] 3 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
  22Q GAIN MUTATED     8   1
  22Q GAIN WILD-TYPE 117  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      8    1
  22Q GAIN WILD-TYPE  117   23
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                8                117
  1                1                 23
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    4  5
  22Q GAIN WILD-TYPE 72 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    5
  22Q GAIN WILD-TYPE   72   84
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                4                 72
  MALE                  5                 84
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     7   0
  22Q GAIN WILD-TYPE 105  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      7    0
  22Q GAIN WILD-TYPE  105   20
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 7                105
  YES                0                 20
[1] 2 2
[1] FALSE
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     9   0
  22Q GAIN WILD-TYPE 137  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      9    0
  22Q GAIN WILD-TYPE  137   13
                                clus
vv                               22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         9                137
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED     6   0   1   0
  22Q GAIN WILD-TYPE 117   2  11   4
D39V10, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                6                117
  R1                0                  2
  R2                1                 11
  RX                0                  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"
D39V11, continuous

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    26   4
  XP GAIN WILD-TYPE 105  23
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               30               128 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                4                23 
$`XP GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-G5-6235 
       10.39        19.99        15.95        36.03        31.00        55.76 
TCGA-AF-2692 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3592 TCGA-AG-3609 
       13.55        16.83        20.02        86.63        34.03        19.99 
TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A032 
       35.01        28.04         1.02        46.03         9.07        38.04 
TCGA-AH-6644 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-6154 TCGA-DC-6156 TCGA-DY-A1H8 
       27.55        78.12        21.01        12.00        31.00        32.61 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6863 
       18.28        17.69        13.64        49.51         0.39        11.87 

$`XP GAIN WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A023 
        8.02        13.94        17.03        17.03        25.97        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       21.24        18.28        26.43        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 
       43.04        37.97        34.49        37.74        29.98        24.36 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.59        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 
        1.02        17.95        36.95        13.02        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
       48.03        25.02        32.02        19.99        36.03        14.04 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        3.98        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       41.00        38.56         2.50        43.20        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        7.17        25.05        26.04        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        3.48         4.18        20.55        19.96        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 
       10.78        17.46        11.97         8.45         9.96        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       28.57        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.39              0.99 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            86.63            129.27 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           20.515            21.110 
[1] "0.4 - 86.6 (20.5)"  "1.0 - 129.3 (21.1)"
[1] "hr=" "1.5"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  XP GAIN MUTATED         3        1         4         0         0         0
  XP GAIN WILD-TYPE      27        7        36         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XP GAIN MUTATED            2          8          3        5         2
  XP GAIN WILD-TYPE          5         17         11       13         5
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                  3                27
  STAGE II                 1                 7
  STAGE IIA                4                36
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               2                 5
  STAGE IIIB               8                17
  STAGE IIIC               3                11
  STAGE IV                 5                13
  STAGE IVA                2                 5
[1] 11  2
[1] TRUE
[1] "dimension of 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  6 18  5
  XP GAIN WILD-TYPE  8 22 94  9
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               1                 8
  T2               6                22
  T3              18                94
  T4               5                 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
  XP GAIN MUTATED   10 12  7
  XP GAIN WILD-TYPE 74 33 26
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              10                74
  N1              12                33
  N2               7                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"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    19   7
  XP GAIN WILD-TYPE 106  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     19    7
  XP GAIN WILD-TYPE  106   17
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              19               106
  1               7                17
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   17 14
  XP GAIN WILD-TYPE 59 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     17   14
  XP GAIN WILD-TYPE   59   75
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              17                59
  MALE                14                75
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   24  2
  XP GAIN WILD-TYPE 88 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     24    2
  XP GAIN WILD-TYPE   88   18
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               24                88
  YES               2                18
[1] 2 2
[1] FALSE
D40V9, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    30   0
  XP GAIN WILD-TYPE 116  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     30    0
  XP GAIN WILD-TYPE  116   13
                                clus
vv                               XP GAIN MUTATED XP GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       30               116
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED    23   1   4   1
  XP GAIN WILD-TYPE 100   1   8   3
D40V10, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              23               100
  R1               1                 1
  R2               4                 8
  RX               1                 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"
D40V11, continuous

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    26   5
  XQ GAIN WILD-TYPE 105  22
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               31               127 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                5                22 
$`XQ GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-A014 TCGA-AG-A015 TCGA-AF-2692 TCGA-AF-5654 
       10.39        19.99        15.95        36.03        13.55        16.83 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3609 TCGA-AG-3881 
       20.02        86.63        34.03         2.01        19.99        19.04 
TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A032 
       35.01        28.04         1.02        46.03         9.07        38.04 
TCGA-AH-6644 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-6154 TCGA-DC-6156 
       27.55        47.44        78.12        21.01        12.00        31.00 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 
       18.28        17.69        13.64         9.96        49.51         0.39 
TCGA-F5-6863 
       11.87 

$`XQ GAIN WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A01N 
        8.02        13.94        17.03        17.03        25.97        31.00 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       51.98        21.24        18.28        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       39.48        17.23        43.04        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       29.98        24.36        24.59        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03        34.03        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        15.95        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98        37.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 
        1.02        17.95        36.95        13.02        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
       48.03        25.02        32.02        19.99        36.03        14.04 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        3.98        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       41.00        38.56         2.50        43.20        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 
        6.05        33.17        13.78        44.78        48.20         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       25.05        26.04        31.00        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        3.48         4.18        20.55        19.96        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 
       10.78        17.46        11.97         8.45        42.35        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       32.19        36.49        19.66        37.18        38.14        12.46 
TCGA-G5-6572 
       47.08 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.39              0.99 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            86.63            129.27 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            19.99             24.00 
[1] "0.4 - 86.6 (20.0)"  "1.0 - 129.3 (24.0)"
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  XQ GAIN MUTATED         4        1         6         0         0         0
  XQ GAIN WILD-TYPE      26        7        34         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XQ GAIN MUTATED            1          7          4        4         2
  XQ GAIN WILD-TYPE          6         18         10       14         5
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  4                26
  STAGE II                 1                 7
  STAGE IIA                6                34
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               1                 6
  STAGE IIIB               7                18
  STAGE IIIC               4                10
  STAGE IV                 4                14
  STAGE IVA                2                 5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XQ GAIN MUTATED    2  4 19  6
  XQ GAIN WILD-TYPE  7 24 93  8
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               2                 7
  T2               4                24
  T3              19                93
  T4               6                 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
  XQ GAIN MUTATED   12 10  8
  XQ GAIN WILD-TYPE 72 35 25
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              12                72
  N1              10                35
  N2               8                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
  XQ GAIN MUTATED    22   6
  XQ GAIN WILD-TYPE 103  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     22    6
  XQ GAIN WILD-TYPE  103   18
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              22               103
  1               6                18
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   17 15
  XQ GAIN WILD-TYPE 59 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     17   15
  XQ GAIN WILD-TYPE   59   74
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              17                59
  MALE                15                74
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   25  2
  XQ GAIN WILD-TYPE 87 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     25    2
  XQ GAIN WILD-TYPE   87   18
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               25                87
  YES               2                18
[1] 2 2
[1] FALSE
D41V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    29   1
  XQ GAIN WILD-TYPE 117  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     29    1
  XQ GAIN WILD-TYPE  117   12
                                clus
vv                               XQ GAIN MUTATED XQ GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       29               117
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  XQ GAIN MUTATED   25  0  3  1
  XQ GAIN WILD-TYPE 98  2  9  3
D41V10, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              25                98
  R1               0                 2
  R2               3                 9
  RX               1                 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"
D41V11, continuous

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   36  8
  1P LOSS WILD-TYPE 95 19
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               44               114 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                8                19 
$`1P LOSS MUTATED`
TCGA-AG-A00H TCGA-BM-6198 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-4110 TCGA-AF-6136 
       25.97        21.24        46.92        17.23        29.98        24.36 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3728 
       65.98        11.84        36.03        24.00        34.03        29.98 
TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3898 
       37.02        19.04        19.99         1.02         1.02        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00Y TCGA-AG-A02G TCGA-AG-A032 
       19.99        28.04        36.03        23.01        38.96        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6621 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 
       38.56        43.20        13.78        47.44        48.20        25.05 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE 
       31.00        13.97        51.98        44.02       126.44       129.27 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 
        3.48        20.55        15.85        11.97        28.57        32.19 
TCGA-F5-6813 TCGA-G5-6572 
       19.66        47.08 

$`1P LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       26.43        39.48        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3574 
       37.74        16.83        20.02        24.59        86.63        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       12.00        32.02         7.07        20.05         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        20.98         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       32.98         0.99         0.99        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 
       35.01        14.01        25.02        32.02        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 
        3.98        46.03        20.98        13.94         6.02        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N 
        9.07         1.02         1.02        49.97         1.94        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       41.00         2.50        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
       33.17        44.78        78.12         7.17        21.01        26.04 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       12.00        31.00        10.98        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       12.62        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
        4.18        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46         8.45         9.96        49.51        42.35 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.39        36.49        37.18        38.14        11.87        12.46 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             1.02              0.39 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           129.27             86.63 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           29.275            19.710 
[1] "1.0 - 129.3 (29.3)" "0.4 - 86.6 (19.7)" 
[1] "hr=" "1.3"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1P LOSS MUTATED         8        1        11         1         0         0
  1P LOSS WILD-TYPE      22        7        29         1         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1P LOSS MUTATED            1          9          6        5         2
  1P LOSS WILD-TYPE          6         16          8       13         5
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  8                22
  STAGE II                 1                 7
  STAGE IIA               11                29
  STAGE IIB                1                 1
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               1                 6
  STAGE IIIB               9                16
  STAGE IIIC               6                 8
  STAGE IV                 5                13
  STAGE IVA                2                 5
[1] 11  2
[1] TRUE
[1] "dimension of 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    1  9 32  3
  1P LOSS WILD-TYPE  8 19 80 11
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               1                 8
  T2               9                19
  T3              32                80
  T4               3                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
  1P LOSS MUTATED   21 15  9
  1P LOSS WILD-TYPE 63 30 24
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              21                63
  N1              15                30
  N2               9                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"
D42V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   34  7
  1P LOSS WILD-TYPE 91 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     34    7
  1P LOSS WILD-TYPE   91   17
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              34                91
  1               7                17
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   19 27
  1P LOSS WILD-TYPE 57 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     19   27
  1P LOSS WILD-TYPE   57   62
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              19                57
  MALE                27                62
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   30  7
  1P LOSS WILD-TYPE 82 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     30    7
  1P LOSS WILD-TYPE   82   13
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               30                82
  YES               7                13
[1] 2 2
[1] FALSE
D42V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    44   0
  1P LOSS WILD-TYPE 102  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     44    0
  1P LOSS WILD-TYPE  102   13
                                clus
vv                               1P LOSS MUTATED 1P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       44               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  1P LOSS MUTATED   31  0  4  1
  1P LOSS WILD-TYPE 92  2  8  3
D42V10, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              31                92
  R1               0                 2
  R2               4                 8
  RX               1                 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"
D42V11, continuous

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    23   4
  1Q LOSS WILD-TYPE 108  23
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               27               131 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                23 
$`1Q LOSS MUTATED`
TCGA-AG-A00H TCGA-BM-6198 TCGA-AF-2687 TCGA-AF-4110 TCGA-AF-A56L TCGA-AF-A56N 
       25.97        21.24        46.92        29.98        65.98        11.84 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 
       36.03        24.00        37.02        19.99         1.02         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-A00Y TCGA-CI-6621 TCGA-CI-6624 
       48.03        19.99        36.03        23.01        13.78        48.20 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6157 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6511 
       25.05        31.00        51.98         3.48        20.55        15.85 
TCGA-EI-7002 TCGA-F5-6702 TCGA-G5-6572 
       11.97        28.57        47.08 

$`1Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       26.43        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        37.74        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 
       86.63        36.03        12.00        32.02         7.07        20.05 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
       20.98         7.99         0.99        29.98        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.04        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       14.01        25.02        32.02        28.04        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 
        3.98        46.03        20.98        13.94         6.02        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       27.55        26.43        19.46         6.05        33.17        44.78 
TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 
       47.44        78.12         7.17        21.01        26.04        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        31.00        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        12.62       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61         4.18        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       17.00        18.28        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        42.35         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       19.66        37.18        38.14        11.87        12.46 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1.02              0.39 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            65.98            129.27 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            25.05             20.05 
[1] "1.0 - 66.0 (25.1)"  "0.4 - 129.3 (20.1)"
[1] "hr=" "1.4"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1Q LOSS MUTATED         6        0         6         1         0         0
  1Q LOSS WILD-TYPE      24        8        34         1         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1Q LOSS MUTATED            0          6          2        4         2
  1Q LOSS WILD-TYPE          7         19         12       14         5
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  6                24
  STAGE II                 0                 8
  STAGE IIA                6                34
  STAGE IIB                1                 1
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               6                19
  STAGE IIIC               2                12
  STAGE IV                 4                14
  STAGE IVA                2                 5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1Q LOSS MUTATED    0  6 19  2
  1Q LOSS WILD-TYPE  9 22 93 12
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               0                 9
  T2               6                22
  T3              19                93
  T4               2                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
  1Q LOSS MUTATED   13  9  5
  1Q LOSS WILD-TYPE 71 36 28
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              13                71
  N1               9                36
  N2               5                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"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    19   5
  1Q LOSS WILD-TYPE 106  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     19    5
  1Q LOSS WILD-TYPE  106   19
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              19               106
  1               5                19
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    9 19
  1Q LOSS WILD-TYPE 67 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9   19
  1Q LOSS WILD-TYPE   67   70
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               9                67
  MALE                19                70
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   19  4
  1Q LOSS WILD-TYPE 93 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     19    4
  1Q LOSS WILD-TYPE   93   16
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               19                93
  YES               4                16
[1] 2 2
[1] FALSE
D43V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    27   0
  1Q LOSS WILD-TYPE 119  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     27    0
  1Q LOSS WILD-TYPE  119   13
                                clus
vv                               1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       27               119
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    21   0   3   1
  1Q LOSS WILD-TYPE 102   2   9   3
D43V10, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              21               102
  R1               0                 2
  R2               3                 9
  RX               1                 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"
D43V11, continuous

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    10   1
  2P LOSS WILD-TYPE 121  26
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               147 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                26 
$`2P LOSS MUTATED`
TCGA-AG-3611 TCGA-AG-A00H TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3881 
       13.94        25.97        24.36        32.02        36.03        19.04 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A02X TCGA-EF-5831 TCGA-F5-6571 
       28.04        36.03        41.00         4.18        42.35 

$`2P LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 
       10.39         8.02        19.99        17.03        17.03        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       36.03        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       37.97        34.49        37.74        29.98        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
        7.07        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98        37.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 
        1.02        48.03        25.02        32.02        19.99        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        61.97        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        12.62       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         3.48        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       17.46        11.97         8.45         9.96        49.51        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             4.18              0.39 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            42.35            129.27 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            28.04             20.91 
[1] "4.2 - 42.4 (28.0)"  "0.4 - 129.3 (20.9)"
[1] "hr=" "1.9"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2P LOSS MUTATED         1        0         7         0         0         0
  2P LOSS WILD-TYPE      29        8        33         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2P LOSS MUTATED            0          1          1        1         0
  2P LOSS WILD-TYPE          7         24         13       17         7
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  1                29
  STAGE II                 0                 8
  STAGE IIA                7                33
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               1                24
  STAGE IIIC               1                13
  STAGE IV                 1                17
  STAGE IVA                0                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P LOSS MUTATED     0   1  10   0
  2P LOSS WILD-TYPE   9  27 102  14
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               0                 9
  T2               1                27
  T3              10               102
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  2P LOSS MUTATED    8  2  1
  2P LOSS WILD-TYPE 76 43 32
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               8                76
  N1               2                43
  N2               1                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     9   1
  2P LOSS WILD-TYPE 116  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      9    1
  2P LOSS WILD-TYPE  116   23
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               9               116
  1               1                23
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    6  5
  2P LOSS WILD-TYPE 70 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    5
  2P LOSS WILD-TYPE   70   84
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               6                70
  MALE                 5                84
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     8   2
  2P LOSS WILD-TYPE 104  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      8    2
  2P LOSS WILD-TYPE  104   18
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                8               104
  YES               2                18
[1] 2 2
[1] FALSE
D44V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     9   1
  2P LOSS WILD-TYPE 137  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      9    1
  2P LOSS WILD-TYPE  137   12
                                clus
vv                               2P LOSS MUTATED 2P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        9               137
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     8   0   1   0
  2P LOSS WILD-TYPE 115   2  11   4
D44V10, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               8               115
  R1               0                 2
  R2               1                11
  RX               0                 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"
D44V11, continuous

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED     7   0
  2Q LOSS WILD-TYPE 124  27
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                7               151 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                0                27 
$`2Q LOSS MUTATED`
TCGA-AG-3611 TCGA-AG-A00H TCGA-AG-3881 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A02X 
       13.94        25.97        19.04        28.04        36.03        41.00 
TCGA-F5-6571 
       42.35 

$`2Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 
       10.39         8.02        19.99        17.03        17.03        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       36.03        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       32.02        19.99        14.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       19.46         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        3.48         4.18        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        49.51        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            13.94              0.39 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            42.35            129.27 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            28.04             20.98 
[1] "13.9 - 42.4 (28.0)" "0.4 - 129.3 (21.0)"
[1] "hr="     "2.7e+07"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2Q LOSS MUTATED         1        0         5         0         0         0
  2Q LOSS WILD-TYPE      29        8        35         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2Q LOSS MUTATED            0          0          1        0         0
  2Q LOSS WILD-TYPE          7         25         13       18         7
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1                29
  STAGE II                 0                 8
  STAGE IIA                5                35
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               0                25
  STAGE IIIC               1                13
  STAGE IV                 0                18
  STAGE IVA                0                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED     0   1   6   0
  2Q LOSS WILD-TYPE   9  27 106  14
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               0                 9
  T2               1                27
  T3               6               106
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  2Q LOSS MUTATED    6  0  1
  2Q LOSS WILD-TYPE 78 45 32
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0               6                78
  N1               0                45
  N2               1                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7   0
  2Q LOSS WILD-TYPE 118  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    0
  2Q LOSS WILD-TYPE  118   24
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               7               118
  1               0                24
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    4  3
  2Q LOSS WILD-TYPE 72 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4    3
  2Q LOSS WILD-TYPE   72   86
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               4                72
  MALE                 3                86
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     5   1
  2Q LOSS WILD-TYPE 107  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    1
  2Q LOSS WILD-TYPE  107   19
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                5               107
  YES               1                19
[1] 2 2
[1] FALSE
D45V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     6   0
  2Q LOSS WILD-TYPE 140  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      6    0
  2Q LOSS WILD-TYPE  140   13
                                clus
vv                               2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        6               140
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED     6   0   0   0
  2Q LOSS WILD-TYPE 117   2  12   4
D45V10, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               6               117
  R1               0                 2
  R2               0                12
  RX               0                 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"
D45V11, continuous

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    11   4
  3P LOSS WILD-TYPE 120  23
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               15               143 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                23 
$`3P LOSS MUTATED`
TCGA-BM-6198 TCGA-G5-6233 TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3583 TCGA-AG-3584 
       21.24        18.28        34.49        29.98        20.05        24.00 
TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-4021 TCGA-AH-6544 TCGA-CI-6619 
       37.02        19.04        17.95         3.98        38.56         6.05 
TCGA-DC-6682 TCGA-DT-5265 TCGA-F5-6810 
       25.05        12.62         0.39 

$`3P LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 
       25.97        15.95        36.03        31.00        51.98        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.97        37.74        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
        7.07        36.03         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        41.00        38.04         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       26.43        19.46        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       44.02        25.97        25.05       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        42.35        28.57        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.39              0.99 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            38.56            129.27 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            20.05             21.01 
[1] "0.4 - 38.6 (20.1)"  "1.0 - 129.3 (21.0)"
[1] "hr=" "2.9"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3P LOSS MUTATED         0        1         3         0         0         0
  3P LOSS WILD-TYPE      30        7        37         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3P LOSS MUTATED            0          2          0        5         1
  3P LOSS WILD-TYPE          7         23         14       13         6
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  0                30
  STAGE II                 1                 7
  STAGE IIA                3                37
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               2                23
  STAGE IIIC               0                14
  STAGE IV                 5                13
  STAGE IVA                1                 6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3P LOSS MUTATED    0  0 13  1
  3P LOSS WILD-TYPE  9 28 99 13
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               0                 9
  T2               0                28
  T3              13                99
  T4               1                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
  3P LOSS MUTATED    4  5  5
  3P LOSS WILD-TYPE 80 40 28
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0               4                80
  N1               5                40
  N2               5                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
  3P LOSS MUTATED     6   6
  3P LOSS WILD-TYPE 119  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      6    6
  3P LOSS WILD-TYPE  119   18
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               6               119
  1               6                18
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    3 12
  3P LOSS WILD-TYPE 73 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3   12
  3P LOSS WILD-TYPE   73   77
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               3                73
  MALE                12                77
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    10   3
  3P LOSS WILD-TYPE 102  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     10    3
  3P LOSS WILD-TYPE  102   17
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               10               102
  YES               3                17
[1] 2 2
[1] FALSE
D46V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    10   3
  3P LOSS WILD-TYPE 136  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     10    3
  3P LOSS WILD-TYPE  136   10
                                clus
vv                               3P LOSS MUTATED 3P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       10               136
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED     7   0   4   1
  3P LOSS WILD-TYPE 116   2   8   3
D46V10, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               7               116
  R1               0                 2
  R2               4                 8
  RX               1                 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"
D46V11, continuous

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     7   3
  3Q LOSS WILD-TYPE 124  24
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               148 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                24 
$`3Q LOSS MUTATED`
TCGA-BM-6198 TCGA-G5-6233 TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3578 TCGA-AG-3583 
       21.24        18.28        34.49        29.98        32.02        20.05 
TCGA-AG-3731 TCGA-AG-4021 TCGA-CI-6619 TCGA-DT-5265 
       37.02         3.98         6.05        12.62 

$`3Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 
       25.97        15.95        36.03        31.00        51.98        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.97        37.74        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       86.63        65.98        11.84        36.03        12.00         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       36.03        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
        2.50        43.20        27.55        26.43        19.46        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       25.05       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             3.98              0.39 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            37.02            129.27 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           20.645            20.995 
[1] "4.0 - 37.0 (20.6)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "3"  
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3Q LOSS MUTATED         0        1         2         0         0         0
  3Q LOSS WILD-TYPE      30        7        38         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3Q LOSS MUTATED            0          1          0        4         1
  3Q LOSS WILD-TYPE          7         24         14       14         6
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  0                30
  STAGE II                 1                 7
  STAGE IIA                2                38
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               1                24
  STAGE IIIC               0                14
  STAGE IV                 4                14
  STAGE IVA                1                 6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED     0   0   9   1
  3Q LOSS WILD-TYPE   9  28 103  13
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0                 9
  T2               0                28
  T3               9               103
  T4               1                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
  3Q LOSS MUTATED    3  3  4
  3Q LOSS WILD-TYPE 81 42 29
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0               3                81
  N1               3                42
  N2               4                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"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     4   4
  3Q LOSS WILD-TYPE 121  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      4    4
  3Q LOSS WILD-TYPE  121   20
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               4               121
  1               4                20
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  8
  3Q LOSS WILD-TYPE 74 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    8
  3Q LOSS WILD-TYPE   74   81
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               2                74
  MALE                 8                81
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     7   2
  3Q LOSS WILD-TYPE 105  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      7    2
  3Q LOSS WILD-TYPE  105   18
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                7               105
  YES               2                18
[1] 2 2
[1] FALSE
D47V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5   4
  3Q LOSS WILD-TYPE 141   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    4
  3Q LOSS WILD-TYPE  141    9
                                clus
vv                               3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        5               141
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED     5   0   3   1
  3Q LOSS WILD-TYPE 118   2   9   3
D47V10, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               5               118
  R1               0                 2
  R2               3                 9
  RX               1                 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"
D47V11, continuous

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   50  7
  4P LOSS WILD-TYPE 81 20
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               57               101 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                7                20 
$`4P LOSS MUTATED`
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6641 TCGA-AF-2687 
       13.94        19.99        25.97        21.24        26.43        46.92 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 
       17.23        43.04        34.49        37.74        29.98        24.36 
TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 
       65.98        36.03        34.03        34.03        34.03         6.05 
TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 
       20.98        29.98        37.02        32.98        19.04         1.02 
TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       17.95        35.01         1.02        48.03        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A02X TCGA-AH-6643 
       36.03        14.04        13.94        23.01        41.00        43.20 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 
        6.05        33.17        48.20        31.00        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 
       10.98        44.02       126.44       129.27        32.61         4.18 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       15.85        16.34        16.41        11.97         8.45        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 
       28.57         0.39        19.66 

$`4P LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 
       10.39         8.02        17.03        17.03        15.95        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2692 
       31.00        51.98        18.28        55.76        39.48        13.55 
TCGA-AF-2693 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N 
       37.97        16.83        20.02        24.59        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00        32.02         7.07        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        46.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 
       15.95        19.99         7.99         0.99         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 
       19.99        36.95        13.02        14.01        25.02        32.02 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 
        1.02         3.98        46.03        20.98         6.02        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       61.97        38.04        38.56         2.50        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
       19.46        13.78        44.78        47.44        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 
       21.01        25.05        26.04        12.00        13.97        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       25.05        25.05        12.62        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       51.48         3.48        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       18.28        17.69        16.31         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 
       13.64        17.46         9.96        49.51        32.19        36.49 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.39              0.99 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           129.27             86.63 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            28.57             19.99 
[1] "0.4 - 129.3 (28.6)" "1.0 - 86.6 (20.0)" 
[1] "hr=" "1.9"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4P LOSS MUTATED        10        1        15         0         0         1
  4P LOSS WILD-TYPE      20        7        25         2         1         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4P LOSS MUTATED            3         11          8        5         4
  4P LOSS WILD-TYPE          4         14          6       13         3
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 10                20
  STAGE II                 1                 7
  STAGE IIA               15                25
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                1                 3
  STAGE IIIA               3                 4
  STAGE IIIB              11                14
  STAGE IIIC               8                 6
  STAGE IV                 5                13
  STAGE IVA                4                 3
[1] 11  2
[1] TRUE
[1] "dimension of 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    2 10 43  4
  4P LOSS WILD-TYPE  7 18 69 10
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               2                 7
  T2              10                18
  T3              43                69
  T4               4                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
  4P LOSS MUTATED   26 19 14
  4P LOSS WILD-TYPE 58 26 19
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              26                58
  N1              19                26
  N2              14                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   46  8
  4P LOSS WILD-TYPE 79 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     46    8
  4P LOSS WILD-TYPE   79   16
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              46                79
  1               8                16
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   26 34
  4P LOSS WILD-TYPE 50 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     26   34
  4P LOSS WILD-TYPE   50   55
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              26                50
  MALE                34                55
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   38 10
  4P LOSS WILD-TYPE 74 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     38   10
  4P LOSS WILD-TYPE   74   10
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               38                74
  YES              10                10
[1] 2 2
[1] FALSE
D48V9, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   54  4
  4P LOSS WILD-TYPE 92  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     54    4
  4P LOSS WILD-TYPE   92    9
                                clus
vv                               4P LOSS MUTATED 4P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       54                92
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED   48  0  2  1
  4P LOSS WILD-TYPE 75  2 10  3
D48V10, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              48                75
  R1               0                 2
  R2               2                10
  RX               1                 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"
D48V11, continuous

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   55  7
  4Q LOSS WILD-TYPE 76 20
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               62                96 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                7                20 
$`4Q LOSS MUTATED`
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6641 TCGA-AF-2687 
       13.94        19.99        25.97        21.24        26.43        46.92 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3592 TCGA-AG-3593 
       29.98        24.36        65.98        36.03        34.03        34.03 
TCGA-AG-3600 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 
        6.05        20.98        29.98        32.98        19.04         1.02 
TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       17.95         1.02        48.03        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 
       14.04        13.94        23.01        41.00        38.56        43.20 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 
        6.05        33.17        13.78        48.20        25.05        31.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE 
       31.00        51.98        10.98        44.02       126.44       129.27 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
       32.61         4.18        17.00        15.85        16.34        16.41 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97         8.45        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 
       36.49        19.66 

$`4Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 
       10.39         8.02        17.03        17.03        15.95        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-5654 
       31.00        51.98        18.28        55.76        39.48        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        24.59        86.63        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       32.02         7.07        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        37.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 
       19.99        36.95        13.02        35.01        14.01        25.02 
TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       32.02         1.02         3.98        46.03        20.98         6.02 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       38.96        61.97        38.04         2.50        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       19.46        44.78        47.44        78.12         7.17        21.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       26.04        12.00        13.97        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       12.62        41.36        57.24        24.13        51.48         3.48 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 
       20.55        19.96        20.91        18.28        17.69        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 
        8.61        11.51        10.78        13.64        17.46         9.96 
TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       49.51        37.18        38.14        11.87        12.46        47.08 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.39              0.99 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           129.27             86.63 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           27.235            19.990 
[1] "0.4 - 129.3 (27.2)" "1.0 - 86.6 (20.0)" 
[1] "hr=" "2.1"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4Q LOSS MUTATED        12        2        17         0         0         1
  4Q LOSS WILD-TYPE      18        6        23         2         1         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4Q LOSS MUTATED            3         12          9        4         4
  4Q LOSS WILD-TYPE          4         13          5       14         3
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 12                18
  STAGE II                 2                 6
  STAGE IIA               17                23
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                1                 3
  STAGE IIIA               3                 4
  STAGE IIIB              12                13
  STAGE IIIC               9                 5
  STAGE IV                 4                14
  STAGE IVA                4                 3
[1] 11  2
[1] TRUE
[1] "dimension of 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    2 12 47  5
  4Q LOSS WILD-TYPE  7 16 65  9
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               2                 7
  T2              12                16
  T3              47                65
  T4               5                 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
  4Q LOSS MUTATED   31 20 15
  4Q LOSS WILD-TYPE 53 25 18
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              31                53
  N1              20                25
  N2              15                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"
D49V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   51  8
  4Q LOSS WILD-TYPE 74 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     51    8
  4Q LOSS WILD-TYPE   74   16
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              51                74
  1               8                16
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   28 39
  4Q LOSS WILD-TYPE 48 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     28   39
  4Q LOSS WILD-TYPE   48   50
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              28                48
  MALE                39                50
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   43  9
  4Q LOSS WILD-TYPE 69 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     43    9
  4Q LOSS WILD-TYPE   69   11
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               43                69
  YES               9                11
[1] 2 2
[1] FALSE
D49V9, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   59  4
  4Q LOSS WILD-TYPE 87  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     59    4
  4Q LOSS WILD-TYPE   87    9
                                clus
vv                               4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       59                87
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED   51  0  2  1
  4Q LOSS WILD-TYPE 72  2 10  3
D49V10, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              51                72
  R1               0                 2
  R2               2                10
  RX               1                 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"
D49V11, continuous

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    21   4
  5P LOSS WILD-TYPE 110  23
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               25               133 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                23 
$`5P LOSS MUTATED`
TCGA-AG-3611 TCGA-G5-6233 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-6136 TCGA-AG-3600 
       13.94        18.28        46.92        43.04        24.36         6.05 
TCGA-AG-3725 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 
       20.98        37.02        19.99         1.02        48.03        28.04 
TCGA-AG-4021 TCGA-AG-A00Y TCGA-CI-6620 TCGA-CI-6621 TCGA-DC-6155 TCGA-DC-6157 
        3.98        23.01        33.17        13.78        13.97        51.98 
TCGA-DC-6158 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-EI-6506 TCGA-EI-6881 TCGA-EI-6885 
       10.98       126.44        57.24        20.55        16.41        13.64 
TCGA-EI-7004 
        8.45 

$`5P LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        21.24        55.76 
TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       26.43        39.48        17.23        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       37.74        29.98        16.83        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       65.98        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       34.03        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01        25.02        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
        6.02        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 
       25.05        26.04        31.00        12.00        31.00        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE 
       25.97        25.05        25.05        12.62        41.36       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
       24.13        51.48        32.61         3.48         4.18        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.31         8.61        11.51        10.78        17.46        11.97 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1.02              0.39 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           126.44            129.27 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            20.55             21.24 
[1] "1.0 - 126.4 (20.6)" "0.4 - 129.3 (21.2)"
[1] "hr=" "1.3"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5P LOSS MUTATED         5        1         6         0         0         1
  5P LOSS WILD-TYPE      25        7        34         2         1         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5P LOSS MUTATED            2          3          3        3         1
  5P LOSS WILD-TYPE          5         22         11       15         6
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  5                25
  STAGE II                 1                 7
  STAGE IIA                6                34
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                1                 3
  STAGE IIIA               2                 5
  STAGE IIIB               3                22
  STAGE IIIC               3                11
  STAGE IV                 3                15
  STAGE IVA                1                 6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5P LOSS MUTATED    1  5 20  1
  5P LOSS WILD-TYPE  8 23 92 13
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               1                 8
  T2               5                23
  T3              20                92
  T4               1                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
  5P LOSS MUTATED   12  8  7
  5P LOSS WILD-TYPE 72 37 26
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              12                72
  N1               8                37
  N2               7                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"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    21   4
  5P LOSS WILD-TYPE 104  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     21    4
  5P LOSS WILD-TYPE  104   20
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              21               104
  1               4                20
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED   16 11
  5P LOSS WILD-TYPE 60 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     16   11
  5P LOSS WILD-TYPE   60   78
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              16                60
  MALE                11                78
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                 0  1
  5P LOSS MUTATED   18  3
  5P LOSS WILD-TYPE 94 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     18    3
  5P LOSS WILD-TYPE   94   17
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               18                94
  YES               3                17
[1] 2 2
[1] FALSE
D50V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    26   1
  5P LOSS WILD-TYPE 120  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     26    1
  5P LOSS WILD-TYPE  120   12
                                clus
vv                               5P LOSS MUTATED 5P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       26               120
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    20   0   2   0
  5P LOSS WILD-TYPE 103   2  10   4
D50V10, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              20               103
  R1               0                 2
  R2               2                10
  RX               0                 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"
D50V11, continuous

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    28   9
  5Q LOSS WILD-TYPE 103  18
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               37               121 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                9                18 
$`5Q LOSS MUTATED`
TCGA-AG-3611 TCGA-AG-4008 TCGA-BM-6198 TCGA-G5-6233 TCGA-AF-2687 TCGA-AF-2690 
       13.94        17.03        21.24        18.28        46.92        17.23 
TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-A56K TCGA-AG-3578 TCGA-AG-3725 
       43.04        37.74        24.36        86.63        32.02        20.98 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 
       29.98        37.02        32.98        19.04        19.99         1.02 
TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A00Y TCGA-AG-A026 
       48.03        28.04        36.03         3.98        23.01         1.94 
TCGA-AG-A02G TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       38.96        33.17        13.97        31.00        51.98        10.98 
TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6881 
       25.05       126.44        57.24        51.48        20.55        16.41 
TCGA-F5-6702 
       28.57 

$`5Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A014 
       10.39         8.02        19.99        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2689 
       36.03        31.00        51.98        55.76        26.43        39.48 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       13.55        37.97        34.49        29.98        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       24.59        65.98        11.84        36.03        12.00         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 
        0.99        15.95        19.99         7.99         0.99         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 
       14.01        25.02        32.02        19.99        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 
       46.03        20.98        13.94         6.02        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
        1.02         1.02        49.97        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        6.05        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE 
       44.02        25.97        25.05        12.62        41.36       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         3.48         4.18        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        49.51        42.35         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             1.02              0.39 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           126.44            129.27 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            28.04             19.99 
[1] "1.0 - 126.4 (28.0)" "0.4 - 129.3 (20.0)"
[1] "hr=" "1.2"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5Q LOSS MUTATED         6        3        12         0         0         1
  5Q LOSS WILD-TYPE      24        5        28         2         1         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5Q LOSS MUTATED            2          4          4        3         4
  5Q LOSS WILD-TYPE          5         21         10       15         3
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  6                24
  STAGE II                 3                 5
  STAGE IIA               12                28
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                1                 3
  STAGE IIIA               2                 5
  STAGE IIIB               4                21
  STAGE IIIC               4                10
  STAGE IV                 3                15
  STAGE IVA                4                 3
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    1  7 30  2
  5Q LOSS WILD-TYPE  8 21 82 12
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               1                 8
  T2               7                21
  T3              30                82
  T4               2                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
  5Q LOSS MUTATED   21 11  8
  5Q LOSS WILD-TYPE 63 34 25
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              21                63
  N1              11                34
  N2               8                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"
D51V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   30  7
  5Q LOSS WILD-TYPE 95 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     30    7
  5Q LOSS WILD-TYPE   95   17
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              30                95
  1               7                17
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   20 20
  5Q LOSS WILD-TYPE 56 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     20   20
  5Q LOSS WILD-TYPE   56   69
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              20                56
  MALE                20                69
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   29  3
  5Q LOSS WILD-TYPE 83 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     29    3
  5Q LOSS WILD-TYPE   83   17
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               29                83
  YES               3                17
[1] 2 2
[1] FALSE
D51V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    38   1
  5Q LOSS WILD-TYPE 108  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     38    1
  5Q LOSS WILD-TYPE  108   12
                                clus
vv                               5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       38               108
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  5Q LOSS MUTATED   29  1  3  0
  5Q LOSS WILD-TYPE 94  1  9  4
D51V10, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              29                94
  R1               1                 1
  R2               3                 9
  RX               0                 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"
D51V11, continuous

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    10   4
  6P LOSS WILD-TYPE 121  23
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               14               144 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4                23 
$`6P LOSS MUTATED`
TCGA-AG-3611 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3584 TCGA-AG-3591 
       13.94        17.23        13.55        34.49        24.00        34.03 
TCGA-AG-3593 TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A011 TCGA-DC-6682 TCGA-DT-5265 
       34.03         3.98        13.94        37.02        25.05        12.62 
TCGA-DY-A1DF TCGA-EI-6883 
       24.13        11.51 

$`6P LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 
       55.76        26.43        46.92        39.48        43.04        37.97 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        29.98        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 
        7.07        36.03        20.05         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y 
       14.04         1.02        46.03        20.98         6.02        23.01 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA 
       51.98        10.98        44.02        25.97        25.05       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        42.35        28.57         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             3.98              0.39 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            37.02            129.27 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           20.615            20.995 
[1] "4.0 - 37.0 (20.6)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "3.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6P LOSS MUTATED         1        1         7         0         1         0
  6P LOSS WILD-TYPE      29        7        33         2         0         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6P LOSS MUTATED            0          0          2        2         0
  6P LOSS WILD-TYPE          7         25         12       16         7
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  1                29
  STAGE II                 1                 7
  STAGE IIA                7                33
  STAGE IIB                0                 2
  STAGE IIC                1                 0
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               0                25
  STAGE IIIC               2                12
  STAGE IV                 2                16
  STAGE IVA                0                 7
[1] 11  2
[1] TRUE
[1] "dimension of 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    0  1 13  0
  6P LOSS WILD-TYPE  9 27 99 14
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               0                 9
  T2               1                27
  T3              13                99
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  6P LOSS MUTATED   10  0  4
  6P LOSS WILD-TYPE 74 45 29
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              10                74
  N1               0                45
  N2               4                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"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    12   2
  6P LOSS WILD-TYPE 113  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     12    2
  6P LOSS WILD-TYPE  113   22
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              12               113
  1               2                22
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    7  7
  6P LOSS WILD-TYPE 69 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      7    7
  6P LOSS WILD-TYPE   69   82
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               7                69
  MALE                 7                82
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     9   4
  6P LOSS WILD-TYPE 103  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9    4
  6P LOSS WILD-TYPE  103   16
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                9               103
  YES               4                16
[1] 2 2
[1] FALSE
D52V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    10   3
  6P LOSS WILD-TYPE 136  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     10    3
  6P LOSS WILD-TYPE  136   10
                                clus
vv                               6P LOSS MUTATED 6P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       10               136
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    10   0   2   1
  6P LOSS WILD-TYPE 113   2  10   3
D52V10, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              10               113
  R1               0                 2
  R2               2                10
  RX               1                 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"
D52V11, continuous

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    19   3
  6Q LOSS WILD-TYPE 112  24
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22               136 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                24 
$`6Q LOSS MUTATED`
TCGA-AG-3611 TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       13.94        18.28        26.43        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3587 
       37.97        34.49        12.00        32.02        24.00        46.03 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A011 
       34.03        34.03         6.05        14.04        13.94        37.02 
TCGA-AH-6544 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6883 
       38.56        25.05        12.62        11.51 

$`6Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        21.24        55.76 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       46.92        39.48        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 
        7.07        36.03        20.05         1.02        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       50.04        12.03         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 
       32.02        19.99        28.04        36.03         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A01J 
       46.03        20.98         6.02        23.01         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.04         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.97        25.05       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         3.48         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             6.05              0.39 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            46.03            129.27 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           24.525            20.980 
[1] "6.0 - 46.0 (24.5)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "1"  
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6Q LOSS MUTATED         4        2         8         0         1         0
  6Q LOSS WILD-TYPE      26        6        32         2         0         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6Q LOSS MUTATED            1          0          3        2         0
  6Q LOSS WILD-TYPE          6         25         11       16         7
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  4                26
  STAGE II                 2                 6
  STAGE IIA                8                32
  STAGE IIB                0                 2
  STAGE IIC                1                 0
  STAGE III                0                 4
  STAGE IIIA               1                 6
  STAGE IIIB               0                25
  STAGE IIIC               3                11
  STAGE IV                 2                16
  STAGE IVA                0                 7
[1] 11  2
[1] TRUE
[1] "dimension of 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    2  3 18  0
  6Q LOSS WILD-TYPE  7 25 94 14
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               2                 7
  T2               3                25
  T3              18                94
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  6Q LOSS MUTATED   15  2  6
  6Q LOSS WILD-TYPE 69 43 27
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              15                69
  N1               2                43
  N2               6                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"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    18   3
  6Q LOSS WILD-TYPE 107  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     18    3
  6Q LOSS WILD-TYPE  107   21
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              18               107
  1               3                21
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    8 15
  6Q LOSS WILD-TYPE 68 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      8   15
  6Q LOSS WILD-TYPE   68   74
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               8                68
  MALE                15                74
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   16  6
  6Q LOSS WILD-TYPE 96 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     16    6
  6Q LOSS WILD-TYPE   96   14
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               16                96
  YES               6                14
[1] 2 2
[1] FALSE
D53V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    16   5
  6Q LOSS WILD-TYPE 130   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     16    5
  6Q LOSS WILD-TYPE  130    8
                                clus
vv                               6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       16               130
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    19   0   1   1
  6Q LOSS WILD-TYPE 104   2  11   3
D53V10, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              19               104
  R1               0                 2
  R2               1                11
  RX               1                 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"
D53V11, continuous

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     3   0
  7Q LOSS WILD-TYPE 128  27
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               155 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                0                27 
$`7Q LOSS MUTATED`
TCGA-AG-3591 TCGA-AG-A008 TCGA-DC-6682 
       34.03        13.94        25.05 

$`7Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       18.28        55.76        26.43        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        24.36        20.02        24.59        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       14.04         1.02         3.98        46.03        20.98         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       33.17        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        31.00        51.98        10.98        44.02        25.97 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        12.62       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         3.48         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            13.94              0.39 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            34.03            129.27 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            25.05             20.98 
[1] "13.9 - 34.0 (25.1)" "0.4 - 129.3 (21.0)"
[1] "hr="     "9200000"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  7Q LOSS MUTATED         1        0         2         0         0         0
  7Q LOSS WILD-TYPE      29        8        38         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  7Q LOSS MUTATED            0          0          0        0         0
  7Q LOSS WILD-TYPE          7         25         14       18         7
D54V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  1                29
  STAGE II                 0                 8
  STAGE IIA                2                38
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               0                25
  STAGE IIIC               0                14
  STAGE IV                 0                18
  STAGE IVA                0                 7
[1] 11  2
[1] TRUE
[1] "dimension of 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 LOSS MUTATED     0   1   2   0
  7Q LOSS WILD-TYPE   9  27 110  14
D54V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               0                 9
  T2               1                27
  T3               2               110
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  7Q LOSS MUTATED    3  0  0
  7Q LOSS WILD-TYPE 81 45 33
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               3                81
  N1               0                45
  N2               0                33
[1] 3 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
  7Q LOSS MUTATED     3   0
  7Q LOSS WILD-TYPE 122  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    0
  7Q LOSS WILD-TYPE  122   24
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               3               122
  1               0                24
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    2  1
  7Q LOSS WILD-TYPE 74 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    1
  7Q LOSS WILD-TYPE   74   88
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               2                74
  MALE                 1                88
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     2   1
  7Q LOSS WILD-TYPE 110  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    1
  7Q LOSS WILD-TYPE  110   19
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                2               110
  YES               1                19
[1] 2 2
[1] FALSE
D54V9, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     2   1
  7Q LOSS WILD-TYPE 144  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    1
  7Q LOSS WILD-TYPE  144   12
                                clus
vv                               7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        2               144
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED     3   0   0   0
  7Q LOSS WILD-TYPE 120   2  12   4
D54V10, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               3               120
  R1               0                 2
  R2               0                12
  RX               0                 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"
D54V11, continuous

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   55 16
  8P LOSS WILD-TYPE 76 11
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               71                87 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16                11 
$`8P LOSS MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       10.39        13.94        17.03        17.03        25.97        15.95 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2690 
       51.98        21.24        18.28        26.43        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6655 
       43.04        13.55        37.97        37.74        24.36        20.02 
TCGA-AF-6672 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 
       24.59        36.03        24.00         1.02        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
       34.03         2.01         6.05         0.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3893 TCGA-AG-3909 
       29.98        32.98         0.99         1.02        35.01        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       28.04        36.03        14.04        23.01        37.02         1.02 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6547 TCGA-CI-6624 
        1.02         1.94        38.96        41.00         2.50        48.20 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12        21.01        25.05        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG 
       10.98        25.05        12.62       126.44       129.27        51.48 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 
        4.18        15.85        16.34        10.78        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 
        9.96        42.35        28.57        19.66        12.46 

$`8P LOSS WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-A015 TCGA-AG-A01N TCGA-G5-6235 TCGA-AF-2687 
        8.02        19.99        36.03        31.00        55.76        46.92 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       34.49        29.98        16.83        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3587 
       36.03        12.00        32.02         7.07        20.05        46.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3731 
       50.04        12.03        15.95        19.99        20.98        37.02 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
        0.99        19.04        19.99        17.95        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4007 
       14.01         1.02        48.03        25.02        32.02         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A016 
        3.98        46.03        20.98        13.94         6.02         9.07 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       49.97        61.97        38.04        38.56        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 
       47.44         7.17        26.04        12.00        31.00        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
       25.97        25.05        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        3.48        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 
       17.69        16.31        16.41         8.61        11.51        13.64 
TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
       17.46        49.51         0.39        32.19        36.49        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       38.14        11.87        47.08 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.99              0.39 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           129.27             86.63 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            21.01             20.98 
[1] "1.0 - 129.3 (21.0)" "0.4 - 86.6 (21.0)" 
[1] "hr=" "2"  
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8P LOSS MUTATED        13        2        17         0         0         3
  8P LOSS WILD-TYPE      17        6        23         2         1         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8P LOSS MUTATED            4         13          7       10         2
  8P LOSS WILD-TYPE          3         12          7        8         5
D55V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 13                17
  STAGE II                 2                 6
  STAGE IIA               17                23
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                3                 1
  STAGE IIIA               4                 3
  STAGE IIIB              13                12
  STAGE IIIC               7                 7
  STAGE IV                10                 8
  STAGE IVA                2                 5
[1] 11  2
[1] TRUE
[1] "dimension of 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 14 51  7
  8P LOSS WILD-TYPE  6 14 61  7
D55V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               3                 6
  T2              14                14
  T3              51                61
  T4               7                 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
  8P LOSS MUTATED   33 25 17
  8P LOSS WILD-TYPE 51 20 16
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              33                51
  N1              25                20
  N2              17                16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   56 11
  8P LOSS WILD-TYPE 69 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     56   11
  8P LOSS WILD-TYPE   69   13
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              56                69
  1              11                13
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   33 42
  8P LOSS WILD-TYPE 43 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     33   42
  8P LOSS WILD-TYPE   43   47
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              33                43
  MALE                42                47
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   49  9
  8P LOSS WILD-TYPE 63 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     49    9
  8P LOSS WILD-TYPE   63   11
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               49                63
  YES               9                11
[1] 2 2
[1] FALSE
D55V9, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   67  5
  8P LOSS WILD-TYPE 79  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     67    5
  8P LOSS WILD-TYPE   79    8
                                clus
vv                               8P LOSS MUTATED 8P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       67                79
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED   56  1  6  2
  8P LOSS WILD-TYPE 67  1  6  2
D55V10, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              56                67
  R1               1                 1
  R2               6                 6
  RX               2                 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"
D55V11, continuous

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     7   2
  8Q LOSS WILD-TYPE 124  25
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               149 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                25 
$`8Q LOSS MUTATED`
TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-3883 TCGA-AG-A00Y TCGA-AG-A02X TCGA-DC-6157 
       13.94        17.03         1.02        23.01        41.00        51.98 
TCGA-DY-A1DG TCGA-EI-6511 TCGA-F5-6813 
       51.48        15.85        19.66 

$`8Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       10.39         8.02        19.99        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       36.03        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04        19.99        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 
        3.98        46.03        20.98        13.94         6.02        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
       26.04        31.00        12.00        13.97        31.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        24.13        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        42.35        28.57         0.39        32.19        36.49 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.02              0.39 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            51.98            129.27 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            19.66             21.01 
[1] "1.0 - 52.0 (19.7)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "1.1"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8Q LOSS MUTATED         4        0         2         0         0         0
  8Q LOSS WILD-TYPE      26        8        38         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8Q LOSS MUTATED            0          2          1        0         1
  8Q LOSS WILD-TYPE          7         23         13       18         6
D56V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  4                26
  STAGE II                 0                 8
  STAGE IIA                2                38
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               2                23
  STAGE IIIC               1                13
  STAGE IV                 0                18
  STAGE IVA                1                 6
[1] 11  2
[1] TRUE
[1] "dimension of 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     0   4   5   1
  8Q LOSS WILD-TYPE   9  24 107  13
D56V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               0                 9
  T2               4                24
  T3               5               107
  T4               1                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
  8Q LOSS MUTATED    6  3  1
  8Q LOSS WILD-TYPE 78 42 32
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               6                78
  N1               3                42
  N2               1                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     9   1
  8Q LOSS WILD-TYPE 116  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      9    1
  8Q LOSS WILD-TYPE  116   23
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               9               116
  1               1                23
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    0 10
  8Q LOSS WILD-TYPE 76 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   10
  8Q LOSS WILD-TYPE   76   79
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               0                76
  MALE                10                79
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     5   1
  8Q LOSS WILD-TYPE 107  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5    1
  8Q LOSS WILD-TYPE  107   19
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                5               107
  YES               1                19
[1] 2 2
[1] FALSE
D56V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    10   0
  8Q LOSS WILD-TYPE 136  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     10    0
  8Q LOSS WILD-TYPE  136   13
                                clus
vv                               8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       10               136
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED     9   0   0   0
  8Q LOSS WILD-TYPE 114   2  12   4
D56V10, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               9               114
  R1               0                 2
  R2               0                12
  RX               0                 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"
D56V11, continuous

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    15   6
  9P LOSS WILD-TYPE 116  21
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               21               137 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                6                21 
$`9P LOSS MUTATED`
TCGA-AG-A014 TCGA-AG-A01N TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-A56L TCGA-AG-3583 
       15.95        31.00        46.92        13.55        65.98        20.05 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-4021 TCGA-AG-A026 
       34.03         6.05        37.02        19.99         3.98         1.94 
TCGA-AG-A02G TCGA-CI-6619 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-6158 TCGA-DC-6160 
       38.96         6.05        48.20        25.05        10.98        44.02 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6514 
       51.48         3.48        16.31 

$`9P LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       25.97        36.03        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       26.43        39.48        17.23        43.04        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        29.98        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       86.63        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       36.03        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
       20.98         7.99         0.99        29.98        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
        0.99        19.04         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       19.99        28.04        36.03        14.04         1.02        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
        1.02         1.02        49.97        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
       33.17        13.78        44.78        47.44        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       21.01        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       51.98        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 
       41.36        57.24       129.27        24.13        32.61         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             1.94              0.39 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            65.98            129.27 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            20.05             21.01 
[1] "1.9 - 66.0 (20.1)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "1.7"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9P LOSS MUTATED         6        1         3         1         0         0
  9P LOSS WILD-TYPE      24        7        37         1         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9P LOSS MUTATED            0          1          3        6         1
  9P LOSS WILD-TYPE          7         24         11       12         6
D57V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  6                24
  STAGE II                 1                 7
  STAGE IIA                3                37
  STAGE IIB                1                 1
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               1                24
  STAGE IIIC               3                11
  STAGE IV                 6                12
  STAGE IVA                1                 6
[1] 11  2
[1] TRUE
[1] "dimension of 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    0  8 13  2
  9P LOSS WILD-TYPE  9 20 99 12
D57V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               0                 9
  T2               8                20
  T3              13                99
  T4               2                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
  9P LOSS MUTATED   12  6  5
  9P LOSS WILD-TYPE 72 39 28
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              12                72
  N1               6                39
  N2               5                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"
D57V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    16   7
  9P LOSS WILD-TYPE 109  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     16    7
  9P LOSS WILD-TYPE  109   17
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              16               109
  1               7                17
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    9 14
  9P LOSS WILD-TYPE 67 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      9   14
  9P LOSS WILD-TYPE   67   75
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               9                67
  MALE                14                75
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   14  3
  9P LOSS WILD-TYPE 98 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     14    3
  9P LOSS WILD-TYPE   98   17
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               14                98
  YES               3                17
[1] 2 2
[1] FALSE
D57V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    21   1
  9P LOSS WILD-TYPE 125  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     21    1
  9P LOSS WILD-TYPE  125   12
                                clus
vv                               9P LOSS MUTATED 9P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       21               125
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    12   1   5   1
  9P LOSS WILD-TYPE 111   1   7   3
D57V10, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              12               111
  R1               1                 1
  R2               5                 7
  RX               1                 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"
D57V11, continuous

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    15   5
  9Q LOSS WILD-TYPE 116  22
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               20               138 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                5                22 
$`9Q LOSS MUTATED`
TCGA-AG-A014 TCGA-AG-A01N TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-A56L TCGA-AG-3583 
       15.95        31.00        46.92        13.55        65.98        20.05 
TCGA-AG-3593 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-4001 TCGA-AG-A026 TCGA-AG-A02G 
       34.03        37.02        19.99        36.03         1.94        38.96 
TCGA-CI-6619 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-6158 TCGA-DC-6160 TCGA-EF-5830 
        6.05        48.20        25.05        10.98        44.02         3.48 
TCGA-EI-6514 TCGA-F5-6702 
       16.31        28.57 

$`9Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       25.97        36.03        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       26.43        39.48        17.23        43.04        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        29.98        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       86.63        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       36.03        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
       19.99        20.98         7.99         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       32.02        19.99        28.04        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
        9.07         1.02         1.02        49.97        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 
       19.46        33.17        13.78        44.78        47.44        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.17        21.01        26.04        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       31.00        51.98        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         4.18        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        42.35         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             1.94              0.39 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            65.98            129.27 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            26.81             20.98 
[1] "1.9 - 66.0 (26.8)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "1.4"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9Q LOSS MUTATED         6        1         4         1         0         0
  9Q LOSS WILD-TYPE      24        7        36         1         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9Q LOSS MUTATED            0          2          2        5         1
  9Q LOSS WILD-TYPE          7         23         12       13         6
D58V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  6                24
  STAGE II                 1                 7
  STAGE IIA                4                36
  STAGE IIB                1                 1
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               0                 7
  STAGE IIIB               2                23
  STAGE IIIC               2                12
  STAGE IV                 5                13
  STAGE IVA                1                 6
[1] 11  2
[1] TRUE
[1] "dimension of 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     0   8  12   3
  9Q LOSS WILD-TYPE   9  20 100  11
D58V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               0                 9
  T2               8                20
  T3              12               100
  T4               3                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
  9Q LOSS MUTATED   13  7  3
  9Q LOSS WILD-TYPE 71 38 30
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              13                71
  N1               7                38
  N2               3                30
[1] 3 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
  9Q LOSS MUTATED    17   6
  9Q LOSS WILD-TYPE 108  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     17    6
  9Q LOSS WILD-TYPE  108   18
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              17               108
  1               6                18
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    9 14
  9Q LOSS WILD-TYPE 67 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9   14
  9Q LOSS WILD-TYPE   67   75
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               9                67
  MALE                14                75
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   15  2
  9Q LOSS WILD-TYPE 97 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     15    2
  9Q LOSS WILD-TYPE   97   18
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               15                97
  YES               2                18
[1] 2 2
[1] FALSE
D58V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    21   1
  9Q LOSS WILD-TYPE 125  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     21    1
  9Q LOSS WILD-TYPE  125   12
                                clus
vv                               9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       21               125
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    13   1   5   1
  9Q LOSS WILD-TYPE 110   1   7   3
D58V10, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              13               110
  R1               1                 1
  R2               5                 7
  RX               1                 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"
D58V11, continuous

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   32  1
  10P LOSS WILD-TYPE 99 26
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                33                125 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 1                 26 
$`10P LOSS MUTATED`
TCGA-AG-A00H TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 
       25.97        26.43        46.92        13.55        34.49        24.59 
TCGA-AF-A56L TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3887 
       65.98        46.03        34.03        34.03        29.98        36.95 
TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A008 TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6544 
        1.02        19.99        13.94         1.02        41.00        38.56 
TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 
       48.20        13.97        31.00        51.98        25.05        25.05 
TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
      129.27         3.48        17.00        16.34        16.31        16.41 
TCGA-EI-7004 TCGA-F5-6702 TCGA-F5-6864 
        8.45        28.57        12.46 

$`10P LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
       55.76        39.48        17.23        43.04        37.97        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N 
       29.98        16.83        24.36        20.02        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        17.95        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        25.02        32.02        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y 
        1.02         3.98        46.03        20.98         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       37.02         9.07         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       61.97        38.04         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       19.46         6.05        33.17        13.78        44.78        47.44 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       12.00        10.98        44.02        25.97        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
       41.36        57.24        24.13        51.48        32.61         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        18.28        15.85        17.69 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        42.35         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        47.08 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              1.02               0.39 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            129.27             126.44 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             25.97              20.55 
[1] "1.0 - 129.3 (26.0)" "0.4 - 126.4 (20.6)"
[1] "hr=" "8"  
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10P LOSS MUTATED         6        0         9         1         0         1
  10P LOSS WILD-TYPE      24        8        31         1         1         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10P LOSS MUTATED            3          6          3        1         2
  10P LOSS WILD-TYPE          4         19         11       17         5
D59V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   6                 24
  STAGE II                  0                  8
  STAGE IIA                 9                 31
  STAGE IIB                 1                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  3
  STAGE IIIA                3                  4
  STAGE IIIB                6                 19
  STAGE IIIC                3                 11
  STAGE IV                  1                 17
  STAGE IVA                 2                  5
[1] 11  2
[1] TRUE
[1] "dimension of 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    1  7 22  4
  10P LOSS WILD-TYPE  8 21 90 10
D59V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                1                  8
  T2                7                 21
  T3               22                 90
  T4                4                 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
  10P LOSS MUTATED   16 11  7
  10P LOSS WILD-TYPE 68 34 26
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               16                 68
  N1               11                 34
  N2                7                 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
  10P LOSS MUTATED   29  3
  10P LOSS WILD-TYPE 96 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     29    3
  10P LOSS WILD-TYPE   96   21
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               29                 96
  1                3                 21
[1] 2 2
[1] FALSE
D59V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   14 20
  10P LOSS WILD-TYPE 62 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     14   20
  10P LOSS WILD-TYPE   62   69
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               14                 62
  MALE                 20                 69
[1] 2 2
[1] FALSE
D59V8, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   20  8
  10P LOSS WILD-TYPE 92 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     20    8
  10P LOSS WILD-TYPE   92   12
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                20                 92
  YES                8                 12
[1] 2 2
[1] FALSE
D59V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    27   6
  10P LOSS WILD-TYPE 119   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     27    6
  10P LOSS WILD-TYPE  119    7
                                clus
vv                               10P LOSS MUTATED 10P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        27                119
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  10P LOSS MUTATED   29  0  0  1
  10P LOSS WILD-TYPE 94  2 12  3
D59V10, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               29                 94
  R1                0                  2
  R2                0                 12
  RX                1                  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"
D59V11, continuous

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   34  3
  10Q LOSS WILD-TYPE 97 24
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                37                121 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 3                 24 
$`10Q LOSS MUTATED`
TCGA-AG-A00H TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 
       25.97        26.43        46.92        13.55        34.49        24.59 
TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 
       65.98        32.02        46.03        34.03        34.03         6.05 
TCGA-AG-3728 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A008 TCGA-AG-A011 
       29.98        36.95         1.02        19.99        13.94        37.02 
TCGA-AG-A020 TCGA-AG-A02X TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 
        1.02        41.00        48.20        13.97        51.98        25.05 
TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6513 
       25.05       129.27        24.13         3.48        17.00        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6864 
       16.31        16.41        11.97        28.57        36.49        12.46 
TCGA-G5-6572 
       47.08 

$`10Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
       55.76        39.48        17.23        43.04        37.97        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N 
       29.98        16.83        24.36        20.02        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       15.95        19.99        20.98         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 
       17.95        13.02        35.01        14.01        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       32.02        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A01J 
       46.03        20.98         6.02        23.01         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       49.97         1.94        38.96        61.97        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
       33.17        13.78        44.78        47.44        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       21.01        25.05        26.04        31.00        12.00        31.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       10.98        44.02        25.97        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       57.24        51.48        32.61         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 
       20.91        18.28        15.85        17.69         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       42.35         0.39        32.19        19.66        37.18        38.14 
TCGA-F5-6863 
       11.87 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              1.02               0.39 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            129.27             126.44 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             25.97              20.05 
[1] "1.0 - 129.3 (26.0)" "0.4 - 126.4 (20.1)"
[1] "hr=" "2.9"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10Q LOSS MUTATED         6        0        12         1         0         1
  10Q LOSS WILD-TYPE      24        8        28         1         1         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10Q LOSS MUTATED            3          6          5        2         1
  10Q LOSS WILD-TYPE          4         19          9       16         6
D60V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   6                 24
  STAGE II                  0                  8
  STAGE IIA                12                 28
  STAGE IIB                 1                  1
  STAGE IIC                 0                  1
  STAGE III                 1                  3
  STAGE IIIA                3                  4
  STAGE IIIB                6                 19
  STAGE IIIC                5                  9
  STAGE IV                  2                 16
  STAGE IVA                 1                  6
[1] 11  2
[1] TRUE
[1] "dimension of 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    1  7 27  2
  10Q LOSS WILD-TYPE  8 21 85 12
D60V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                1                  8
  T2                7                 21
  T3               27                 85
  T4                2                 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
  10Q LOSS MUTATED   19 10  8
  10Q LOSS WILD-TYPE 65 35 25
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               19                 65
  N1               10                 35
  N2                8                 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"
D60V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   33  2
  10Q LOSS WILD-TYPE 92 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     33    2
  10Q LOSS WILD-TYPE   92   22
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               33                 92
  1                2                 22
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   15 23
  10Q LOSS WILD-TYPE 61 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     15   23
  10Q LOSS WILD-TYPE   61   66
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               15                 61
  MALE                 23                 66
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   22  9
  10Q LOSS WILD-TYPE 90 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     22    9
  10Q LOSS WILD-TYPE   90   11
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                22                 90
  YES                9                 11
[1] 2 2
[1] FALSE
D60V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    31   6
  10Q LOSS WILD-TYPE 115   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     31    6
  10Q LOSS WILD-TYPE  115    7
                                clus
vv                               10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        31                115
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  10Q LOSS MUTATED   32  0  0  1
  10Q LOSS WILD-TYPE 91  2 12  3
D60V10, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               32                 91
  R1                0                  2
  R2                0                 12
  RX                1                  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"
D60V11, continuous

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    20   3
  11P LOSS WILD-TYPE 111  24
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                23                135 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                 24 
$`11P LOSS MUTATED`
TCGA-AF-2691 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3581 
       43.04        29.98        24.36        24.59        32.02         7.07 
TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-A008 
        6.05        32.98        19.04        17.95         1.02        13.94 
TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-DC-6155 TCGA-DC-6156 
        1.02        41.00        38.56        43.20        13.97        31.00 
TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6881 TCGA-F5-6813 
       12.62        24.13        17.00        16.41        19.66 

$`11P LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       18.28        55.76        26.43        46.92        39.48        17.23 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 
       13.55        37.97        34.49        37.74        16.83        20.02 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3582 
       86.63        65.98        11.84        36.03        12.00        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99        19.99         1.02        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01        48.03        25.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       28.04        36.03        14.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       20.98         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 
       49.97         1.94        38.96        61.97        38.04         2.50 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 
       25.05        26.04        31.00        12.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        51.48        32.61         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
       28.57         0.39        32.19        36.49        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              1.02               0.39 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             43.20             129.27 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             19.66              21.01 
[1] "1.0 - 43.2 (19.7)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "1"  
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11P LOSS MUTATED         6        1         2         0         0         1
  11P LOSS WILD-TYPE      24        7        38         2         1         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11P LOSS MUTATED            2          3          5        1         2
  11P LOSS WILD-TYPE          5         22          9       17         5
D61V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   6                 24
  STAGE II                  1                  7
  STAGE IIA                 2                 38
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 1                  3
  STAGE IIIA                2                  5
  STAGE IIIB                3                 22
  STAGE IIIC                5                  9
  STAGE IV                  1                 17
  STAGE IVA                 2                  5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11P LOSS MUTATED    1  6 13  4
  11P LOSS WILD-TYPE  8 22 99 10
D61V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                1                  8
  T2                6                 22
  T3               13                 99
  T4                4                 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
  11P LOSS MUTATED    9  7  8
  11P LOSS WILD-TYPE 75 38 25
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                9                 75
  N1                7                 38
  N2                8                 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"
D61V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    19   2
  11P LOSS WILD-TYPE 106  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     19    2
  11P LOSS WILD-TYPE  106   22
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               19                106
  1                2                 22
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   11 13
  11P LOSS WILD-TYPE 65 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     11   13
  11P LOSS WILD-TYPE   65   76
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               11                 65
  MALE                 13                 76
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   14  5
  11P LOSS WILD-TYPE 98 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     14    5
  11P LOSS WILD-TYPE   98   15
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                14                 98
  YES                5                 15
[1] 2 2
[1] FALSE
D61V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    18   4
  11P LOSS WILD-TYPE 128   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     18    4
  11P LOSS WILD-TYPE  128    9
                                clus
vv                               11P LOSS MUTATED 11P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        18                128
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    18   0   0   1
  11P LOSS WILD-TYPE 105   2  12   3
D61V10, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               18                105
  R1                0                  2
  R2                0                 12
  RX                1                  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"
D61V11, continuous

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    24   4
  11Q LOSS WILD-TYPE 107  23
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                28                130 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                 23 
$`11Q LOSS MUTATED`
TCGA-AG-3611 TCGA-BM-6198 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 
       13.94        21.24        43.04        13.55        37.97        29.98 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3591 TCGA-AG-3594 
       24.36        24.59        32.02         7.07        34.03         2.01 
TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-A008 
        6.05        32.98        19.04        17.95         1.02        13.94 
TCGA-AG-A020 TCGA-AH-6544 TCGA-AH-6643 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
        1.02        38.56        43.20        13.97        10.98        44.02 
TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6881 
       12.62        24.13        17.00        16.41 

$`11Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 
       26.43        46.92        39.48        17.23        34.49        37.74 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       16.83        20.02        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       12.00        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03        34.03        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99        19.99         1.02        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01        48.03        25.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       28.04        36.03        14.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       20.98         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        2.50        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       21.01        25.05        26.04        31.00        12.00        31.00 
TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       51.98        25.97        25.05        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        51.48        32.61         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              1.02               0.39 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             44.02             129.27 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            18.495             22.010 
[1] "1.0 - 44.0 (18.5)"  "0.4 - 129.3 (22.0)"
[1] "hr=" "1.2"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11Q LOSS MUTATED         8        1         6         0         0         1
  11Q LOSS WILD-TYPE      22        7        34         2         1         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11Q LOSS MUTATED            2          4          4        1         1
  11Q LOSS WILD-TYPE          5         21         10       17         6
D62V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   8                 22
  STAGE II                  1                  7
  STAGE IIA                 6                 34
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 1                  3
  STAGE IIIA                2                  5
  STAGE IIIB                4                 21
  STAGE IIIC                4                 10
  STAGE IV                  1                 17
  STAGE IVA                 1                  6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED    1  8 19  2
  11Q LOSS WILD-TYPE  8 20 93 12
D62V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                1                  8
  T2                8                 20
  T3               19                 93
  T4                2                 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
  11Q LOSS MUTATED   15  9  6
  11Q LOSS WILD-TYPE 69 36 27
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               15                 69
  N1                9                 36
  N2                6                 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"
D62V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    24   1
  11Q LOSS WILD-TYPE 101  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     24    1
  11Q LOSS WILD-TYPE  101   23
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               24                101
  1                1                 23
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   14 16
  11Q LOSS WILD-TYPE 62 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     14   16
  11Q LOSS WILD-TYPE   62   73
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               14                 62
  MALE                 16                 73
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   20  6
  11Q LOSS WILD-TYPE 92 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     20    6
  11Q LOSS WILD-TYPE   92   14
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                20                 92
  YES                6                 14
[1] 2 2
[1] FALSE
D62V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    21   5
  11Q LOSS WILD-TYPE 125   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     21    5
  11Q LOSS WILD-TYPE  125    8
                                clus
vv                               11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        21                125
  RECTAL MUCINOUS ADENOCARCINOMA                5                  8
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    22   0   0   1
  11Q LOSS WILD-TYPE 101   2  12   3
D62V10, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               22                101
  R1                0                  2
  R2                0                 12
  RX                1                  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"
D62V11, continuous

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    14   6
  12P LOSS WILD-TYPE 117  21
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                20                138 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                 21 
$`12P LOSS MUTATED`
TCGA-AF-3913 TCGA-AF-2691 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3591 TCGA-AG-3593 
       10.39        43.04        29.98        24.36        34.03        34.03 
TCGA-AG-3728 TCGA-AG-3898 TCGA-AG-4021 TCGA-AG-A00Y TCGA-DC-6155 TCGA-DC-6158 
       29.98        48.03         3.98        23.01        13.97        10.98 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 
       24.13        51.48        20.91        17.00        16.31        16.41 
TCGA-F5-6702 TCGA-F5-6812 
       28.57        36.49 

$`12P LOSS WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
       55.76        26.43        46.92        39.48        17.23        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       37.97        34.49        37.74        16.83        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       15.95        19.99        20.98         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 
        1.02        46.03        20.98        13.94         6.02        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       25.05        26.04        31.00        12.00        31.00        51.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       41.36        57.24       129.27        32.61         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.55        19.96        18.28        15.85        17.69        16.34 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        49.51        42.35         0.39        32.19 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              3.98               0.39 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             51.48             129.27 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            24.245             20.765 
[1] "4.0 - 51.5 (24.2)"  "0.4 - 129.3 (20.8)"
[1] "hr=" "2.2"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12P LOSS MUTATED         2        1         7         0         0         0
  12P LOSS WILD-TYPE      28        7        33         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12P LOSS MUTATED            2          3          3        2         3
  12P LOSS WILD-TYPE          5         22         11       16         4
D63V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   2                 28
  STAGE II                  1                  7
  STAGE IIA                 7                 33
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                2                  5
  STAGE IIIB                3                 22
  STAGE IIIC                3                 11
  STAGE IV                  2                 16
  STAGE IVA                 3                  4
[1] 11  2
[1] TRUE
[1] "dimension of 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  2 19  1
  12P LOSS WILD-TYPE  8 26 93 13
D63V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                1                  8
  T2                2                 26
  T3               19                 93
  T4                1                 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
  12P LOSS MUTATED   10  8  5
  12P LOSS WILD-TYPE 74 37 28
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               10                 74
  N1                8                 37
  N2                5                 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"
D63V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    17   4
  12P LOSS WILD-TYPE 108  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     17    4
  12P LOSS WILD-TYPE  108   20
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               17                108
  1                4                 20
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   12 11
  12P LOSS WILD-TYPE 64 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     12   11
  12P LOSS WILD-TYPE   64   78
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               12                 64
  MALE                 11                 78
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   15  3
  12P LOSS WILD-TYPE 97 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     15    3
  12P LOSS WILD-TYPE   97   17
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                15                 97
  YES                3                 17
[1] 2 2
[1] FALSE
D63V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    22   0
  12P LOSS WILD-TYPE 124  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     22    0
  12P LOSS WILD-TYPE  124   13
                                clus
vv                               12P LOSS MUTATED 12P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        22                124
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    19   0   1   0
  12P LOSS WILD-TYPE 104   2  11   4
D63V10, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               19                104
  R1                0                  2
  R2                1                 11
  RX                0                  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"
D63V11, continuous

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    17   6
  12Q LOSS WILD-TYPE 114  21
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                23                135 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 6                 21 
$`12Q LOSS MUTATED`
TCGA-AG-A014 TCGA-G5-6233 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-6136 
       15.95        18.28        43.04        34.49        29.98        24.36 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3898 TCGA-AG-4001 TCGA-AG-4021 
       34.03        34.03        29.98        48.03        36.03         3.98 
TCGA-AG-A00Y TCGA-AH-6544 TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DF TCGA-DY-A1DG 
       23.01        38.56        13.97        10.98        24.13        51.48 
TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6812 
       17.00        16.31        16.41        28.57        36.49 

$`12Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       25.97        36.03        31.00        51.98        21.24        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 
       26.43        46.92        39.48        17.23        13.55        37.97 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       37.74        16.83        20.02        24.59        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       20.98         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       19.99        28.04        14.04         1.02        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       13.94         6.02        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       33.17        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       31.00        51.98        44.02        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 
       12.62       126.44        41.36        57.24       129.27        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
        3.48         4.18        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        17.69        16.34         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       42.35         0.39        32.19        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              3.98               0.39 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             51.48             129.27 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             28.57              20.55 
[1] "4.0 - 51.5 (28.6)"  "0.4 - 129.3 (20.6)"
[1] "hr=" "1.8"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12Q LOSS MUTATED         3        0         9         0         0         0
  12Q LOSS WILD-TYPE      27        8        31         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12Q LOSS MUTATED            2          2          2        1         3
  12Q LOSS WILD-TYPE          5         23         12       17         4
D64V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   3                 27
  STAGE II                  0                  8
  STAGE IIA                 9                 31
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                2                  5
  STAGE IIIB                2                 23
  STAGE IIIC                2                 12
  STAGE IV                  1                 17
  STAGE IVA                 3                  4
[1] 11  2
[1] TRUE
[1] "dimension of 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 LOSS MUTATED    1  3 19  1
  12Q LOSS WILD-TYPE  8 25 93 13
D64V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                1                  8
  T2                3                 25
  T3               19                 93
  T4                1                 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
  12Q LOSS MUTATED   12  7  5
  12Q LOSS WILD-TYPE 72 38 28
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               12                 72
  N1                7                 38
  N2                5                 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"
D64V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    18   4
  12Q LOSS WILD-TYPE 107  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     18    4
  12Q LOSS WILD-TYPE  107   20
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               18                107
  1                4                 20
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED   10 14
  12Q LOSS WILD-TYPE 66 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     10   14
  12Q LOSS WILD-TYPE   66   75
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               10                 66
  MALE                 14                 75
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED   16  4
  12Q LOSS WILD-TYPE 96 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     16    4
  12Q LOSS WILD-TYPE   96   16
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                16                 96
  YES                4                 16
[1] 2 2
[1] FALSE
D64V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    22   1
  12Q LOSS WILD-TYPE 124  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     22    1
  12Q LOSS WILD-TYPE  124   12
                                clus
vv                               12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        22                124
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    19   0   1   0
  12Q LOSS WILD-TYPE 104   2  11   4
D64V10, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               19                104
  R1                0                  2
  R2                1                 11
  RX                0                  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"
D64V11, continuous

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED     4   2
  13Q LOSS WILD-TYPE 127  25
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                152 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 25 
$`13Q LOSS MUTATED`
TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-4021 TCGA-AG-A020 TCGA-DY-A0XA 
       34.03         2.01         6.05         3.98         1.02       126.44 

$`13Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       18.28        55.76        26.43        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        24.36        20.02        24.59        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       50.04        12.03         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        9.07         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       26.04        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        3.48         4.18        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              1.02               0.39 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            126.44             129.27 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             5.015             21.125 
[1] "1.0 - 126.4 (5.0)"  "0.4 - 129.3 (21.1)"
[1] "hr=" "2.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  13Q LOSS MUTATED         0        0         3         0         0         1
  13Q LOSS WILD-TYPE      30        8        37         2         1         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  13Q LOSS MUTATED            0          0          1        1         0
  13Q LOSS WILD-TYPE          7         25         13       17         7
D65V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   0                 30
  STAGE II                  0                  8
  STAGE IIA                 3                 37
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 1                  3
  STAGE IIIA                0                  7
  STAGE IIIB                0                 25
  STAGE IIIC                1                 13
  STAGE IV                  1                 17
  STAGE IVA                 0                  7
[1] 11  2
[1] TRUE
[1] "dimension of 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     0   0   6   0
  13Q LOSS WILD-TYPE   9  28 106  14
D65V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                0                  9
  T2                0                 28
  T3                6                106
  T4                0                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  13Q LOSS MUTATED    3  1  2
  13Q LOSS WILD-TYPE 81 44 31
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                3                 81
  N1                1                 44
  N2                2                 31
[1] 3 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
  13Q LOSS MUTATED     5   1
  13Q LOSS WILD-TYPE 120  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      5    1
  13Q LOSS WILD-TYPE  120   23
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0                5                120
  1                1                 23
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    4  2
  13Q LOSS WILD-TYPE 72 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    2
  13Q LOSS WILD-TYPE   72   87
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                4                 72
  MALE                  2                 87
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     2   2
  13Q LOSS WILD-TYPE 110  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    2
  13Q LOSS WILD-TYPE  110   18
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 2                110
  YES                2                 18
[1] 2 2
[1] FALSE
D65V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     4   2
  13Q LOSS WILD-TYPE 142  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    2
  13Q LOSS WILD-TYPE  142   11
                                clus
vv                               13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                         4                142
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED     4   0   1   0
  13Q LOSS WILD-TYPE 119   2  11   4
D65V10, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0                4                119
  R1                0                  2
  R2                1                 11
  RX                0                  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"
D65V11, continuous

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   54  9
  14Q LOSS WILD-TYPE 77 18
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                63                 95 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 9                 18 
$`14Q LOSS MUTATED`
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       17.03        17.03        25.97        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-6672 
       26.43        39.48        17.23        13.55        37.74        24.59 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       65.98        11.84        36.03        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3881 
       34.03        50.04         6.05         0.99         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-4001 
        1.02        17.95        35.01         1.02        48.03        36.03 
TCGA-AG-4005 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       14.04         6.02        23.01         1.94        38.96        38.04 
TCGA-AH-6544 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 
       38.56         6.05        33.17        47.44        48.20         7.17 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
       25.05        31.00        13.97        51.98        10.98        25.05 
TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6513 
       25.05       129.27        51.48        20.55        17.00        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 
       16.31        16.41        10.78        11.97        42.35         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6863 
       32.19        36.49        11.87 

$`14Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A014 TCGA-AG-A015 
       10.39         8.02        13.94        19.99        15.95        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       31.00        51.98        46.92        43.04        37.97        34.49 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3574 
       29.98        16.83        24.36        20.02        86.63        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00        32.02         7.07        20.05        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
        2.01        12.03         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 
        7.99        29.98        37.02        32.98         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       36.95        13.02        14.01        25.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       28.04         1.02         3.98        46.03        20.98        13.94 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N 
       37.02         9.07         1.02         1.02        49.97        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       41.00         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 
       13.78        44.78        78.12        21.01        26.04        12.00 
TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       31.00        44.02        25.97        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
       57.24        24.13        32.61         3.48         4.18        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 
       20.91        18.28        15.85        17.69         8.61        11.51 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       13.64        17.46         8.45         9.96        49.51        28.57 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        12.46        47.08 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.39               0.99 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            129.27             126.44 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             24.59              20.91 
[1] "0.4 - 129.3 (24.6)" "1.0 - 126.4 (20.9)"
[1] "hr=" "1.4"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  14Q LOSS MUTATED        10        1        21         0         0         1
  14Q LOSS WILD-TYPE      20        7        19         2         1         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  14Q LOSS MUTATED            4         11          6        7         2
  14Q LOSS WILD-TYPE          3         14          8       11         5
D66V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  10                 20
  STAGE II                  1                  7
  STAGE IIA                21                 19
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 1                  3
  STAGE IIIA                4                  3
  STAGE IIIB               11                 14
  STAGE IIIC                6                  8
  STAGE IV                  7                 11
  STAGE IVA                 2                  5
[1] 11  2
[1] TRUE
[1] "dimension of 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    3 10 49  4
  14Q LOSS WILD-TYPE  6 18 63 10
D66V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                3                  6
  T2               10                 18
  T3               49                 63
  T4                4                 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
  14Q LOSS MUTATED   32 23 11
  14Q LOSS WILD-TYPE 52 22 22
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               32                 52
  N1               23                 22
  N2               11                 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"
D66V6, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   51  9
  14Q LOSS WILD-TYPE 74 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     51    9
  14Q LOSS WILD-TYPE   74   15
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               51                 74
  1                9                 15
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   28 39
  14Q LOSS WILD-TYPE 48 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     28   39
  14Q LOSS WILD-TYPE   48   50
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               28                 48
  MALE                 39                 50
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   42 11
  14Q LOSS WILD-TYPE 70  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     42   11
  14Q LOSS WILD-TYPE   70    9
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                42                 70
  YES               11                  9
[1] 2 2
[1] FALSE
D66V9, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   64  1
  14Q LOSS WILD-TYPE 82 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     64    1
  14Q LOSS WILD-TYPE   82   12
                                clus
vv                               14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        64                 82
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  14Q LOSS MUTATED   48  2  3  2
  14Q LOSS WILD-TYPE 75  0  9  2
D66V10, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               48                 75
  R1                2                  0
  R2                3                  9
  RX                2                  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"
D66V11, continuous

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   58 12
  15Q LOSS WILD-TYPE 73 15
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                70                 88 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                12                 15 
$`15Q LOSS MUTATED`
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-BM-6198 
       13.94        19.99        17.03        17.03        25.97        21.24 
TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 
       18.28        26.43        46.92        43.04        13.55        37.74 
TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 
       29.98        24.59        65.98        32.02        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3725 
       24.00        46.03        34.03        34.03         6.05        20.98 
TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3893 TCGA-AG-3896 
       29.98         0.99        19.04        19.99        35.01         1.02 
TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00Y 
       25.02        19.99        28.04        14.04        13.94        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       37.02         1.02         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 TCGA-CL-5918 
       38.56        43.20         6.05        13.78        47.44         7.17 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DC 
       21.01        31.00        13.97        51.98        25.05        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 
       57.24        24.13         3.48         4.18        15.85        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 
       16.41        11.51        10.78        13.64        11.97        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       28.57        32.19        36.49        19.66 

$`15Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       10.39         8.02        15.95        36.03        31.00        51.98 
TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 
       55.76        39.48        17.23        37.97        34.49        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.36        20.02        86.63        11.84        36.03        12.00 
TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        7.07         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       32.98         0.99         1.02        17.95        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 
       14.01        48.03        32.02        36.03         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 
       46.03        20.98         6.02         9.07         1.02        49.97 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       61.97         2.50        27.55        26.43        19.46        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
       44.78        48.20        78.12        25.05        26.04        12.00 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       31.00        10.98        44.02        25.97        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
      126.44       129.27        51.48        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 
       20.91        17.00        18.28        17.69        16.34         8.61 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 
       17.46         8.45         9.96        49.51         0.39        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.99               0.39 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             65.98             129.27 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            23.505             20.285 
[1] "1.0 - 66.0 (23.5)"  "0.4 - 129.3 (20.3)"
[1] "hr=" "1.1"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  15Q LOSS MUTATED        10        1        20         1         1         1
  15Q LOSS WILD-TYPE      20        7        20         1         0         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  15Q LOSS MUTATED            4         13          8        9         2
  15Q LOSS WILD-TYPE          3         12          6        9         5
D67V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  10                 20
  STAGE II                  1                  7
  STAGE IIA                20                 20
  STAGE IIB                 1                  1
  STAGE IIC                 1                  0
  STAGE III                 1                  3
  STAGE IIIA                4                  3
  STAGE IIIB               13                 12
  STAGE IIIC                8                  6
  STAGE IV                  9                  9
  STAGE IVA                 2                  5
[1] 11  2
[1] TRUE
[1] "dimension of 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    4  9 54  5
  15Q LOSS WILD-TYPE  5 19 58  9
D67V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                4                  5
  T2                9                 19
  T3               54                 58
  T4                5                  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
  15Q LOSS MUTATED   33 23 16
  15Q LOSS WILD-TYPE 51 22 17
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               33                 51
  N1               23                 22
  N2               16                 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"
D67V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   55 10
  15Q LOSS WILD-TYPE 70 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     55   10
  15Q LOSS WILD-TYPE   70   14
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               55                 70
  1               10                 14
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   29 43
  15Q LOSS WILD-TYPE 47 46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     29   43
  15Q LOSS WILD-TYPE   47   46
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               29                 47
  MALE                 43                 46
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   49 10
  15Q LOSS WILD-TYPE 63 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     49   10
  15Q LOSS WILD-TYPE   63   10
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                49                 63
  YES               10                 10
[1] 2 2
[1] FALSE
D67V9, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   64  5
  15Q LOSS WILD-TYPE 82  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     64    5
  15Q LOSS WILD-TYPE   82    8
                                clus
vv                               15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        64                 82
  RECTAL MUCINOUS ADENOCARCINOMA                5                  8
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED   54  1  4  2
  15Q LOSS WILD-TYPE 69  1  8  2
D67V10, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               54                 69
  R1                1                  1
  R2                4                  8
  RX                2                  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"
D67V11, continuous

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     8   1
  16P LOSS WILD-TYPE 123  26
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                149 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 26 
$`16P LOSS MUTATED`
TCGA-G5-6233 TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3609 TCGA-AG-3881 TCGA-AG-4005 
       18.28        32.02        34.03        19.99        19.04        14.04 
TCGA-DC-6682 TCGA-F5-6811 TCGA-F5-6814 
       25.05        32.19        37.18 

$`16P LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       55.76        26.43        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       13.55        37.97        34.49        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        1.02        46.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       14.01         1.02        48.03        25.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       28.04        36.03         1.02         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       19.46         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
        9.96        49.51        42.35        28.57         0.39        36.49 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        38.14        11.87        12.46        47.08 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             14.04               0.39 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             37.18             129.27 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             25.05              20.98 
[1] "14.0 - 37.2 (25.1)" "0.4 - 129.3 (21.0)"
[1] "hr=" "1.2"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16P LOSS MUTATED         0        0         6         0         0         0
  16P LOSS WILD-TYPE      30        8        34         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16P LOSS MUTATED            0          0          1        1         0
  16P LOSS WILD-TYPE          7         25         13       17         7
D68V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   0                 30
  STAGE II                  0                  8
  STAGE IIA                 6                 34
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                0                  7
  STAGE IIIB                0                 25
  STAGE IIIC                1                 13
  STAGE IV                  1                 17
  STAGE IVA                 0                  7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED     0   0   9   0
  16P LOSS WILD-TYPE   9  28 103  14
D68V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                0                  9
  T2                0                 28
  T3                9                103
  T4                0                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  16P LOSS MUTATED    6  0  3
  16P LOSS WILD-TYPE 78 45 30
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                6                 78
  N1                0                 45
  N2                3                 30
[1] 3 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
  16P LOSS MUTATED     8   1
  16P LOSS WILD-TYPE 117  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      8    1
  16P LOSS WILD-TYPE  117   23
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                8                117
  1                1                 23
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    5  4
  16P LOSS WILD-TYPE 71 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5    4
  16P LOSS WILD-TYPE   71   85
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                5                 71
  MALE                  4                 85
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     8   1
  16P LOSS WILD-TYPE 104  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      8    1
  16P LOSS WILD-TYPE  104   19
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 8                104
  YES                1                 19
[1] 2 2
[1] FALSE
D68V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     7   1
  16P LOSS WILD-TYPE 139  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7    1
  16P LOSS WILD-TYPE  139   12
                                clus
vv                               16P LOSS MUTATED 16P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                         7                139
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED     7   0   0   0
  16P LOSS WILD-TYPE 116   2  12   4
D68V10, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0                7                116
  R1                0                  2
  R2                0                 12
  RX                0                  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"
D68V11, continuous

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    13   1
  16Q LOSS WILD-TYPE 118  26
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                144 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 26 
$`16Q LOSS MUTATED`
TCGA-G5-6233 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3600 TCGA-AG-3609 
       18.28        24.59        32.02        34.03         6.05        19.99 
TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-4005 TCGA-DC-6682 
        7.99        32.98        19.04         1.02        14.04        25.05 
TCGA-F5-6811 TCGA-F5-6814 
       32.19        37.18 

$`16Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       55.76        26.43        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       13.55        37.97        34.49        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       24.36        20.02        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        15.95        20.98         0.99        29.98        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99        19.99        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       19.99        28.04        36.03         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       26.04        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        44.02        25.97        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        3.48         4.18        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        42.35        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       36.49        19.66        38.14        11.87        12.46        47.08 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              1.02               0.39 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             37.18             129.27 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            22.290             20.995 
[1] "1.0 - 37.2 (22.3)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "1.6"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16Q LOSS MUTATED         3        0         6         0         0         0
  16Q LOSS WILD-TYPE      27        8        34         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16Q LOSS MUTATED            0          0          2        2         0
  16Q LOSS WILD-TYPE          7         25         12       16         7
D69V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   3                 27
  STAGE II                  0                  8
  STAGE IIA                 6                 34
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                0                  7
  STAGE IIIB                0                 25
  STAGE IIIC                2                 12
  STAGE IV                  2                 16
  STAGE IVA                 0                  7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED     0   3  10   1
  16Q LOSS WILD-TYPE   9  25 102  13
D69V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                0                  9
  T2                3                 25
  T3               10                102
  T4                1                 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
  16Q LOSS MUTATED    9  0  5
  16Q LOSS WILD-TYPE 75 45 28
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                9                 75
  N1                0                 45
  N2                5                 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"
D69V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    12   1
  16Q LOSS WILD-TYPE 113  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     12    1
  16Q LOSS WILD-TYPE  113   23
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               12                113
  1                1                 23
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    7  7
  16Q LOSS WILD-TYPE 69 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7    7
  16Q LOSS WILD-TYPE   69   82
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                7                 69
  MALE                  7                 82
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    10   3
  16Q LOSS WILD-TYPE 102  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     10    3
  16Q LOSS WILD-TYPE  102   17
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                10                102
  YES                3                 17
[1] 2 2
[1] FALSE
D69V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    12   1
  16Q LOSS WILD-TYPE 134  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     12    1
  16Q LOSS WILD-TYPE  134   12
                                clus
vv                               16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        12                134
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    11   0   0   0
  16Q LOSS WILD-TYPE 112   2  12   4
D69V10, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               11                112
  R1                0                  2
  R2                0                 12
  RX                0                  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"
D69V11, continuous

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   80 18
  17P LOSS WILD-TYPE 51  9
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                98                 60 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                18                  9 
$`17P LOSS MUTATED`
TCGA-AG-3611 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 
       13.94        17.03        25.97        15.95        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       21.24        55.76        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       37.97        34.49        37.74        29.98        24.36        20.02 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3582 
       86.63        65.98        11.84        12.00        32.02        36.03 
TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 
       24.00        34.03        34.03         2.01        50.04         0.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       20.98         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
       19.04         1.02        17.95        35.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 
       32.02        19.99        28.04        36.03        14.04         3.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A026 
       13.94         6.02        23.01        37.02         1.02         1.94 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 
       41.00        38.56        43.20        27.55        26.43         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6155 
       33.17        13.78        44.78         7.17        25.05        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       10.98        44.02        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        51.48         3.48         4.18 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        18.28        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       16.41        11.51        10.78        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6814 
       49.51        42.35        28.57         0.39        19.66        37.18 
TCGA-F5-6863 TCGA-F5-6864 
       11.87        12.46 

$`17P LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-A015 TCGA-G5-6233 
       10.39         8.02        19.99        17.03        36.03        18.28 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3581 
       26.43        46.92        16.83        24.59        36.03         7.07 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3599 TCGA-AG-3600 
       20.05         1.02        46.03        34.03        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
       15.95        19.99        29.98         0.99        19.99        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       13.02        14.01        25.02         1.02        46.03        20.98 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
        9.07         1.02        49.97        38.96        61.97        38.04 
TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 
        2.50        19.46        47.44        48.20        78.12        21.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 
       26.04        31.00        12.00        31.00        51.98        25.97 
TCGA-DC-6682 TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6882 
       25.05        32.61        20.55        19.96        15.85         8.61 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6861 TCGA-G5-6572 
       13.64        17.46        32.19        36.49        38.14        47.08 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.39               0.99 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            129.27              78.12 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            21.110             20.995 
[1] "0.4 - 129.3 (21.1)" "1.0 - 78.1 (21.0)" 
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17P LOSS MUTATED        14        5        29         2         1         2
  17P LOSS WILD-TYPE      16        3        11         0         0         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17P LOSS MUTATED            4         17         10       11         4
  17P LOSS WILD-TYPE          3          8          4        7         3
D70V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  14                 16
  STAGE II                  5                  3
  STAGE IIA                29                 11
  STAGE IIB                 2                  0
  STAGE IIC                 1                  0
  STAGE III                 2                  2
  STAGE IIIA                4                  3
  STAGE IIIB               17                  8
  STAGE IIIC               10                  4
  STAGE IV                 11                  7
  STAGE IVA                 4                  3
[1] 11  2
[1] TRUE
[1] "dimension of 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 16 76 10
  17P LOSS WILD-TYPE  7 12 36  4
D70V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                2                  7
  T2               16                 12
  T3               76                 36
  T4               10                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  17P LOSS MUTATED   53 30 20
  17P LOSS WILD-TYPE 31 15 13
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               53                 31
  N1               30                 15
  N2               20                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   79 15
  17P LOSS WILD-TYPE 46  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     79   15
  17P LOSS WILD-TYPE   46    9
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               79                 46
  1               15                  9
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   51 54
  17P LOSS WILD-TYPE 25 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     51   54
  17P LOSS WILD-TYPE   25   35
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               51                 25
  MALE                 54                 35
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   70 11
  17P LOSS WILD-TYPE 42  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     70   11
  17P LOSS WILD-TYPE   42    9
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                70                 42
  YES               11                  9
[1] 2 2
[1] FALSE
D70V9, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   95  6
  17P LOSS WILD-TYPE 51  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     95    6
  17P LOSS WILD-TYPE   51    7
                                clus
vv                               17P LOSS MUTATED 17P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        95                 51
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   75  2  8  3
  17P LOSS WILD-TYPE 48  0  4  1
D70V10, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               75                 48
  R1                2                  0
  R2                8                  4
  RX                3                  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"
D70V11, continuous

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    22   5
  17Q LOSS WILD-TYPE 109  22
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                27                131 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 22 
$`17Q LOSS MUTATED`
TCGA-AG-3611 TCGA-AG-A00H TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-AF-4110 
       13.94        25.97        51.98        21.24        55.76        29.98 
TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3591 TCGA-AG-3896 TCGA-AG-3902 
       24.36        65.98        36.03        34.03         1.02        32.02 
TCGA-AG-3999 TCGA-AG-A008 TCGA-AG-A02X TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6683 
       28.04        13.94        41.00        13.97        10.98        25.05 
TCGA-DT-5265 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6512 TCGA-EI-6881 
       12.62        24.13         3.48         4.18        17.69        16.41 
TCGA-EI-6883 TCGA-F5-6702 TCGA-F5-6814 
       11.51        28.57        37.18 

$`17Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 
       10.39         8.02        19.99        17.03        17.03        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 
       36.03        31.00        18.28        26.43        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        37.97        34.49        37.74 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       16.83        20.02        24.59        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00        32.02         7.07        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-4001 
       35.01        14.01        48.03        25.02        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       14.04         1.02         3.98        46.03        20.98         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        61.97        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       21.01        25.05        26.04        31.00        12.00        31.00 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC 
       51.98        44.02        25.97        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       57.24       129.27        51.48        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        18.28        15.85        16.34        16.31 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        8.61        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        42.35         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        38.14        11.87        12.46        47.08 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              1.02               0.39 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             65.98             129.27 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             24.36              20.91 
[1] "1.0 - 66.0 (24.4)"  "0.4 - 129.3 (20.9)"
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17Q LOSS MUTATED         4        1         6         1         1         0
  17Q LOSS WILD-TYPE      26        7        34         1         0         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17Q LOSS MUTATED            2          6          3        2         2
  17Q LOSS WILD-TYPE          5         19         11       16         5
D71V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   4                 26
  STAGE II                  1                  7
  STAGE IIA                 6                 34
  STAGE IIB                 1                  1
  STAGE IIC                 1                  0
  STAGE III                 0                  4
  STAGE IIIA                2                  5
  STAGE IIIB                6                 19
  STAGE IIIC                3                 11
  STAGE IV                  2                 16
  STAGE IVA                 2                  5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17Q LOSS MUTATED    0  5 20  3
  17Q LOSS WILD-TYPE  9 23 92 11
D71V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                  9
  T2                5                 23
  T3               20                 92
  T4                3                 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
  17Q LOSS MUTATED   13 10  5
  17Q LOSS WILD-TYPE 71 35 28
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               13                 71
  N1               10                 35
  N2                5                 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"
D71V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    21   3
  17Q LOSS WILD-TYPE 104  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     21    3
  17Q LOSS WILD-TYPE  104   21
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               21                104
  1                3                 21
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   10 18
  17Q LOSS WILD-TYPE 66 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10   18
  17Q LOSS WILD-TYPE   66   71
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               10                 66
  MALE                 18                 71
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   20  4
  17Q LOSS WILD-TYPE 92 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     20    4
  17Q LOSS WILD-TYPE   92   16
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                20                 92
  YES                4                 16
[1] 2 2
[1] FALSE
D71V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    25   2
  17Q LOSS WILD-TYPE 121  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     25    2
  17Q LOSS WILD-TYPE  121   11
                                clus
vv                               17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        25                121
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    21   1   2   2
  17Q LOSS WILD-TYPE 102   1  10   2
D71V10, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               21                102
  R1                1                  1
  R2                2                 10
  RX                2                  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"
D71V11, continuous

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   102  20
  18P LOSS WILD-TYPE  29   7
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               122                 36 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                20                  7 
$`18P LOSS MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       15.95        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       34.49        37.74        29.98        24.36        20.02        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 
       65.98        11.84        36.03        12.00         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       20.05        24.00        46.03        34.03        34.03        34.03 
TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 
       50.04         0.99        15.95        20.98         7.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       37.02        32.98         0.99        19.99         1.02        36.95 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       35.01         1.02        48.03        25.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A008 
       28.04        36.03         1.02         3.98        46.03        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
        6.02        23.01        37.02         9.07         1.02         1.02 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        41.00        38.04        38.56        43.20        27.55 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       26.43         6.05        33.17        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        25.05       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        51.48         3.48         4.18        20.55 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6465 
       16.41        11.51        10.78        13.64        11.97        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6863 TCGA-F5-6864 
       11.87        12.46 

$`18P LOSS WILD-TYPE`
TCGA-AG-3580 TCGA-AG-A015 TCGA-AF-2693 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3578 
        8.02        36.03        37.97        16.83        24.59        32.02 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3727 
        1.02         2.01        12.03         6.05        19.99         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4005 
        0.99        19.04        17.95        13.02        14.01        14.04 
TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 
       20.98        49.97        38.96        61.97         2.50        19.46 
TCGA-CI-6621 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 
       13.78        12.62        32.61        19.96        20.91         8.61 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6572 
       17.46         8.45         9.96        37.18        38.14        47.08 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.39               0.99 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            129.27              61.97 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            25.035             17.705 
[1] "0.4 - 129.3 (25.0)" "1.0 - 62.0 (17.7)" 
[1] "hr=" "1.7"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18P LOSS MUTATED        21        5        32         2         1         2
  18P LOSS WILD-TYPE       9        3         8         0         0         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18P LOSS MUTATED            5         21         11       15         7
  18P LOSS WILD-TYPE          2          4          3        3         0
D72V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  21                  9
  STAGE II                  5                  3
  STAGE IIA                32                  8
  STAGE IIB                 2                  0
  STAGE IIC                 1                  0
  STAGE III                 2                  2
  STAGE IIIA                5                  2
  STAGE IIIB               21                  4
  STAGE IIIC               11                  3
  STAGE IV                 15                  3
  STAGE IVA                 7                  0
[1] 11  2
[1] TRUE
[1] "dimension of 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    5 21 90 11
  18P LOSS WILD-TYPE  4  7 22  3
D72V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                5                  4
  T2               21                  7
  T3               90                 22
  T4               11                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  18P LOSS MUTATED   63 37 26
  18P LOSS WILD-TYPE 21  8  7
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               63                 21
  N1               37                  8
  N2               26                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   95 22
  18P LOSS WILD-TYPE 30  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     95   22
  18P LOSS WILD-TYPE   30    2
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               95                 30
  1               22                  2
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   59 69
  18P LOSS WILD-TYPE 17 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     59   69
  18P LOSS WILD-TYPE   17   20
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               59                 17
  MALE                 69                 20
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   88 15
  18P LOSS WILD-TYPE 24  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     88   15
  18P LOSS WILD-TYPE   24    5
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                88                 24
  YES               15                  5
[1] 2 2
[1] FALSE
D72V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   119   7
  18P LOSS WILD-TYPE  27   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    119    7
  18P LOSS WILD-TYPE   27    6
                                clus
vv                               18P LOSS MUTATED 18P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       119                 27
  RECTAL MUCINOUS ADENOCARCINOMA                7                  6
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  18P LOSS MUTATED   95  2 11  3
  18P LOSS WILD-TYPE 28  0  1  1
D72V10, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               95                 28
  R1                2                  0
  R2               11                  1
  RX                3                  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"
D72V11, continuous

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   109  22
  18Q LOSS WILD-TYPE  22   5
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               131                 27 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                22                  5 
$`18Q LOSS MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       15.95        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       37.97        34.49        37.74        29.98        24.36        20.02 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 
        7.07        36.03        20.05        24.00        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 
       34.03        34.03         2.01        50.04         0.99        15.95 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3893 
        0.99        19.04        19.99         1.02        36.95        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
        1.02        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A008 
       36.03        14.04         1.02         3.98        46.03        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
        6.02        23.01        37.02         9.07         1.02         1.02 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        41.00        38.04        38.56        43.20        27.55 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       26.43         6.05        33.17        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        25.05       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        51.48         3.48         4.18        20.55 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       16.31        16.41        11.51        10.78        13.64        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       36.49        19.66        11.87        12.46        47.08 

$`18Q LOSS WILD-TYPE`
TCGA-AG-3580 TCGA-AG-A015 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3586 TCGA-AG-3599 
        8.02        36.03        16.83        24.59         1.02        12.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3894 
        6.05        19.99         0.99        17.95        13.02        14.01 
TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 
       20.98        49.97        38.96        61.97         2.50        19.46 
TCGA-CI-6621 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 
       13.78        12.62        32.61        19.96         8.61        17.46 
TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
        9.96        37.18        38.14 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.39               0.99 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            129.27              61.97 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             24.36              17.46 
[1] "0.4 - 129.3 (24.4)" "1.0 - 62.0 (17.5)" 
[1] "hr=" "1.6"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18Q LOSS MUTATED        22        6        35         2         1         3
  18Q LOSS WILD-TYPE       8        2         5         0         0         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18Q LOSS MUTATED            5         22         11       16         7
  18Q LOSS WILD-TYPE          2          3          3        2         0
D73V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  22                  8
  STAGE II                  6                  2
  STAGE IIA                35                  5
  STAGE IIB                 2                  0
  STAGE IIC                 1                  0
  STAGE III                 3                  1
  STAGE IIIA                5                  2
  STAGE IIIB               22                  3
  STAGE IIIC               11                  3
  STAGE IV                 16                  2
  STAGE IVA                 7                  0
[1] 11  2
[1] TRUE
[1] "dimension of 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    5 22 97 12
  18Q LOSS WILD-TYPE  4  6 15  2
D73V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                5                  4
  T2               22                  6
  T3               97                 15
  T4               12                  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                 N0 N1 N2
  18Q LOSS MUTATED   68 39 28
  18Q LOSS WILD-TYPE 16  6  5
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               68                 16
  N1               39                  6
  N2               28                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   102  23
  18Q LOSS WILD-TYPE  23   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    102   23
  18Q LOSS WILD-TYPE   23    1
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              102                 23
  1               23                  1
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   65 73
  18Q LOSS WILD-TYPE 11 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     65   73
  18Q LOSS WILD-TYPE   11   16
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               65                 11
  MALE                 73                 16
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   96 15
  18Q LOSS WILD-TYPE 16  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     96   15
  18Q LOSS WILD-TYPE   16    5
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                96                 16
  YES               15                  5
[1] 2 2
[1] FALSE
D73V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   124  10
  18Q LOSS WILD-TYPE  22   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    124   10
  18Q LOSS WILD-TYPE   22    3
                                clus
vv                               18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       124                 22
  RECTAL MUCINOUS ADENOCARCINOMA               10                  3
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   102   2  11   3
  18Q LOSS WILD-TYPE  21   0   1   1
D73V10, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              102                 21
  R1                2                  0
  R2               11                  1
  RX                3                  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"
D73V11, continuous

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    18   4
  19P LOSS WILD-TYPE 113  23
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                22                136 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 23 
$`19P LOSS MUTATED`
TCGA-AG-4008 TCGA-G5-6233 TCGA-AF-2687 TCGA-AF-4110 TCGA-AG-3608 TCGA-AG-3725 
       17.03        18.28        46.92        29.98        15.95        20.98 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-A016 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 
       32.98        19.04         9.07        48.20        25.05        31.00 
TCGA-DC-6155 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6513 TCGA-EI-6883 
       13.97        24.13        51.48         3.48        16.34        11.51 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 
       13.64        11.97        42.35        28.57 

$`19P LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-A00H 
       10.39         8.02        13.94        19.99        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        21.24        55.76 
TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       26.43        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        37.74        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       34.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        6.05         0.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       37.02         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         1.02         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       13.78        44.78        47.44        78.12         7.17        21.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       26.04        12.00        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       25.97        25.05        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       57.24       129.27        32.61         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 
       20.91        17.00        18.28        15.85        17.69        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       16.41         8.61        10.78        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       49.51         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              3.48               0.39 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             51.48             129.27 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            20.010             21.125 
[1] "3.5 - 51.5 (20.0)"  "0.4 - 129.3 (21.1)"
[1] "hr=" "1.3"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19P LOSS MUTATED         3        1         5         1         1         1
  19P LOSS WILD-TYPE      27        7        35         1         0         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19P LOSS MUTATED            1          2          2        3         3
  19P LOSS WILD-TYPE          6         23         12       15         4
D74V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   3                 27
  STAGE II                  1                  7
  STAGE IIA                 5                 35
  STAGE IIB                 1                  1
  STAGE IIC                 1                  0
  STAGE III                 1                  3
  STAGE IIIA                1                  6
  STAGE IIIB                2                 23
  STAGE IIIC                2                 12
  STAGE IV                  3                 15
  STAGE IVA                 3                  4
[1] 11  2
[1] TRUE
[1] "dimension of 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    0  4 18  2
  19P LOSS WILD-TYPE  9 24 94 12
D74V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                0                  9
  T2                4                 24
  T3               18                 94
  T4                2                 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
  19P LOSS MUTATED   11  6  7
  19P LOSS WILD-TYPE 73 39 26
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               11                 73
  N1                6                 39
  N2                7                 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"
D74V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    18   5
  19P LOSS WILD-TYPE 107  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     18    5
  19P LOSS WILD-TYPE  107   19
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               18                107
  1                5                 19
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   12 12
  19P LOSS WILD-TYPE 64 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     12   12
  19P LOSS WILD-TYPE   64   77
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               12                 64
  MALE                 12                 77
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   18  1
  19P LOSS WILD-TYPE 94 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     18    1
  19P LOSS WILD-TYPE   94   19
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                18                 94
  YES                1                 19
[1] 2 2
[1] FALSE
D74V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    22   0
  19P LOSS WILD-TYPE 124  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     22    0
  19P LOSS WILD-TYPE  124   13
                                clus
vv                               19P LOSS MUTATED 19P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        22                124
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    19   0   1   0
  19P LOSS WILD-TYPE 104   2  11   4
D74V10, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               19                104
  R1                0                  2
  R2                1                 11
  RX                0                  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"
D74V11, continuous

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    18   3
  19Q LOSS WILD-TYPE 113  24
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                21                137 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 24 
$`19Q LOSS MUTATED`
TCGA-G5-6233 TCGA-AF-2687 TCGA-AF-4110 TCGA-AG-3591 TCGA-AG-3608 TCGA-AG-3725 
       18.28        46.92        29.98        34.03        15.95        20.98 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-4001 TCGA-AG-A011 TCGA-CI-6624 TCGA-DC-4745 
       32.98        19.04        36.03        37.02        48.20        21.01 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6513 TCGA-EI-6883 
       25.05        31.00        24.13         3.48        16.34        11.51 
TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 
       11.97        42.35        28.57 

$`19Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       55.76        26.43        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.97        34.49        37.74        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        6.05         0.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       37.02         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       25.02        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 
       44.78        47.44        78.12         7.17        26.04        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        31.00        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
      129.27        51.48        32.61         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 
       20.91        17.00        18.28        15.85        17.69        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
       16.41         8.61        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        49.51         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              3.48               0.39 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             48.20             129.27 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             25.05              20.55 
[1] "3.5 - 48.2 (25.1)"  "0.4 - 129.3 (20.6)"
[1] "hr=" "1.1"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19Q LOSS MUTATED         3        1         6         1         1         1
  19Q LOSS WILD-TYPE      27        7        34         1         0         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19Q LOSS MUTATED            0          3          2        1         2
  19Q LOSS WILD-TYPE          7         22         12       17         5
D75V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   3                 27
  STAGE II                  1                  7
  STAGE IIA                 6                 34
  STAGE IIB                 1                  1
  STAGE IIC                 1                  0
  STAGE III                 1                  3
  STAGE IIIA                0                  7
  STAGE IIIB                3                 22
  STAGE IIIC                2                 12
  STAGE IV                  1                 17
  STAGE IVA                 2                  5
[1] 11  2
[1] TRUE
[1] "dimension of 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    0  3 17  2
  19Q LOSS WILD-TYPE  9 25 95 12
D75V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                0                  9
  T2                3                 25
  T3               17                 95
  T4                2                 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
  19Q LOSS MUTATED   12  4  6
  19Q LOSS WILD-TYPE 72 41 27
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               12                 72
  N1                4                 41
  N2                6                 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"
D75V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    19   2
  19Q LOSS WILD-TYPE 106  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     19    2
  19Q LOSS WILD-TYPE  106   22
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               19                106
  1                2                 22
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   12 10
  19Q LOSS WILD-TYPE 64 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     12   10
  19Q LOSS WILD-TYPE   64   79
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               12                 64
  MALE                 10                 79
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   17  2
  19Q LOSS WILD-TYPE 95 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     17    2
  19Q LOSS WILD-TYPE   95   18
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                17                 95
  YES                2                 18
[1] 2 2
[1] FALSE
D75V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    20   0
  19Q LOSS WILD-TYPE 126  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     20    0
  19Q LOSS WILD-TYPE  126   13
                                clus
vv                               19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        20                126
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    19   0   0   0
  19Q LOSS WILD-TYPE 104   2  12   4
D75V10, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               19                104
  R1                0                  2
  R2                0                 12
  RX                0                  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"
D75V11, continuous

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    13   6
  20P LOSS WILD-TYPE 118  21
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                139 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                 21 
$`20P LOSS MUTATED`
TCGA-G5-6641 TCGA-AF-4110 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 
       26.43        29.98        86.63        11.84        36.03        32.02 
TCGA-AG-3600 TCGA-AG-3902 TCGA-AG-4022 TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G 
        6.05        32.02        46.03         1.02         1.94        38.96 
TCGA-DC-4749 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-EI-6511 TCGA-F5-6571 
       25.05        25.05        41.36        57.24        15.85        42.35 
TCGA-F5-6702 
       28.57 

$`20P LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       18.28        55.76        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 
       13.55        37.97        34.49        37.74        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 
       20.02        24.59        65.98        12.00         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        25.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        1.02         3.98        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
       37.02         9.07         1.02        49.97        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       19.46         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
       48.20        78.12         7.17        21.01        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DF 
       25.97        25.05        12.62       126.44       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        18.28        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 
       11.97         8.45         9.96        49.51         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              1.02               0.39 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             86.63             129.27 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             29.98              20.05 
[1] "1.0 - 86.6 (30.0)"  "0.4 - 129.3 (20.1)"
[1] "hr=" "1.6"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  20P LOSS MUTATED         1        5         7         0         0         0
  20P LOSS WILD-TYPE      29        3        33         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  20P LOSS MUTATED            1          5          2        1         2
  20P LOSS WILD-TYPE          6         20         12       17         5
D76V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   1                 29
  STAGE II                  5                  3
  STAGE IIA                 7                 33
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 0                  4
  STAGE IIIA                1                  6
  STAGE IIIB                5                 20
  STAGE IIIC                2                 12
  STAGE IV                  1                 17
  STAGE IVA                 2                  5
[1] 11  2
[1] TRUE
[1] "dimension of 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    1  2 18  3
  20P LOSS WILD-TYPE  8 26 94 11
D76V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                1                  8
  T2                2                 26
  T3               18                 94
  T4                3                 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
  20P LOSS MUTATED   13  8  3
  20P LOSS WILD-TYPE 71 37 30
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               13                 71
  N1                8                 37
  N2                3                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    20   2
  20P LOSS WILD-TYPE 105  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     20    2
  20P LOSS WILD-TYPE  105   22
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               20                105
  1                2                 22
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED   11 13
  20P LOSS WILD-TYPE 65 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     11   13
  20P LOSS WILD-TYPE   65   76
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               11                 65
  MALE                 13                 76
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    11   4
  20P LOSS WILD-TYPE 101  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     11    4
  20P LOSS WILD-TYPE  101   16
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                11                101
  YES                4                 16
[1] 2 2
[1] FALSE
D76V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    21   2
  20P LOSS WILD-TYPE 125  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     21    2
  20P LOSS WILD-TYPE  125   11
                                clus
vv                               20P LOSS MUTATED 20P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        21                125
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    19   1   2   0
  20P LOSS WILD-TYPE 104   1  10   4
D76V10, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               19                104
  R1                1                  1
  R2                2                 10
  RX                0                  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"
D76V11, continuous

Clustering(77) Variable = 21Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   50 12
  21Q LOSS WILD-TYPE 81 15
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                62                 96 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                12                 15 
$`21Q LOSS MUTATED`
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A01N TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2687 
       17.03        17.03        31.00        18.28        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       39.48        17.23        29.98        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       86.63        11.84        12.00         7.07        36.03        24.00 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 
       46.03        34.03        34.03        12.03         6.05        19.99 
TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 
       20.98        29.98        19.04        19.99         1.02        48.03 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-A020 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       19.99        36.03         1.02        38.96        61.97        41.00 
TCGA-AH-6643 TCGA-CI-6621 TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6158 
       43.20        13.78        48.20        21.01        13.97        10.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
       25.05        25.05       126.44        57.24       129.27        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       32.61        20.55        20.91        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       16.41        11.97         8.45        42.35         0.39        36.49 
TCGA-F5-6814 TCGA-F5-6863 
       37.18        11.87 

$`21Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A00H TCGA-AG-A014 
       10.39         8.02        13.94        19.99        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-AF-2691 TCGA-AF-2692 
       36.03        51.98        21.24        55.76        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-A56L TCGA-AG-3574 
       37.97        34.49        37.74        16.83        65.98        36.03 
TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 
       32.02        20.05         1.02        34.03         2.01        50.04 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
        0.99        15.95         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 
       35.01        14.01        25.02        32.02        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         9.07         1.02        49.97         1.94 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.04        38.56         2.50        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17        44.78        47.44        78.12         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       25.05        26.04        31.00        12.00        31.00        51.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DF TCGA-EF-5830 
       44.02        25.97        12.62        41.36        24.13         3.48 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-6882 
        4.18        19.96        17.00        18.28        16.31         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        13.64        17.46         9.96        49.51 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       28.57        32.19        19.66        38.14        12.46        47.08 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.39               0.99 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            129.27              78.12 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            22.505             20.515 
[1] "0.4 - 129.3 (22.5)" "1.0 - 78.1 (20.5)" 
[1] "hr=" "1"  
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  21Q LOSS MUTATED         9        4        16         0         0         2
  21Q LOSS WILD-TYPE      21        4        24         2         1         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  21Q LOSS MUTATED            5         13          6        7         2
  21Q LOSS WILD-TYPE          2         12          8       11         5
D77V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   9                 21
  STAGE II                  4                  4
  STAGE IIA                16                 24
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 2                  2
  STAGE IIIA                5                  2
  STAGE IIIB               13                 12
  STAGE IIIC                6                  8
  STAGE IV                  7                 11
  STAGE IVA                 2                  5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS MUTATED    1 14 48  4
  21Q LOSS WILD-TYPE  8 14 64 10
D77V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                1                  8
  T2               14                 14
  T3               48                 64
  T4                4                 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
  21Q LOSS MUTATED   30 23 14
  21Q LOSS WILD-TYPE 54 22 19
D77V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               30                 54
  N1               23                 22
  N2               14                 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"
D77V6, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   55  7
  21Q LOSS WILD-TYPE 70 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     55    7
  21Q LOSS WILD-TYPE   70   17
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               55                 70
  1                7                 17
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   33 35
  21Q LOSS WILD-TYPE 43 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     33   35
  21Q LOSS WILD-TYPE   43   54
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               33                 43
  MALE                 35                 54
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   42  9
  21Q LOSS WILD-TYPE 70 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     42    9
  21Q LOSS WILD-TYPE   70   11
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                42                 70
  YES                9                 11
[1] 2 2
[1] FALSE
D77V9, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   62  3
  21Q LOSS WILD-TYPE 84 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     62    3
  21Q LOSS WILD-TYPE   84   10
                                clus
vv                               21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        62                 84
  RECTAL MUCINOUS ADENOCARCINOMA                3                 10
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED   53  0  4  0
  21Q LOSS WILD-TYPE 70  2  8  4
D77V10, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               53                 70
  R1                0                  2
  R2                4                  8
  RX                0                  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"
D77V11, continuous

Clustering(78) Variable = 22Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   43 10
  22Q LOSS WILD-TYPE 88 17
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                53                105 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                10                 17 
$`22Q LOSS MUTATED`
TCGA-AG-3611 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2692 
       13.94        25.97        21.24        18.28        26.43        13.55 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3578 
       29.98        24.36        24.59        65.98        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3725 TCGA-AG-3728 
        7.07        20.05        34.03        34.03        20.98        29.98 
TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-3909 
       37.02        19.99         1.02        17.95         1.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A020 TCGA-AG-A026 
       28.04        36.03        14.04         3.98         1.02         1.94 
TCGA-AG-A02G TCGA-AH-6544 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6624 
       38.96        38.56        27.55         6.05        13.78        48.20 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       21.01        31.00        13.97        10.98        44.02        25.05 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6512 
       25.05        41.36        51.48         4.18        20.55        17.69 
TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6863 
       16.41        28.57         0.39        36.49        11.87 

$`22Q LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 
       10.39         8.02        19.99        17.03        17.03        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2689 
       36.03        31.00        51.98        55.76        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 
       17.23        43.04        37.97        34.49        37.74        16.83 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3584 
       20.02        86.63        11.84        36.03        36.03        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3892 
       32.98         0.99         0.99        19.04        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4007 
       35.01        14.01        48.03        25.02        32.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
        9.07         1.02        49.97        61.97        41.00        38.04 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
        2.50        43.20        26.43        19.46        33.17        44.78 
TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
       47.44        78.12         7.17        25.05        26.04        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD 
       31.00        51.98        25.97        12.62       126.44        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 
      129.27        24.13        32.61         3.48        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 
       17.00        18.28        15.85        16.34        16.31         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
        9.96        49.51        42.35        32.19        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       38.14        12.46        47.08 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.39               0.99 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             65.98             129.27 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             21.01              20.98 
[1] "0.4 - 66.0 (21.0)"  "1.0 - 129.3 (21.0)"
[1] "hr=" "1.6"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  22Q LOSS MUTATED         7        2        13         0         0         2
  22Q LOSS WILD-TYPE      23        6        27         2         1         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  22Q LOSS MUTATED            3         13          3        7         3
  22Q LOSS WILD-TYPE          4         12         11       11         4
D78V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   7                 23
  STAGE II                  2                  6
  STAGE IIA                13                 27
  STAGE IIB                 0                  2
  STAGE IIC                 0                  1
  STAGE III                 2                  2
  STAGE IIIA                3                  4
  STAGE IIIB               13                 12
  STAGE IIIC                3                 11
  STAGE IV                  7                 11
  STAGE IVA                 3                  4
[1] 11  2
[1] TRUE
[1] "dimension of 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    1  9 42  5
  22Q LOSS WILD-TYPE  8 19 70  9
D78V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                1                  8
  T2                9                 19
  T3               42                 70
  T4                5                  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
  22Q LOSS MUTATED   22 24 10
  22Q LOSS WILD-TYPE 62 21 23
D78V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               22                 62
  N1               24                 21
  N2               10                 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"
D78V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   41  9
  22Q LOSS WILD-TYPE 84 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     41    9
  22Q LOSS WILD-TYPE   84   15
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               41                 84
  1                9                 15
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   26 32
  22Q LOSS WILD-TYPE 50 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     26   32
  22Q LOSS WILD-TYPE   50   57
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               26                 50
  MALE                 32                 57
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   38  6
  22Q LOSS WILD-TYPE 74 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     38    6
  22Q LOSS WILD-TYPE   74   14
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                38                 74
  YES                6                 14
[1] 2 2
[1] FALSE
D78V9, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   52  4
  22Q LOSS WILD-TYPE 94  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     52    4
  22Q LOSS WILD-TYPE   94    9
                                clus
vv                               22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        52                 94
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED   41  1  5  1
  22Q LOSS WILD-TYPE 82  1  7  3
D78V10, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               41                 82
  R1                1                  1
  R2                5                  7
  RX                1                  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"
D78V11, continuous

Clustering(79) Variable = XP LOSS MUTATION ANALYSIS
D79V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    21   4
  XP LOSS WILD-TYPE 110  23
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               25               133 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                4                23 
$`XP LOSS MUTATED`
TCGA-BM-6198 TCGA-AF-2693 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 
       21.24        37.97        11.84        12.00        32.02        24.00 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3881 
       34.03        34.03         2.01         6.05        32.98        19.04 
TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A02X TCGA-AH-6544 TCGA-CI-6623 
        3.98        13.94        23.01        41.00        38.56        47.44 
TCGA-DC-6155 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EI-7002 
       13.97        44.02        12.62        57.24       129.27        11.97 
TCGA-F5-6571 
       42.35 

$`XP LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 
       25.97        15.95        36.03        31.00        51.98        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       55.76        26.43        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3581 
       20.02        24.59        86.63        65.98        36.03         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3598 
       36.03        20.05         1.02        46.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99        29.98        37.02         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
        1.02        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       36.03        14.04         1.02        46.03        20.98         6.02 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       38.96        61.97        38.04         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 
       31.00        12.00        31.00        51.98        10.98        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG 
       25.05        25.05       126.44        41.36        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         3.48         4.18        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        49.51        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             2.01              0.39 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           129.27            126.44 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            24.00             20.91 
[1] "2.0 - 129.3 (24.0)" "0.4 - 126.4 (20.9)"
[1] "hr=" "1.3"
D79V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  XP LOSS MUTATED         6        3        10         0         0         0
  XP LOSS WILD-TYPE      24        5        30         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XP LOSS MUTATED            1          2          2        3         0
  XP LOSS WILD-TYPE          6         23         12       15         7
D79V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                  6                24
  STAGE II                 3                 5
  STAGE IIA               10                30
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               1                 6
  STAGE IIIB               2                23
  STAGE IIIC               2                12
  STAGE IV                 3                15
  STAGE IVA                0                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XP LOSS MUTATED    1  6 21  0
  XP LOSS WILD-TYPE  8 22 91 14
D79V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               1                 8
  T2               6                22
  T3              21                91
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  XP LOSS MUTATED   19  4  5
  XP LOSS WILD-TYPE 65 41 28
D79V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              19                65
  N1               4                41
  N2               5                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"
D79V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    22   4
  XP LOSS WILD-TYPE 103  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     22    4
  XP LOSS WILD-TYPE  103   20
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              22               103
  1               4                20
[1] 2 2
[1] FALSE
D79V7, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   15 13
  XP LOSS WILD-TYPE 61 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     15   13
  XP LOSS WILD-TYPE   61   76
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              15                61
  MALE                13                76
[1] 2 2
[1] FALSE
D79V8, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   16  5
  XP LOSS WILD-TYPE 96 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     16    5
  XP LOSS WILD-TYPE   96   15
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               16                96
  YES               5                15
[1] 2 2
[1] FALSE
D79V9, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    22   4
  XP LOSS WILD-TYPE 124   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     22    4
  XP LOSS WILD-TYPE  124    9
                                clus
vv                               XP LOSS MUTATED XP LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       22               124
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED    19   0   2   1
  XP LOSS WILD-TYPE 104   2  10   3
D79V10, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              19               104
  R1               0                 2
  R2               2                10
  RX               1                 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"
D79V11, continuous

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    19   4
  XQ LOSS WILD-TYPE 112  23
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               23               135 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                23 
$`XQ LOSS MUTATED`
TCGA-AG-A01N TCGA-BM-6198 TCGA-AF-2693 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 
       31.00        21.24        37.97        11.84        12.00        32.02 
TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-4021 TCGA-AG-A008 
       24.00        34.03         6.05        32.98         3.98        13.94 
TCGA-AG-A00Y TCGA-AG-A02X TCGA-AH-6544 TCGA-DC-6155 TCGA-DC-6160 TCGA-DT-5265 
       23.01        41.00        38.56        13.97        44.02        12.62 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EI-7002 TCGA-F5-6571 
       57.24       129.27        32.61        11.97        42.35 

$`XQ LOSS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       25.97        15.95        36.03        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        37.74        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 
       24.59        86.63        65.98        36.03         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
       20.05         1.02        46.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       50.04        12.03         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        29.98        37.02         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       19.99        28.04        36.03        14.04         1.02        46.03 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       20.98         6.02        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 
       49.97         1.94        38.96        61.97        38.04         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       21.01        25.05        26.04        31.00        12.00        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       51.98        10.98        25.97        25.05        25.05       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       41.36        24.13        51.48         3.48         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       13.64        17.46         8.45         9.96        49.51        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             3.98              0.39 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           129.27            126.44 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            31.00             20.55 
[1] "4.0 - 129.3 (31.0)" "0.4 - 126.4 (20.6)"
[1] "hr=" "1.2"
D80V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  XQ LOSS MUTATED         5        3         7         0         0         0
  XQ LOSS WILD-TYPE      25        5        33         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XQ LOSS MUTATED            2          2          2        4         0
  XQ LOSS WILD-TYPE          5         23         12       14         7
D80V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  5                25
  STAGE II                 3                 5
  STAGE IIA                7                33
  STAGE IIB                0                 2
  STAGE IIC                0                 1
  STAGE III                0                 4
  STAGE IIIA               2                 5
  STAGE IIIB               2                23
  STAGE IIIC               2                12
  STAGE IV                 4                14
  STAGE IVA                0                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XQ LOSS MUTATED    0  8 18  0
  XQ LOSS WILD-TYPE  9 20 94 14
D80V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               0                 9
  T2               8                20
  T3              18                94
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  XQ LOSS MUTATED   16  5  5
  XQ LOSS WILD-TYPE 68 40 28
D80V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              16                68
  N1               5                40
  N2               5                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"
D80V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    19   5
  XQ LOSS WILD-TYPE 106  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     19    5
  XQ LOSS WILD-TYPE  106   19
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              19               106
  1               5                19
[1] 2 2
[1] FALSE
D80V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   15 11
  XQ LOSS WILD-TYPE 61 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     15   11
  XQ LOSS WILD-TYPE   61   78
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              15                61
  MALE                11                78
[1] 2 2
[1] FALSE
D80V8, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   15  4
  XQ LOSS WILD-TYPE 97 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     15    4
  XQ LOSS WILD-TYPE   97   16
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               15                97
  YES               4                16
[1] 2 2
[1] FALSE
D80V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    22   3
  XQ LOSS WILD-TYPE 124  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     22    3
  XQ LOSS WILD-TYPE  124   10
                                clus
vv                               XQ LOSS MUTATED XQ LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       22               124
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    17   0   3   1
  XQ LOSS WILD-TYPE 106   2   9   3
D80V10, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              17               106
  R1               0                 2
  R2               3                 9
  RX               1                 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"
D80V11, continuous
